Cohort 1 (NSCLC cohort) \r\n* Ability to undergo a fresh tumor biopsy for the purpose of screening for this clinical trial (including able and willing to give valid written consent) to ability or to provide an available archival tumor sample taken less than 3 months prior to study enrollment (and not obtained prior to progression on a PD-1/PD-L1 inhibitor) if a fresh tumor biopsy is not feasible with an acceptable clinical risk; tumor lesions used for fresh biopsies should be the same lesions to be irradiated when possible and should not be the same lesions used as Response Evaluation Criteria in Solid Tumors (RECIST) target lesions, unless there are no other lesions accessible; additional, optional archival tumor tissue is also requested from before the prior PD-1 directed therapy
Availability of a representative formalin-fixed, paraffin-embedded (FFPE) tumor specimen in paraffin blocks (preferred) or at least 20 unstained slides (for detailed tissue requirements at screening)
All subjects must have adequate archival tissue available prior to registration (i.e., at least 20 unstained slides or paraffin block); if acceptable archival tissue is not available, the subject must be willing to consent to providing a core or excisional biopsy for research prior to registration for protocol therapy; if archival tissue is not available and there are no sites amenable to biopsy, enrollment must be discussed with the sponsor-investigator on a case by case basis
Have documented IDH1 gene-mutated disease (from a fresh tumor biopsy or the most recent banked tumor tissue available) based on central laboratory testing (R132C/L/G/H/S mutation variants tested).
Tissue blocks or slides must be sent for all patients; if tissue blocks or slides are unavailable, the study chair must be notified prior to enrollment
Willingness to release archival tissue sample for research purposes, if available
For patients enrolled via local molecular testing, an archival or fresh tumor tissue (unless medically contraindicated) is required to be submitted for independent central molecular testing at Ignyta's CLIA laboratory post-enrollment
Tissue blocks or slides must be sent for all patients; if tissue blocks or slides are unavailable, the study chair must be notified prior to enrollment
Tissue blocks or slides must be sent if available; if tissue blocks or slides are unavailable, the study chair must be notified prior to study enrollment
Patient must consent to provision of, and Investigator(s) must confirm access to and agree to submit a representative formalin fixed paraffin block of tumor tissue in order that the specific correlative marker assays may be conducted. Submission of the tissue does not have to occur prior to randomization. Where local center regulations prohibit submission of blocks of tumor tissue, two 2 mm cores of tumor from the block and 10-30 unstained slides of whole sections of representative tumor tissue are preferred. Where two 2 mm cores of tumor from the block are unavailable, 10-30 unstained slides of whole sections of representative tumor tissue alone are acceptable. Where no previously resected or biopsied tumor tissue exists or is available, on the approval of the Sponsor/designated CRO, the patient may still be considered eligible for the study.
Optional tumor biopsies: Patients will be asked permission (consent) to provide tissue from a recent (within 6 weeks of study entry) archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion; in addition, for on-study biopsies (after one week and after 7 weeks of initiating study therapy) and for baseline tumor biopsy if an archival tissue sample is not available: willingness to undergo biopsies will be asked; patients who consent to provide tumor biopsies for research should have tumors deemed relatively safely accessible for biopsies with low likelihood of complication
Part C: Archived paraffin-embedded tissue (20 unstained slides or a tumor block) from a prior resection must be available as a control for correlative studies; if tissue blocks or slides are unavailable, the study chair must be notified prior to enrollment
Tissue blocks or slides must be sent if available, with exclusions; if tissue blocks or slides are unavailable, the study chair must be notified prior to study enrollment
Tumor tissue samples must be available for submission to the sponsor prior to study treatment.
Unless the pre-screening was performed at Yale Clinical Molecular Pathology Lab (YCMPL), patients must have TCC tumor tissue available for submission in a form of at least 10 unstained slides or formalin-fixed paraffin-embedded (FFPE) block (FFPE block highly recommended and preferred) along with a buccal swab; if the number of slides is less than 10, a biopsy should be considered; if a biopsy is deemed unsafe, the case may be discussed with the study principal investigator (PI) and approval must be given for eligibility
Patients must have archived formalin-fixed paraffin-embedded (FFPE) tumor tissue specimen from the residual disease on the definitive surgical specimen available for PAM50 analysis for stratification\r\n* Tumor tissue specimen from the definitive surgery has been collected and is ready to ship to the ECOG-American College of Radiology Imaging Network (ACRIN) Central Biorepository and Pathology Facility (CBPF) within 21 weeks post-surgery\r\n* The Molecular Diagnostics Laboratory (MDL) at MD Anderson Cancer Center will perform the PAM50 analysis and notify the ECOG-American College of Radiology Imaging Network (ACRIN) operations office within three (3) weeks of receipt of the tumor tissue specimen via secure electronic messaging to the ECOG-ACRIN database; results will not be reported to the submitting institution\r\n* NOTE: Tissue must and can be submitted any time during screening period, even if patient is getting radiation\r\n* NOTE: Every effort should be made to submit the tumor tissue specimen to the ECOG-ACRIN CBPF immediately
ELIGIBILITY CRITERIA FOR RANDOMIZATION (STEP 1): Must have PAM50 analysis by digital mRNA quantitation on the formalin-fixed paraffin-embedded tumor tissue specimen (FFPE) of the residual disease in the breast resected at the time of definitive surgery completed
Patients must have adequate tumor tissue available, defined as >= 20% tumor cells and >= 0.2 mm^3 tumor volume\r\n* The local interpreting pathologist must review the specimen\r\n* The pathologist must sign the S1400 Local Pathology Review Form confirming tissue adequacy prior to screening/pre-screening registration\r\n* Patients must agree to have this tissue submitted to Foundation Medicine for common broad platform Clinical Laboratory Improvement Act (CLIA) biomarker profiling and c-MET IHC; if archival tumor material is exhausted, then a new fresh tumor biopsy that is formalin-fixed and paraffin-embedded (FFPE) must be obtained; a tumor block or FFPE slides 4-5 microns thick must be submitted; bone biopsies are not allowed; if FFPE slides are to be submitted, at least 12 unstained slides plus an H&E stained slide, or 13 unstained slides must be submitted; however it is strongly recommended that 20 FFPE slides be submitted; Note: previous next-generation deoxyribonucleic acid (DNA) sequencing (NGS) will be repeated if done outside this study for sub-study assignment; patients must agree to have any tissue that remains after NGS testing retained for the use of the translational medicine (TM) studies (if such TM studies are defined) within any sub-study the patient is enrolled in
Paraffin tissue samples obtained by transurethral resection of muscle-invasive bladder tumor, upper tract resection, cystectomy/nephrectomy/ureterectomy, or nephroureterectomy must be available; this specimen submission is mandatory prior to registration as results will be used for stratification
Patients must have a formalin-fixed, paraffin-embedded (FFPE) tumor block OR 1 representative hematoxylin and eosin (H&E) and 20 unstained sarcoma tissue slides available for submission to central pathology review; this review is mandatory prior to registration to confirm eligibility
Patients must be offered the opportunity to submit archival tissue for translational medicine; patients must also be willing to undergo biopsies and submit fresh tissue and blood for translational medicine
A paraffin-embedded surgical tumor tissue specimen has been located is available for shipment to Foundation Medicine, Inc. following pre-registration\r\n* NOTE: Complete the EA3132-specific FoundationOne requisition form
Formalin fixed, paraffin embedded (FFPE) tumor sample from the primary tumor, mandatory\r\n* NOTE: for adjuvant patients this refers to the surgical specimen; for neoadjuvant patients, both the pre-treatment core biopsy and the surgical specimen with residual disease are requested but only one is mandatory; if the surgery tumor blocks are available, but cannot be submitted, sites may submit a portion of invasive tumor from the original block, either by taking at least one core of at least 3 mm in diameter, or by splitting the original block in two parts, and re-embedding one in a new block for central submission; if blocks containing pre-neoadjuvant treatment core biopsies are available but cannot be submitted, sections mounted on glass slides prepared from the block can be provided; if tumor sample can't be provided as requested above or if it's not available, approval by study team for patient's entry into the trial is required
Patients must have a minimum of five, available unstained slides from the residual (post-neoadjuvant) invasive tumor in primary site or lymph node; (these will be submitted to determine PD-L1 expression) the tumor tissue must be adequate for PD-L1 testing, which typically requires a minimum of 100 cancer cells per slide\r\n* NOTE: Initial order for specimen kits should be placed at least two weeks prior to registering the first patient at each site
Sufficient tissue and blood must be available to submit for required biology studies
Specimen Submission: Patients must have sufficient tissue available for the required biology study
Patients must have adequate tumor tissue to meet the minimum requirement for submission
Enrolling institutions are reminded that submission of pre-treatment serum, tumor tissue and whole blood is required
An adequate amount of archived tumor tissue, either from primary colorectal cancer site or metastatic lesions, for central confirmation of dMMR status:\r\n* Either whole or part of the formalin-fixed paraffin-embedded (FFPE) block containing tumor tissue; or\r\n* At least 8 unstained slides containing tumor sections
Patient must have archived formalin-fixed paraffin-embedded (FFPE) tumor tissue specimen from the original diagnostic biopsy available for submission to Adaptive Biotechnologies for ClonoSEQ ID molecular marker identification of unique clonal immunoglobulin deoxyribonucleic acid (DNA) sequence\r\n* NOTE: Patients for whom the molecular marker is identified will have peripheral blood collected after completion of induction (patient’s disease status is PR or CR) and submitted to Adaptive Biotechnologies for minimal residual disease (MRD) assessment
Tumor tissue that is determined by central pathology review prior to step 2 registration to be of sufficient quantity for central analysis of MGMT status
Surgical formalin-fixed paraffin-embedded (FFPE) specimen must be available for submission to GenomeDx for genomic analysis on Decipher GRID platform; Note: if Decipher results have already been obtained, in lieu of tissue, results must be submitted to GenomeDx for validation
Patient must be willing to have tissue specimens submitted for translational medicine studies
Patients must have undergone adequate (definitive) breast surgery for the current malignancy. FFPE tumor tissue block must be confirmed to be received at the central sample repository prior to randomization.
Willing and able to undergo a biopsy of at least one metastatic site or primary prostate; adequate archival metastatic tissue can be used if available in lieu of a biopsy if done when patient had CRPC; fresh or archival tissue must be obtained within 6 months of treatment start\r\n* RB positive as determined by local lab immunohistochemistry (IHC) testing (performed per lab manual) and if available, ship 10 slide (5 micron thickness) or alternatively the tissue block to Thomas Jefferson University (TJU) and 1 hematoxylin and eosin (H&E) slide
Archival tumor tissue or a newly obtained biopsy must be available prior to the first dose of study drug for biomarker analysis. In the case archival tissue cannot be provided, participants with inaccessible tumors for biopsy specimens can be enrolled without a biopsy upon consultation and agreement by the sponsor Note: In case of submitting unstained cut slides, freshly cut slides should be submitted to the testing laboratory within 14 days from when the slides are cut
For patients with solid tumors, either archival tumor tissue must be available or patient must consent to undergo on-study tumor biopsy before administration of first dose
A representative formalin-fixed, paraffin-embedded tumor specimen in paraffin blocks, or at least 20 unstained slides with an associated pathology report documenting ER, PR, and HER2 negativity. Participants with fewer than 20 unstained slides available at baseline, and not fewer than 12 unstained slides will be eligible upon discussion with Medical Monitor
For the expansion portion of the study: patients must have tissue that is amenable to biopsy and must be willing to undergo research biopsy; patients who undergo an attempted research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are not required to undergo a repeat biopsy in order to continue on protocol
Subjects with ED SCLC must consent to provide available archived formalin fixed paraffin embedded (FFPE) tissue sample of SCLC lesion (primary or metastatic) for central review and biomarker analysis.
Provide adequate tissue (core or incisional/excisional biopsy) prior to starting study treatment; this tissue will be used for PD-L1 analysis; fresh tissue or archival tissue sample can be used; if adequate tissue cannot be safely obtained than the patient may still be enrolled on the trial after discussion with the study principal investigator as long as fine-needle aspiration (FNA) was done to confirm recurrent/second primary head and neck squamous cell carcinoma (HNSCC)
Archival tissue must be procured if available
Participants must have fifteen blank (unstained) slides or a diagnostic tissue block must be available for external quality assurance by the AMC Core Pathology Laboratory
The patient must have at least 1 block of tissue or 15 unstained slides at a minimum available for central pathology review and molecular profiling of the tissue sample
Availability of tumor specimen block or 30 unstained slides from diagnosis of muscle-invasive disease. Patients with fewer than 30 slides available may be enrolled after discussion with the principal investigator.
Ability to provide adequate tissue sample
At least 1 site of disease must be accessible to provide repeat biopsies for tumor tissue for sequence and immunological analysis. This site may be a target lesion as long as it will not be made unmeasurable by the biopsy procedure.
Willing to undergo core needle or incisional biopsy to obtain fresh tumor tissue specimens
Subjects must have histologic or cytological confirmation of a malignancy that is advanced (metastatic and/or unresectable) with measurable disease per Response Evaluation Criteria in Solid Tumors (RECIST) version (v)1.1; acquisition of existing formalin fixed paraffin embedded (FFPE) tumor tissue by study investigators is not mandatory for enrolment on the trial; patients without previous histologic/cytologic confirmation must have freshly obtained biopsy for routine pathologic evaluation before enrolment on the study
Willingness to undergo biopsy; if biopsy is not felt to be possible or safe, permission must be received from Dr. Tung to forgo a biopsy; in that event, formalin fixed, paraffin embedded (FFPE) tumor sample from a prior metastatic biopsy (preferable) or from the primary tumor tissue will be collected, unless none is available and Dr. Tung provides approval; if paraffin blocks are unable to be sent to for analysis due to institutional policy, 15 unstained paraffin slides may be sent instead; a formal eligibility exception is not needed as long as approval is granted and documented by Dr. Tung
Have PD-L1 expression level determined from the subject's archival tissue or fresh tumor specimen
Provide tumor tissue sample.
Cohort A Dose Expansion (Ribociclib + PDR001): Participants with accessible tumor lesion(s) must be willing to undergo two research biopsies: one prior to treatment initiation and one after 7 weeks of protocol therapy; participants who undergo an attempted on-treatment research biopsy and in whom inadequate tissue is obtained are still eligible to receive protocol therapy; they will not be required to undergo a repeat research biopsy attempt
Expansion Cohort B (Ribociclib + PDR001 + Fulvestrant): Participants with accessible tumor lesion(s) must be willing to undergo two research biopsies: one prior to treatment initiation and one after 7 weeks of protocol therapy; participants who undergo an attempted on-treatment research biopsy and in whom inadequate tissue is obtained are still eligible to receive protocol therapy; they will not be required to undergo a repeat research biopsy attempt
Willingness to provide archival tumor samples; if sample is not available, a biopsy should be considered in patients with safely accessible disease; participants who undergo an attempted research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are not required to undergo repeat biopsy in order to continue on protocol
Must consent to allow the acquisition of existing formalin-fixed paraffin-embedded (FFPE) tumor tissue, either a block or unstained slides, for performance of correlative studies
Availability of archival or fresh tumor specimen that is suitable for analysis. Acceptable samples must have been acquired using core needle biopsy or excisional biopsy. Samples that were acquired using fine needle aspiration are not acceptable.
Tumor tissue sample is required within 6 months prior to study enrollment; tissue sample may be fresh (core needle, excisional, or incisional biopsy), or archival if obtained within 6 months prior to enrollment; if a tissue sample is available but it has been > 6 months and there has been no intervening therapy, the principal investigator may approve the sample after discussion; PD-L1 IHC testing will be performed on the tumor tissue, but positivity on the PD-L1 IHC testing is not required to enroll in the study
In the dose expansion cohort patients should be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion (pre-treatment) and a post-induction period biopsy; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; patients for whom newly-obtained samples cannot be provided (e.g., inaccessible, subject safety concern, or unwilling to undergo biopsy) may submit an archived specimen only upon agreement from the sponsor; post-induction\r\nbiopsy will be collected at the end of the Induction period, approximately 12 weeks from the start of study treatment (sometime between cycle 4 day 15 – cycle 4 day 21, prior to the re-staging scan)
Have a safely biopsiable tumor lesion and be willing to undergo a pre-treatment and on-treatment core biopsy\r\n* Pretreatment tissue should be collected via core biopsy, ideally of a non-target lesion\r\n* Patients may not have intervening systemic anti-cancer therapy between the time of pre-treatment biopsy/resection and initiating study treatment
Patients must have a tumor tissue form indicating availability of archived tissue from a previous surgery for glioblastoma, completed and signed by a pathologist
Available and adequate baseline tumor tissue sample
Dose Escalation Cohort: archived tumor tissue or fresh tumor biopsy.
Expanded Cohort: archived tumor tissue and fresh tumor biopsy.
1 cm^3 of available tissue for N=5 patients for correlative tissue studies; patients can enroll regardless of their tissue availability being checked beforehand but at least 5 patients will need to have sufficient tissue by study accrual completion; tissue availability will be checked after patients are successfully enrolled
All subjects must have archival tissue confirmed as available for enrollment; subjects who are TKI naive who do not have archival tissue may undergo a fresh tumor biopsy in lieu of the archival tissue requirement; the archival tissue requirement may be waived for subjects after discussion with the principal investigator
Must be able to provide tumor tissue obtained within 6 months of study enrollment. If such tissue is not available, a newly obtained core or excisional biopsy of a tumor lesion must be performed.
Must be willing to undergo an incisional, excisional, or core needle lymph node or tissue biopsy or provide a lymph node or tissue biopsy from the most recent available archival tissue.
Availability of formalin-fixed paraffin-embedded (FFPE) tumor block (preferred) or at least 25 unstained slides, collected ?3 months prior to randomization, with an associated pathology report, if available
Have available archival tumor or be willing to undergo diagnostic biopsy at screening. Sample must be of suitable quality and quantity to satisfy group assignment and biomarker endpoints.
Able to provide tissue from a newly obtained core or excisional biopsy of a chest wall tumor lesion; newly-obtained is defined as a specimen any time after the last systemic or local therapy utilized to treat the disease; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the study chair
Availability of a cancerous lesion amenable to biopsy and willing to undergo a pre-treatment biopsy
Agreement to allow the use of archival tissue from pre-ASCT tumor biopsies\r\n* If unavailable, exceptions may be granted with study principal investigator (PI) approval
Subject has consented to provide archival formalin-fixed, paraffin-embedded (FFPE) tumor block; if archival tissue is not available, Subject must consent to tumor biopsy.
Participants enrolling in the dose expansion must have tissue that is amenable to biopsy and be willing to undergo a fresh tissue biopsy at baseline; participants who undergo an attempted research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are not required to undergo a repeat biopsy in order to continue on protocol
Patients must have a tissue block (or 26 unstained slides) available with adequate tumor to perform multiplex immunohistochemistry and nucleic acids analyses (i.e. whole exome sequencing); patients with only a previous fine-needle aspirate are ineligible for enrollment
Patients who do not have available tissue for immunohistochemistry and nucleic acids analyses
Patients with inadequate tissue for analysis
Be willing to allow the use of archival formalin-fixed paraffin-embedded tumor tissue for correlative analyses\r\n* Note: The archived tumor tissue specimens may be from prior surgery or from prior diagnostic biopsy of primary or metastatic tumor specimen; unavailability of archived tissue will not render subject ineligible for study
Tissue from a prior craniotomy or biopsy for clinical genetic sequencing (at least one formalin-fixed, paraffin-embedded [FFPE] block or 15 unstained slides); patients previously assessed for genetic sequencing who meet requirements do not need to have additional tissue available for prospective genetic screening
Patient has received at least one prior line of systemic therapy in the recurrent/metastatic setting; the study chair may grant exceptions to the mandatory biopsy should the treating physician deem that a biopsy is not feasible or unsafe for the patient, and archival tissue is available and provided for study purposes; a conversation with the study chair is required to obtain an exception
For participants enrolling the phase IIa part of the study, accessible tumor lesion(s) for the purpose of research biopsy and willingness to undergo a research biopsy before treatment initiation and at the time of disease progression, as well as a single research blood sample before initiation of therapy; participants who undergo an attempted on-treatment research biopsy and in whom inadequate tissue is obtained are still eligible to receive protocol therapy; they will not be required to undergo a repeat research biopsy attempt
For participants enrolling the phase Ib part of the study, willingness to provide archival tumor samples when available
Have sufficient archival formalin-fixed paraffin-embedded (FFPE) tumor tissue available for planned analyses
Willing to provide a tumor sample via biopsy from a metastatic site of disease to be collected at screening if safe and feasible per treating investigator discretion; adequate archival metastatic tissue can be used if available in lieu of baseline biopsy if done when patient had CRPC
RANDOMIZED PHASE II CLINICAL TRIAL: Have provided tissue from a newly obtained biopsy (an archival tissue sample may be substituted if new biopsy cannot be obtained and by discretion of principal investigator only) obtained from a focus of metastatic disease (a tumor lesion in newly diagnosed metastatic TNBC de novo is acceptable) and agreed to providing a second newly obtained biopsy after completion of 2 cycles of the study drugs
Patients who are willing and able to comply with the protocol and study procedures including willingness to undergo tumor biopsy for tumor cells before therapy to assess for CD30 status (unless archival tumor tissue from orchiectomy or other previous sample is not obtainable despite efforts to do so and a fresh tumor biopsy is not feasible)
Archival tissue block or unstained slides (from primary or metastatic site) must be available, otherwise fresh tissue biopsy sample will be collected for patients with accessible tumors
All patients should submit an archival tumor biopsy specimen (collected at diagnosis or relapse); patients who have no tumor tissue available may be permitted to participate after discussion with the principal investigator
Known mutation of Rb in tumor tissue
Subjects have archival tumor tissue available or are willing to undergo a baseline biopsy prior to treatment
Phase II subjects must be willing to provide a tissue biopsy prior to registration if archived HCC tumor tissue is not available for correlative studies
Tissue blocks or slides must be sent if available, for patients who consent for the optional correlative pathology studies, with the exception of intrinsic brain stem tumors, optic pathway gliomas, or subjects with pineal tumors; for consenting patients, if tissue blocks or slides are unavailable, the study chair must be notified prior to study enrollment
Participants must have accessible tumors and consent to repeated biopsy for performance of correlative tissue studies
A biopsy of the tumor tissue obtained at anytime from the initial diagnosis to study entry. Although a fresh biopsy obtained during screening is preferred, archival tumor specimen is acceptable if it is not feasible to obtain a fresh biopsy. For Part 1B and Part 2B, any archival tumor specimen must have been obtained within 3 months of starting study drug.
Willing to provide a tumor sample via biopsy from a metastatic site of disease to be collected at screening if safe and feasible per discretion of treating investigator; adequate archival metastatic tissue can be used, if available, in lieu of baseline biopsy if done when patient had CRPC; patients without a site amenable to biopsy and lack of archival tissue may still join the study
Availability of a tumor tissue specimen. If no archived tumor tissue is available, then a de novo biopsy is required for patient participation.
Participants must have sufficient tissue from prior surgery revealing glioblastoma or variants for confirmation of diagnosis and correlative studies; the following amount of tissue is required:\r\n* 15 (5 um thick) unstained formalin fixed paraffin embedded (FFPE) sections\r\n* 1-2 hematoxylin and eosin (H&E) stained slides, or additional unstained 5 um slide(s) for staining\r\n* NOTE: the overall principal investigator (PI) will allow for up to 2 participants to enroll with insufficient tissue; if a site is hoping to enroll a patient with less than the tissue required, prospective approval by the overall PI is required
Willing to provide archival or fresh tumor biopsy at Screening and Week 10
Availability of formalin-fixed paraffin-embedded (FFPE) tumor tissue block.
Patients with pathologically documented metastatic triple negative breast cancer (TNBC), eligible for treatment with paclitaxel. Paraffin-embedded tissue must be available from metastatic sites, if reasonably accessible, or from the primary tumor, to confirm the diagnosis of TNBC and for correlative studies (only on metastatic tissue). Fifteen slides can be obtained if the full block is not available to be sent or released. TNBC will be defined as breast cancer with <1% ER+ and <1% PgR+ cells, and HER2 immunohistochemistry score of 0 or 1+ and/or in situ hybridization (ISH) with HER2 gene copy number <4 or a ratio of less than 2 between HER2 gene copy number and centromere of chromosome 17. Patients whose metastatic disease is TNBC are eligible even when their primary tumor expressed hormone receptors and/or HER2.
For subjects with melanoma, archived or freshly biopsied tumor tissue (preferred) must be obtained prior to enrollment; tissue shipment tracking information should be provided before administration of study treatment is initiated; however, if shipping will be delayed and tissue shipment tracking information is unavailable, study drug may be administered prior to tissue receipt pending discussion with principal investigator
Availability of diagnostic tumor tissue specimens for correlative studies
Prior to initiation of study agents, study participants will be highly encouraged to undergo a baseline research core biopsy of their breast tumor; if this is not possible or the patient refuses, the pre-treatment tumor sample must be obtained from their archival diagnostic core biopsy; if definitive surgery is not performed at day 21-27 after study treatment, a second post-treatment research core biopsy will need to be obtained from their breast tumor; for patients undergoing surgery, the second biopsy will be removed from the breast tumor tissue excised during their operation; Note: In the event that the baseline breast tumor biopsy performed for research purposes does not yield adequate tumor tissue for analysis of the primary and secondary endpoints, tissue will be requested from the patient's archival clinical diagnostic core biopsy if it is available; the patient will still remain on study and complete protocol therapy as planned in this unlikely event
Biopsy of a primary or metastatic lesion must have been performed within the past two years; sufficient pathologic material must be available to enable whole exome sequencing at the time of study entry; patients with biopsy samples older than 2 years must undergo a fresh tumor biopsy or should receive approval for enrollment from the principal investigator
Provide tissue for biomarker analysis from a newly or recently-obtained biopsy (within 90 days of Study Day 1) of a tumor lesion not previously irradiated
Patients must have an adequate tumor tissue sample prior to enrollment available for correlative studies as defined below: core needle biopsy or incisional biopsy samples that can provide >= 5 unstained sections of 5 micron thickness; fine needle aspiration (FNA) sample alone is not sufficient
Adequate archival frozen or fixed tissue available from primary or metastatic site for genotypic analysis (at least 15 unstained slides and/or tumor block)
Have available archival formalin-fixed paraffin-embedded block(s) containing tumor or at least 20 unstained slides containing tumor.
Availability of at least 12 unstained slides from archival FFPE tumor tissue.
Available tumor tissue for biomarker analysis
Participants must have archival tumor tissue available. Participants without archival tissue may be enrolled at the discretion of the principal investigator
PHASE II: Tumor tissue for correlative studies is required for all patients except those with NF1 and LGG (stratum 2) unless surgery was performed prior to enrollment or any patient with optic pathway glioma (stratum 2 or 3), for whom tumor tissue is optional
Have available formalin-fixed paraffin embedded (FFPE) tumor tissue sample blocks for submission. If blocks are not available, have unstained slides for submission for central programmed death-ligand 1 (PD-L1) testing.
Participants must be able and willing to undergo a pre-treatment tumor tissue biopsy; participants must also be willing to undergo an on-treatment tumor tissue biopsy if clinically feasible
Participants must have a tumor tissue sample available (formalin-fixed paraffin embedded [FFPE] tissue block or unstained slides); may be newly obtained or obtained within 6 months prior to enrollment (without systemic therapy given after the sample was obtained); participants without sufficient archival tissue may be enrolled following successful completion of the pre-treatment tumor tissue biopsy; tissue must be a core needle biopsy, excisional, or incisional biopsy; fine needle aspirates (FNA) or malignant effusions are not adequate; bone biopsies without a soft tissue component are not adequate
Willingness and availability to submit formalin-fixed paraffin-embedded (FFPE) tissue for central confirmation of HER2 positivity and central assessment of PD-L1 status. This can be from archival tissue from unresectable loco-regional or metastatic disease obtained =< 1 year prior to enrollment or new tissue material from a recently obtained surgical or diagnostic biopsy. Tissue obtained for the biopsy must not have been previously irradiated. If a patient does not have any available archival tissue =< 1 year old and the treating investigator does not feel that it would be safe to perform a fresh biopsy, the requirement for a fresh biopsy may be waived after discussion with the Principal Investigator.
Tumor tissue for mandatory pre-treatment and on-treatment biopsies.
Participants must have biopsy tissue at time of diagnosis available for targeted next-generation sequencing; the testing does not have to be completed prior to study enrollment; biopsy can be performed at an outside institution as long as sufficient tissue is available
Must agree to provide archival or newly obtained tumor tissue sample prior to the start of treatment in this study
Willing to provide archived tissue for correlative studies. If no archived sample is available the patient will still be eligible
Willing to provide blood and tissue from diagnostic biopsy and at the time of surgery
PHASE II INCLUSION CRITERIA: Patients with tumor tissue uptake during NETSPOT PET that is equal to or higher than that in normal hepatic tissue (grade >= 2) will be eligible; it is recommended that NETSPOT PET be obtained before initiation of chemotherapy, but NETSPOT PET obtained during or after completion of chemotherapy could be used for screening purpose
Confirmed availability of tumor tissue blocks or freshly cut tissue slides for NaPi2b testing.
Be willing to provide tissue from a newly obtained core needle or excisional biopsy; newly-obtained is defined as a specimen obtained up to and including 90 days prior to treatment day 1; subjects for whom newly obtained samples cannot be provided may be enrolled only with agreement by the overall principal investigator (PI)
Has provided archival tumor tissue sample or newly obtained core or excisional biopsy of a tumor lesion not previously irradiated
All subjects must agree to pre- and on-treatment tumor biopsies; subjects in whom biopsy is technically not feasible or in whom would result in unacceptable risk, in the opinion of the investigator, may be exempted from the biopsy requirement with discussion with the principal investigator; use of outside archived tumor tissue for a\r\nbaseline biopsy is not permitted
Sufficient tissue from diagnostic tumor/ lymph node biopsy (from within 2 months prior to ICF signature) must be available for translational research purposes or subject is willing to undergo core needle or incisional/ excisional biopsy during Screening.
Previously obtained archival tumor tissue, or tissue obtained by endoscopically guided core biopsy at screening
If a fresh tissue sample is provided, a blood sample is required.
Representative formalin-fixed, paraffin-embedded (FFPE) tumor specimen in paraffin blocks (preferred) or at least 20 unstained slides, with an associated pathology report documenting ER, PgR, and HER2 negativity
ENROLLMENT TO THE DOSE ESCALATION, EXPANSION AND PART II: The availability of archival tissue to evaluate retrospectively the participant’s retinoblastoma (Rb) status; the requirement is a minimum of 5 unstained slides with each tissue cut measuring 4 microns in width; ideally 15 slides will be requested; patients without available archival tissue may be enrolled at the discretion of the principal investigator
Must agree to provide tumor tissue sample, either from a previous surgery or biopsy within 6 months or fresh, prior to the start of treatment in this study
Participants must have biopsy tissue at time of diagnosis available for next-generation sequencing testing at the Dana-Farber Cancer Institute; biopsy can be performed at an outside institution as long as sufficient tissue is available
Agreement to allow the use of archival tissue from diagnostic tumor biopsies will be retrieved and submitted post-enrollment \r\n* If unavailable, exceptions may be granted with study principal investigator (PI) approval.
Willing to provide archived tissue, if available, from a previous diagnostic biopsy
Participants must have archival tumor tissue available; participants without archival tissue may be enrolled at the discretion of the principal investigator
Must have provided tumor tissue sample, as follows:
For participants entering Ph1a: have submitted, if available, an archival tumor tissue sample.
For participants entering Ph1b: have submitted, a sample from a newly obtained core or excisional biopsy of a tumor lesion or a recent biopsy defined by 6 months of study enrollment (Ph1b).
Be willing to provide tissue from an archival tissue specimen in selected patients, where available
Participants must agree to undergo a research biopsy, if tumor is safely accessible, at baseline; participants can be exempt if archival tumor tissue has been collected within 12 months of study enrollment that the principal investigator deems it appropriate/sufficient for analysis on this protocol; biopsy of a lesion outside of the potential radiation treatment field is preferred to maintain consistency across cohorts
Participants must have archival tissue from the primary tumor or metastases available for correlative studies; either a paraffin block or twenty unstained slides are acceptable; if twenty slides are not available, a lesser amount may be acceptable after discussion with the principal investigator
Memorial Sloan Kettering (MSK) patient has tissue available from a previous biopsy for the evaluation of potential predictive biomarkers; if tissue is not available for MSK patient, a new tumor specimen will need to be obtained prior to the start of study treatment; if archived tissue is available, participating site patient will provide for the evaluation of potential predictive biomarkers; if tissue is not available for participating site patient, a new tumor specimen is optional prior to the start of study treatment
Consent to provide an archival tumor tissue sample (if available) and to undergo baseline and on treatment tumor biopsies for pharmacodynamic biomarker analysis
Tumor tissue from biopsy following progression on the most recent TKI available for mutation analysis; if tissue is inadequate for exploratory research testing, patient may enroll with permission of principal investigator
Availability of an archival FFPE tissue specimen.
If tumor is accessible and outside the field of radiation, the participant must be willing to undergo a research biopsy at baseline and around their second cycle of pembrolizumab; participants for whom newly-obtained samples cannot be provided (e.g. inaccessible or safety concern) must be willing to submit an archival specimen
Either a formalin fixed paraffin block or a minimum of ten 5-micron tissue section’s (slides) of tumor biopsy sample must be available for biomarker evaluation from baseline and repeat esophagogastroduodenoscopy (EGD)
Archival tissue of tumors (slides or blocks [blocks preferred]) must be available for analysis; If tissue is not available, patients willing to undergo a pre-treatment biopsy may enroll
Availability of a tissue block from initial breast cancer diagnosis and/or metastatic recurrence; if a tissue block is not available, 10-20 unstained slides may be provided as an alternative; if unstained slides will be provided, they should not be sent until specifically requested by the Dana-Farber Cancer Institute (DFCI) study coordinator; if archival tumor tissue is not available, a fresh biopsy may be performed
All patients with biopsy-accessible disease must be willing to undergo paired research biopsies; these biopsies will occur 5-48 hours after the cycle (C)1 day (D)1 cisplatin dose (i.e. C1D2 or C1D3) and 5-8 hours (hrs) (+/- 24 hrs) after the last dose of AZD1775 on C2D3; the exact timing of the biopsy relative to receipt of study treatment should be accurately recorded\r\n* Biopsies may be done with local anesthesia or intravenous conscious sedation, according to standard institutional guidelines\r\n* Research biopsies requiring general anesthesia are not allowed on this protocol unless a biopsy is being obtained simultaneously for clinical reasons, in the judgment of the patients’ treating physician\r\n* Patients who undergo an attempted on-treatment research biopsy and in whom inadequate tissue is obtained are still eligible to continue protocol therapy; they will not be required to undergo a repeat biopsy attempt\r\n* If dosing is delayed placing the biopsy outside of the allowable window, the biopsy should be rescheduled to be within the window; if not feasible, the biopsy should be obtained as close to within the window as possible\r\n* Fine needle aspirates (FNA) is not allowed
Tissue blocks or slides must be sent; if tissue blocks or slides are unavailable, the study chair must be notified prior to enrollment
Patients must have archived tumor tissue from prior tumor biopsy or surgical resections available for submission that is sufficient to complete molecular profiling
Tissue blocks or slides must be sent; if tissue blocks or slides are unavailable, the study chair must be notified prior to enrollment
Availability of an archival or new pre-treatment tissue sample is required if molecular testing was not performed by Foundation Medicine. Any available tumor tissue sample can be submitted. The tissue sample must be submitted within 4 weeks after enrollment Erlotinib
For patients where molecular testing was not performed using Foundation Medicine, submission of an archival or new pretreatment tissue sample is mandatory. For patients where molecular testing was performed using Foundation Medicine, submission of an archival or new pretreatment tissue sample is required, if available. The tissue sample must be submitted within 4 weeks after enrollment
Tissue from the initial diagnosis or recurrence must be made available for correlative testing
Confirmation of availability of FFPE tumor specimen with adequate tumor tissue (either one paraffin embedded tissue block OR 10 5-micron unstained slides from the block on regular (non-plus) slides and 1 hematoxylin and eosin [H&E] slide)
Tissue availability must be verified prior to registration; if tissue is unavailable, the study chair must be notified prior to enrollment; tissue blocks or slides will be sent to Dana Farber Cancer Institute; NF-1 patients, as well as those with optic pathway, including chiasmatic-hypothalamic lesions (with or without NF-1) are not required to have a biopsy; all others are, if deemed safe by their clinical team\r\n* Note: All patients who have tissue available must also have a pre-treatment blood sample collected
Patients must have 10 representative hematoxylin and eosin (H&E) stained thyroid tissue slides OR tumor block available for submission to central pathology review; this review is mandatory prior to registration to confirm eligibility
Newly obtained tumor tissue biopsy and archived tumor tissue, if available, must be collected for central pathology determination of LIV-1 expression
Only patients with available archival tumor tissue must consent to provision of, and Investigator(s) must confirm access to and agree to submit a representative formalin fixed paraffin block of tumor tissue in order that the specific correlative marker assays (Correlative Studies) of this protocol may be conducted. Submission of the tissue does not have to occur prior to randomization. Where local center regulations prohibit submission of blocks of tumor tissue, two 2 mm cores of tumor from the block and 5-20 unstained slides of whole sections of representative tumor tissue are preferred. Where it is not possible to obtain two 2 mm cores of tumor from the block, 5-20 unstained slides of representative tumor tissue are also acceptable. Where no previously resected or biopsied tumor tissue exists or is available, on the approval of the Sponsor/designated CRO, the patient may still be considered eligible for the study.
Tissue (or lymph node biopsy for rrcHL participants) available from an archival tissue sample or, if appropriate, a newly obtained core or excisional biopsy of a tumor lesion not previously irradiated
Consent to provide a formalin-fixed paraffin-embedded (FFPE) tissue block (preferred) or a minimum of 15 (20 preferred) freshly cut unstained tumor slides from the most recently collected, available tumor tissue accompanied by an associated pathology report (with tumor content information, Gleason score, and disease staging) for PTEN IHC and NGS testing and for other protocol-mandated secondary and exploratory assessments. If only 12-14 slides are available, the patient may still be eligible for the study, after discussion with and approval by the Medical Monitor. Cytologic or fine-needle aspiration samples are not acceptable. Tumor tissue from bone metastases is not acceptable
The participant must be willing to undergo the three required research biopsies over the course of protocol therapy; participants who undergo an attempted research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are not required to undergo a repeat biopsy in order to continue on protocol
Patients must consent to analysis on archival tissue
The subject is willing to undergo a core needle biopsy during screening and during Cycle 2, Study Week 5. Archival tumor samples are requested, but are not required for eligibility.
Patients must have adequate archival material from a previous biopsy to determine EGFR mutation status and Cripto-1 expression, or undergo a biopsy of fresh tissue of the primary cancer or a metastatic site in order to make these determinations, if archival material is not available
Confirmed availability of archived FFPE tumor tissue block, or a minimum of 15 slides. If archived FFPE tissue is not available, then fresh tumor sample may be obtained in accordance with local institutional practice for tumor biopsies.
Participants enrolled into Part 2 must have tumor tissue available for correlative studies. Fresh tumor biopsy is preferred. Archival tissue must meet the following criteria: archival sections within 4 months of sectioning that have been stored at 2 degree to 8 degree Celsius in the dark or archival tumor blocks within 5 years of collection. Participants without tissues meeting the aforementioned archived tissue criteria must undergo a fresh biopsy
Documentation of BRAFv600 mutation-positive status in melanoma tumor tissue (archival or newly obtained) through use of a clinical mutation test approved by the local health authority
Able to provide a fresh formalin-fixed, paraffin-embedded (FFPE) tumor sample for central evaluation of HER2 status prior to enrolment; if a fresh biopsy is not feasible, sponsor approval is required and archived tumor biopsy must be provided for centralized testing by sponsor
For Parts 1 and 3, eligibility may be based on local read of fresh or archived tumor biopsy. Archived or fresh FFPE biopsy must be provided for retrospective centralized review.
Formalin-fixed paraffin embedded (FFPE) tumor tissue from previous biopsy is requested, but not mandatory
Availability of archival tumor tissue for biomarkers analysis (formalin-fixed paraffin-embedded [FFPE] block or cell block will be required); specimen from primary site will be allowed; patients must have at least 10 slides available; repeat biopsy to obtain sufficient tissue for 10 slides is allowed
Patients must have tumor block or slides available for testing, and tumor must be glucocorticoid receptor positive (defined as GR >= 10% moderate to strong staining by central lab); a formalin-fixed, paraffin-embedded surgical or core needle biopsy obtained from the primary tumor or from a metastasis and containing viable tumor tissue is required for this evaluation; fine needle aspirates or other alternative cytology samples are not acceptable
Has provided tumor tissue from locations not radiated prior to biopsy.
Patient is able to provide tissue from diagnostic core biopsy of tumor lesion(s)\r\n* Notes:\r\n** 4 cores may be taken for lesions > 1.5 cm, otherwise 2 cores may be taken from recent biopsy\r\n** Patient can be registered, randomized, and start study treatment prior to specimen shipment
Availability of an archival tumor tissue sample. If archival tumour tissue is not available, then tissue from a fresh biopsy can be used.
Patients must provide written consent to allow a core needle biopsy samples of tumor tissue (primary or metastatic) to be obtained during baseline for analysis of mutations associated with his/her malignancy, and for correlation studies; if available, patients may elect to provide a formalin fixed paraffin embedded (FFPE) tissue block (from his/her primary or metastatic tumor) obtained within 45 days prior to written consent for the clinical trial granting release of the paraffin block; planned to undergo standard surgical resection for potential cure or for palliation when applicable
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 30 days prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the principal investigator
Disease that can be accessed by a bronchoscopic, surgical or percutaneous biopsy, eligible for biopsy from safety perspective, and agrees to biopsy prior to study; the pre-study biopsy can be waived if there is an archival biopsy specimen that was obtained after the most recent therapy or if the risks of biopsy are judged to be excessive by the study principal investigator (PI)
Be required to provide tissue from a newly obtained biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to study registration; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from principal investigator (PI)
Archival tumor sample available; tissue from an fine-needle aspiration (FNA) is allowed but tumor tissue from a core needle biopsy is preferred
Availability of 20 archival formalin-fixed paraffin embedded (FFPE) tumor tissue slides (15 of 10 uM thick sections, and 5 of 5 uM thick sections)
Tumor tissue available if biopsy consent not provided, if no archival tumor tissue available and pt provides consent, pre-dose biopsy will be done
Tumor tissue receptive to Wnt signalling in biopsy
Patients must have verbal or documented acknowledgement of availability of unstained slides or paraffin block tissue from archived tumor specimen; if not available the patient will undergo a fresh biopsy
Subject’s archival prostate biopsy specimen is available, and subject consents to provide tissue for study endpoint analysis; the prostate biopsy slides or blocks must be available prior to starting any study treatment
Patient must consent to the access, review and analysis of previous medical and cancer history, including tumor archival tissue (if available) and imaging data by the sponsor or a third party nominated by the sponsor.
PHASE I: Must be willing to provide tumor tissue biopsy samples (may be fresh or archival paraffin embedded) at baseline
PHASE IB: Must be willing to provide tumor tissue biopsy samples (may be fresh or archival paraffin embedded) at baseline
Patients enrolled in the escalation and expansion phases will be required to have archival tissue available for analysis.
Patients must have adequate pre-trial formalin-fixed paraffin-embedded (FFPE) tumor material available for use in the biology studies mutational analysis and genome wide sequencing for each stratum\r\n* Patients with DIPG who have tissue available are requested to submit similar tissue as patients in other strata; however, this is not required for eligibility
INCLUSION CRITERIA FOR STRATUM C: Patients must have adequate pre-trial FFPE tumor material available and be willing to provide a blood sample for use in the genome wide sequencing studies; while tissue is required for genome-wide sequencing of tumor and germline samples, patients will be deemed eligible for the study with a minimum of approximately 10 unstained slides for the planned analysis
Locally or centrally confirmed CEA expression in archival tumor tissue
Willingness to undergo tumor biopsy if the patient does not have a known familial cancer syndrome (MEN1, VHL and NF1) or archival tissue available
Formalin fixed paraffin embedded tumor tissue (preferably from current recurrence) must be available to assess Rb1 protein status prior to enrollment; only patients with recurrent diffuse intrinsic brain stem glioma (DIPG) can be enrolled without the need for available tumor tissue for Rb1 protein status confirmation
Tissue for correlative studies must be available (paraffinized or frozen), but confirmation at screening is not needed; archival tissue may be used instead of a fresh biopsy at baseline if it already exists
Diagnostic primary tumor tissue must be available for ERCC1 staining
Patients must have tumor evidence of somatic genomic molecular alteration in EGFR, HER2, ERBB3, or ERBB4, from a test result generated in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory; the tumor tissue sample used to generate the qualifying report must be from a muscle-invasive or higher stage urinary tract cancer specimen (metastatic tissue is also acceptable); final determination about whether a specific tissue source or molecular genomic finding meets criteria as a qualifying result rests with the central study principal investigator (PI)
Patients with breast tumors that are AR+ (?10% staining by immunohisto-chemistry). Archived tumor tissue from a primary biopsy or metastatic lesion for centralized determination of AR expression is mandatory. If tissue is limited, the additional correlative testing is optional. If tissue is not available, a patient will not be eligible for enrollment into the study. Patients may enroll based on local laboratory AR assessment, but will need to submit tissue for confirmation at the central laboratory.
Patients must have measurable disease or evaluable disease for the escalation phase; for the 6 additional patients enrolled at maximum tolerated dose (MTD) for further evaluation of pharmacokinetic (PK) and pharmacodynamic (PD) endpoints (Expansion Arm A), for the 6-patient breast cancer gene (BRCA)-mutation expansion arm, patients must have measurable disease; however, tumor biopsies are optional; for Expansion Arm B, patients must have tumor amenable to biopsy (excisional or incision biopsies of skin or head and neck [H & N] lesions under visualization) and willingness to undergo a tumor biopsy or patient will be undergoing a procedure due to medical necessity during which the tissue may be collected, or tumor biopsy tissue from a previous research study or medical care is available for submission at registration; criteria for the submission of tissue are:\r\n* Tissue must have been collected within 3 months prior to registration\r\n* Patient has not received any intervening therapy for their cancer since the collection of the tumor sample\r\n* Tumor tissue must meet the minimum requirements
Parts B2, B3 & B6 only: Must have adequate tumor tissue sample from archival biopsy available, or willingness to undergo a fresh tumor biopsy
Microsatellite instability (MSI) phenotype of archival tissue biopsy determined by treating institution by polymerase chain reaction (PCR) and immunohistochemistry (IHC) assay
All pathologic diagnoses of subjects from all enrolling sites will be confirmed with tissue block review of previously obtained specimens by Scott VandenBerg, M.D., Ph.D; this will be done in order to assure uniformity in the above subtypes for these sometimes difficult to diagnose tumors; once consent is obtained, subjects’ tissue/slides and corresponding pathology report should be forwarded for central review at University of California at San Diego (UCSD)
Archival tissue block or unstained tumor tissue available for correlative studies
Tumor tissue from the resected site of disease must be provided for biomarker analyses; in order to be treated, a patient must have tissue available for PD-L1 expression analysis by immunohistochemistry (ICH) as determined by the New York University Langone Medical Center (NYULMC) Pathology lab; if insufficient tumor tissue content is provided for analysis, acquisition of additional archived tumor tissue (block and/or slides) for the biomarker analysis is required
Patients must have confirmation of folate receptor-a (FR-alpha) positivity by immunohistochemistry (IHC) (? 25% of tumor staining at ? 2 + intensity) on archival tissue or recent biopsy.
Patients must be willing and able to undergo tissue biopsy for research\r\n* If tumor tissue obtained from the biopsy is deemed inadequate, and the patient is unwilling or unable to have another biopsy, the patient may be considered for enrollment if archival tumor tissue is provided and deemed of adequate quality; this must occur prior to any treatment with rucaparib or mirvetuximab soravtansine\r\n* If biopsy is deemed unsafe to attempt or to perform, and if archival tumor tissue is available and deemed of adequate quality, the patient may enroll on trial\r\n* Biopsy must be of solid tumor tissue; ascites is not acceptable
Archival tumor samples must be available and sufficient for diagnostic and genetic testing; if archival sample insufficient for testing, subject must have lesions amenable to biopsy and be willing to undergo biopsy
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion
Be willing to provide a tissue sample for pre-treatment intra-tumoral assessment of proinflammatory and immunosuppressive factors;
Have pre-resection tissue (Esophagogastroduodenoscopy [EGD] or EUS biopsy from the diagnosis) available
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion. Newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1. Participants for whom newly-obtained samples cannot be provided (e.g. inaccessible or participant safety concern) may submit an archived specimen only upon agreement from the Sponsor
Agreement to access archival tissue or agreement for tumor biopsy prior to treatment
Tumor tissue from an unresectable or metastatic site of disease must be provided for biomarker analyses
Availability of a recent formalin-fixed, paraffin-embedded (FFPE) tumor tissue block; a recently obtained archival FFPE tumor tissue block (if an FFPE tissue block cannot be provided, 15 unstained slides [10 minimum] will be acceptable) from a primary or metastatic tumor resection or biopsy can be provided if it was obtained within 3 years of trial screening; patients with tumor specimens older than 3 years may still be eligible if deemed so by study sponsor
Be willing to provide tissue from an on-treatment fine-needle aspiration (FNA) or core biopsy of a tumor lesion; subjects must consent to on-treatment biopsy prior to initiation of clinical trial, however in subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may still continue on study
Archival tissue for PD-L1 staining (alternatively a new biopsy [core] at baseline can be used); a minimum of 10 slides is required (unless approval from the principal investigator [PI] is obtained)
Willingness to provide paraffin-embedded tissue blocks of ovarian cancer
Insufficient tissue on diagnostic core breast biopsy for analysis
Representative formalin-fixed paraffin-embedded (FFPE) tumor specimens (metastatic specimens preferable but if not available primary tumor specimens that are at least muscle-invasive are acceptable) in paraffin blocks (blocks preferred) or at least 15 unstained slides. If archival tissue is not available, subjects may be considered for enrollment on a case by case basis after discussion with the sponsor-investigator
Other bone and soft tissue sarcomas cohort only: Subjects with other soft tissue sarcomas who have received at least one line of therapy.
All subjects must have adequate archival tissue available prior to registration (i.e., at least 15 unstained slides or paraffin block). Archival tissue should represent invasive or metastatic urothelial cancer with a preference for metastatic tissue if available. Subjects without adequate tissue may be considered on a case by case basis after discussion with the sponsor-investigator.
Untreated/pretreatment archival tumor tissue must be available for correlative analyses
Consent to provide mandatory paired tissue biopsies, obtained within 6 weeks prior to the first study dose of CORT125281 and/or enzalutamide and at Cycle 2 Day 1 (soft tissue biopsy is preferred, when possible)
Archival sample or fresh biopsy or tumor effusion must be available for confirmation of diagnosis
Available primary tumor tissue for CMS4 biomarker assessment.
Be willing to provide archived tumor tissue; tissue from the most obtained core or excisional biopsy of a tumor lesion is preferred; 20 unstained slides are preferred but a minimum of 15 slides will be acceptable; if adequate tissue is not present the patient may consent to a newly obtained biopsy
Patients must consent to a research biopsy of tumor tissue at baseline, for conduct of correlative studies; in cases where a fresh biopsy is not feasible (i.e., if an accessible site cannot be biopsied with acceptable clinical risk), archival tissue may be submitted instead, after discussion with and approval by the principal investigator
Subjects are to have tumor tissue sample available at central lab for PD -L1 immunohistochemical (IHC) testing during the screening period; subjects can initiate therapy before the result of IHC testing; the tumor tissue sample must be a core needle biopsy, excisional or incisional biopsy; it may be fresh or archival if obtained within 6 months prior to enrollment, and there can have been no systemic therapy (e.g., adjuvant or neoadjuvant chemotherapy) given after the sample was obtained
Subjects must be willing to undergo 2 sets of core needle biopsies (pre-treatment and at 6-8 weeks on therapy) if there are lesions amenable to biopsy; subjects without a lesion amendable to biopsy will still be permitted to enroll provided they have an archival tumor sample for PD-L1 IHC testing; an optional core biopsy will be requested at progression (Stage 2 only)
Arm A: Patients with glioma who are positive for the H3 K27M mutation (positive testing in CLIA laboratory) and have completed at least one line of prior therapy. Evidence of progression is not required so that ONC201 may be administered to patients in the maintenance setting or to patients with recurrent disease. No more than two prior episodes of recurrence from radiotherapy and/or chemotherapy are allowed. Use of bevacizumab solely for treatment of radiation necrosis, pseudoprogression, or treatment effect will not be considered a recurrence. Post-mortem biopsy is required if H3 K27M status of tumor is unknown and archival tumor tissue not available. Arm B: Patients with newly diagnosed diffuse intrinsic pontine glioma (DIPG), defined as tumors with a pontine epicenter and diffuse involvement of the pons, are eligible with or without histologic confirmation. Post-mortem biopsy is required if H3 K27M status of tumor is unknown and archival tumor tissue not available.
Archival tumor specimen: All subjects in Arm A must submit at least 5 unstained slides from a tumor specimen that harbors H3 K27M mutation. For subjects in Arm B, at least 5 unstained slides must be submitted if archival tissue is available from the DIPG. For subjects in any arm, if no archival tumor tissue is available, or if H3 K27M status of tumor is unknown, then subjects must agree to submit a post-mortem biopsy specimen.
Subjects must consent to provide archival tumor tissue (initial and subsequent tumor biopsy samples, if possible) for correlative biomarker studies
CD30 staining is to be performed on fresh biopsy or archival formalin-fixed paraffin-embedded (FFPE) tissue however CD30 positivity is not required for eligibility
Patients must have available and be willing to provide formalin fixed paraffin embedded tissue sample from archival tissue (patients who can’t provide archival tissue will be offered an optional biopsy; lack of tissue will not be exclusionary)
Tissue specimen available for B7-H3 and PD-L1 expression testing
Consents to provide tumor tissue sample for the measurement of recent TROP2 levels by immunohistochemistry, which means archived sample following last treatment or pre-DS1062a treatment biopsy (there is no minimum TROP2 expression level required for inclusion)
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion (phase II dose expansion cohort only); newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the Sponsor
Have submitted an evaluable tissue sample for biomarker analysis from a newly obtained core, incisional, or excisional biopsy of a tumor lesion not previously irradiated. The tumor tissue submitted for analysis must be from a single tumor tissue specimen and of sufficient quantity and quality to allow biomarker study. A newly obtained tumor specimen, defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1, for biomarker characterization will be required for enrollment of all subjects. Tissue from tumor progressing at a site of prior radiation may be allowed for biomarker characterization upon agreement from Merck. Subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the Merck.
Must have a tumor lesion safely accessible for biopsy per the investigator’s discretion; while a soft tissue metastasis is preferred for a biopsy, a bone metastasis is allowed for biopsy as long as enough cores can be obtained; a biopsied lesion cannot be used for target lesion for response assessment
DLL3-expressing malignancy based on central immunohistochemical (IHC) testing of representative baseline tumor tissue (archived tissue or on-study biopsy). Positive is defined as staining in ? 1% of tumor cells.
Availability of tumor tissue is mandatory for study eligibility. The participant must have consented to provide archived formalin-fixed paraffin-embedded tumor tissue or be subject to a pre-treatment re-biopsy of primary or metastatic tumor tissue for future central pathology review and translational research (if archived tissue is unavailable).
A representative, formalin-fixed, paraffin-embedded (FFPE) tumor specimen in a paraffin block (preferred) or 20 slides containing unstained, freshly cut, serial sections must be submitted along with an associated pathology report prior to study entry. If 20 slides are not available or the tissue block is not of sufficient size, the patient may still be eligible for the study, after discussion with and approval by the Medical Monitor
Must have provided adequate tissue per the following: Nephrectomy only: tissue from nephrectomy (required); Synchronous M1 NED: tissue from nephrectomy (required) AND, metastasectomy tissue (if available); Metachronous M1 NED: tissue from metastasectomy (required) AND, nephrectomy tissue (if available).
Have tumor tissue for PD L1 expression testing, and for oropharyngeal cancer have results from testing of HPV p16 status.
Agreement to provide mandatory archival tissue or fresh biopsy.
Availability of archival tumor biopsy sample or willing to provide fresh biopsy if not available.
Patients must have a tumor tissue form indicating availability of archived tissue from initial resection at diagnosis of glioblastoma completed and signed by a pathologist; availability of tissue is not a requirement for study participation
Fresh or archived tumor tissue sample available for target expression analysis. [Phase 1b only: Subjects' tumor tissue must test positive for target expression.]
Adequate archival tissue from a biopsy performed after progression of disease on previous EGFR TKI; or willing to undergo a new tumor biopsy prior to registration (for the dose escalation portion only this requirement can be waived if T790M status has already been determined using a local assay)
PHASE II: Tumor tissue for correlative studies is required for all patients except those with NF1 and LGG (stratum 2) or any patient with optic pathway glioma (stratum 2 or 3), for whom tumor tissue is optional
Patients with sporadic (non NF-1 associated), histologically diagnosed progressive, recurrent or refractory non-optic pathway pilocytic astrocytoma who have pre- treatment tumor tissue available for BRAF analysis
Available archival formalin-fixed paraffin-embedded (FFPE) from a prior biopsy or, participant must be willing to have a tissue biopsy taken at a clinic visit prior to start of study treatment
Have archival tissue where available
In addition, patients enrolled on the clinical trial must be willing and able to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; patients for whom newly obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor
Availability of a representative formalin-fixed paraffin-embedded (FFPE) tumour block (preferred) or at least 25 unstained slides with an associated pathology report, if available
Availability of a paraffin-embedded or frozen tumor-tissue block with a minimum of 1 cm^2 of tumor surface area, or 20 unstained slides from the glioblastoma tissue specimen if a tumor block cannot be submitted
Tumor sample must be available for PD-L1 testing; archival tissue within 3 months of study enrollment will be used; if archival tissue is unavailable, a fresh biopsy will be taken
Available tumor samples:\r\n* A formalin-fixed paraffin-embedded (FFPE) tumor tissue block from a de novo tumor biopsy obtained during screening will be required (biopsied tumor lesion should not be a Response Evaluation Criteria in Solid Tumors [RECIST] target lesion); alternatively, a recently obtained archival FFPE tumor tissue block (cut slides not\r\nacceptable) from a primary or metastatic tumor resection or biopsy can be provided if the following criteria are met: 1) the biopsy or resection was performed within 1 year of enrollment AND 2) the patient has not received any intervening systemic anticancer treatment from the time the tissue was obtained and randomization onto the\r\ncurrent study\r\n* Availability of an archival FFPE tumor tissue block from primary tumor resection specimen (if not provided per above); if an FFPE tissue block cannot be provided, 15 unstained slides (10 minimum) will be acceptable
Agreement to provide archival primary or metastatic tumor tissue if available
Have a histologically confirmed diagnosis of:\r\n* Arm 1: melanoma, with =< 5 measurable (as defined by Response Assessment in Neuro-Oncology-Bone Marrow [RANO-BM]) new brain metastases clinically eligible for stereotactic radiosurgery (SRS); tissue diagnosis of the brain metastasis is not required for enrollment if history and imaging is consistent with melanoma and a histopathology is available from the systemic disease; however, a biopsy or surgical excision of one or more of the brain lesions may be performed, if clinically indicated; patient must consent to providing tissue from archival biopsy tissue or newly obtained excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1\r\n* Arm 2: newly diagnosed glioblastoma (World Health Organization [WHO] grade IV)
Archival tumor (up to 10 unstained slides) will be obtained, whenever available for additional biomarker analyses
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; if a freshly procured research specimen has already been made available to the Pollack Lab prior to consent as part of another sample collection research protocol, may be omitted with approval of the primary investigator so long as the patient has not received anti-cancer therapy or immunosuppressive therapy since the biopsy sample was collected
Mandatory tumor tissue must be submitted
Able to submit an archival tumor specimen (primary or metastatic site) and a discussion is documented with trial investigator at screening that patient will consider providing tissue from a newly obtained core or excisional biopsy of a tumor lesion at baseline and a second biopsy 9 weeks after starting trial treatment, unless tumor is considered inaccessible or biopsy is otherwise considered not in the patients best interest. Participation in this trial is not contingent on patient consenting to optional tumor biopsies.
Be willing to provide tissue from archival biopsy tissue or newly obtained excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1
Baseline archival tumor specimen available or willingness to undergo a pretreatment tumor biopsy to obtain the specimen.
A formalin fixed tissue block or equivalent of 24 slides of the tumor sample for analyses by Adaptive Sequenta and NeoGenomics must be available for analysis
Have biopsiable disease; be willing to provide tissue from a newly obtained biopsy of a tumor lesion; newly obtained is defined as a specimen obtained up to 28 days prior to initiation of treatment on day 1
Availability of a paraffin-embedded or frozen tumor-tissue block with a minimum of 1 cm^2 of tumor surface area, or 20 unstained slides from the tumor tissue specimen if a tumor block cannot be submitted
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion. Newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1. Subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen.
Archived or freshly biopsied primary and/or bone metastatic tumor tissue available in paraffin-embedded blocks or slides that is expected to yield 9 slides
Have sufficient available material from archived formalin-fixed paraffin-embedded tumor tissue for biomarker-related studies. If such tissue is not available, a newly obtained core or excisional biopsy of a tumor lesion must be performed.
Prostate biopsy. If previous biopsy has been performed within 3 months of screening, second biopsy procedure will not be required, if archival biopsies and at least one formalin fixed paraffin embedded biopsy tissue block containing tumor is available.
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion. Newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1. Subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen.
The formalin-fixed paraffin-embedded (FFPE) tumor tissue block must be available to be sent for retrospective central pathology review after registration)
Willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion in appropriate low risk cutaneous lesions\r\n* NOTE: if the tissue biopsy is deemed to be of increased risk for the patient, the biopsy should not be performed and is optional\r\n* NOTE: newly-obtained is defined as a specimen obtained up to 42 days prior to registration where no anti-cancer therapy after the specimen was obtained and registration
Patients should be willing to provide a newly obtained fresh core biopsy of a tumor lesion. Not required if there is a recently obtained fresh specimen on an Institutional Review Board (IRB) approved correlated trial up to 6 weeks (42 days) prior to initiation of treatment on day 1.
Archival tissue from a previous biopsy will be required
At least one prior surgery with available archival formalin-fixed paraffin-embedded (FFPE) tumor blocks
A formalin fixed tissue block or at least 15 slides of tumor sample (archival or fresh) must be available for performance of correlative studies; NOTE: Patient must be willing to have a pre-treatment tumor biopsy if adequate archival tissue is not available
Is willing to provide archival tumor tissue from a biopsy performed within 6 months of progression during treatment with erlotinib, gefitinib, or afatinib OR has at least one lesion, not previously irradiated, amenable to core biopsy and is willing to undergo screening tumor biopsy.
Adequate tumor tissue (archival or fresh) must be available for correlative studies\r\n* NOTE: Tumor tissue may be from any previously collected tissue and adequacy is at the discretion of the Principal Investigator; if prior tissue is not available, patient must be willing to undergo baseline tumor biopsy
Patients must agree to have a biopsy of non-bone metastatic tissue at baseline, and there must be a lesion that can be biopsied with acceptable clinical risk as judged by the investigator\r\n* Patients with unsuccessful baseline biopsies or inconclusive DNA damage repair status testing (either MSI or FA/BRCA signature) may undergo an additional biopsy attempt (at the same or a different site, determined by the investigator)\r\n* Patients with previously identified homozygous deletion or deleterious germline or somatic mutation(s) in DNA damage repair gene(s) (such as BRCA1, BRCA2, and ATM) identified in a Clinical Laboratory Improvement Act (CLIA)-certified laboratory are allowed in Group 2\r\n** Somatic mutation(s) in DNA damage repair gene(s) needs to be identified on the biopsy of a castration-resistant metastatic site\r\n** Archival formalin-fixed paraffin-embedded (FFPE) tissue will be requested for determination of MSI and FA/BRCA signature status\r\n*** A formalin-fixed paraffin-embedded (FFPE) tumor specimen in a paraffin block (preferred) or at least 10 slides containing unstained, freshly cut, serial sections must be submitted along with an associated pathology report before study enrollment\r\n*** If archival FFPE tissue is unable to be obtained or is insufficient, patients will be required to undergo biopsy of a metastatic site if feasible for determination of MSI and FA/BRCA signature status\r\n* Patients with germline mutation(s) in mismatch repair (MMR) gene(s) (i.e. Lynch syndrome), or have previously identified MSI-high tumor by polymerase chain reaction (PCR) or MMR deficient tumor by immunohistochemistry (IHC) are also allowed in Group 2\r\n** Archival FFPE tissue will be requested for determination of FA/BRCA signature status\r\n*** A formalin-fixed paraffin-embedded (FFPE) tumor specimen in a paraffin block (preferred) or at least 10 slides containing unstained, freshly cut, serial sections must be submitted along with an associated pathology report before study enrollment\r\n** If archival FFPE tissue is unable to be obtained or is insufficient, patients will be required to undergo biopsy of a metastatic site if feasible for determination of FA/BRCA signature status.
Patients must be willing to provide archival tissue from prior biopsy or surgery for prostate cancer, if available\r\n* A formalin-fixed paraffin-embedded (FFPE) tumor specimen in a paraffin block (preferred) or at least 10 slides containing unstained, freshly cut, serial sections must be submitted along with an associated pathology report before study enrollment
Be willing to consider providing fresh tissue for biomarker analysis, and, based on the adequacy of the tissue sample quality, for assessment of biomarker status. Repeat samples may be required if adequate tissue is not provided. Newly obtained biopsy specimens are preferred to archived samples and formalin-fixed, paraffin-embedded block specimens are preferred to slides. Note: Information on 1 tumor biopsy sample is mandatory and is as follows: (1) To determine eligibility, historical (diagnostic) tumor biopsy official pathology report +/- an archival sample. Additional biopsy samples, preferably obtained from the same localized region, are highly desirable when feasible at the following time points: (2) Sample before the first dose of study treatment, (3) Sample after completion of Cycle 2 but before the start of Cycle 3 dosing, and (4) Sample either at the time of response or at the End of Study Visit (if no response).
Institutional confirmation of pathology on core biopsy (not cytology or fine needle aspiration) or laparoscopic biopsy performed at Memorial Sloan Kettering Cancer Center (MSKCC) with sufficient tissue for analysis, and willingness to undergo repeat biopsy if diagnostic biopsy was performed at an outside hospital
Patients must have available tissue (archived formalin-fixed paraffin embedded [FFPE] blocks or fresh frozen biopsy from primary tumor or metastatic tumor biopsy) for correlative studies; tissue source needs to be located and available at the time of registration (tissue needs to be submitted within 3 weeks of study initiation); patients will not be able to start study drugs without tissue availability
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion
Adequate archival tissue (metastatic tissue sample is preferable but primary tumor tissue will be acceptable) or willing to undergo pre-treatment biopsy (for central confirmation of molecular alteration and PTEN immunohistochemical assessment) if adequate archival tissue is unavailable
Adequate tissue specimens for correlative biomarker analysis; the patient should be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to120 days prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the principal investigator
Patient's tissue must be positive for p16 by immunohistochemical staining (> 70% staining); fine needle aspiration (FNA) biopsy specimens may be used as the sole diagnostic tissue if formalin fixed paraffin-embedded cell block material is available for p16 immunohistochemistry
Availability of archival tumor tissue from the thyroid cancer primary or metastasis (a tissue block or a minimum of 30 unstained slides would be required; patients with less archival tissue available may still be eligible for the study after discussion with the Memorial Sloan-Kettering [MSK] principal investigator)
The subject must have an archived tissue sample such as a prior surgical sample or biopsy sample that is adequate for testing
Be willing to provide archival tissue (if available) for correlative studies\r\n* Note: The archived tumor tissue specimens may be from metastatic tumor specimen (first choice); in alternative, we can consider tissue from prior surgery or from prior diagnostic biopsy (second choice); unavailability of archived tissue will not render subject ineligible for study
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion. Newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1. Subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor
Pathological diagnosis should be obtained by incisional or excisional tissue biopsy; core biopsy is only permissible if obtaining an incisional or excisional is not possible and if the grade can be assessed on the core biopsy
Histologically confirmed, metastatic or unresectable neuroendocrine carcinoma of non-pulmonary origin, high grade as indicated by Ki-67 > 20% and/or > 20 mitoses/10 hpf; patients must have existing Ki67 results from archival tissue or available tissue for Ki-67 testing; if no archival tissue is available the subject must agree to a fresh biopsy for testing to qualify for the study
Provision of suitable tumor tissue for the analysis of Axl kinase expression and PD-L1 expression.
Formalin fixed, paraffin-embedded (FFPE) tumor tissue block or unstained slides of tumor sample (archival) - Biopsy should be excisional, incisional, or core. Needle aspiration is insufficient.
Available tumor tissue for pathologic review and correlative studies; tumor tissue (localized or metastatic) does not need to be received but rather identified and available (slides and/or blocks) to be sent to Duke
Have archived tissue available or be willing to undergo a fresh biopsy during screening, if deemed feasible by the investigator/study principle investigator (PI); if neither available, the patients enrollment must be reviewed and approved by the PI
Representative formalin-fixed paraffin-embedded (FFPE) tumor specimens in paraffin blocks (blocks are preferred) or at least 4 unstained slides, with an associated pathology report, for central testing of tumor PD-L1 expression a) Tumor tissue should be of good quality based on total and viable tumor content. Fine needle aspiration, brushing, cell pellet from pleural effusion, bone metastases, and lavage samples are not acceptable. For core-needle biopsy specimens, at least three cores should be submitted for evaluation. b) Patients who do not have tissue specimens meeting eligibility requirements may undergo a biopsy during the screening period. Acceptable samples include core needle biopsies for deep tumor tissue (minimum of three cores) or excisional, incisional, punch, or forceps biopsies for cutaneous, subcutaneous, or mucosal lesions. c) Tumor tissue from bone metastases is not evaluable for PD-L1 expression and is therefore not acceptable
Subjects must agree to allow use of any pre-treatment tissue remaining after definitive diagnosis is made (ie, archival and or fresh tissue) for research purposes; in addition, subjects must consent to allow use of their residual post-operative tissue for research purposes
The tumor tissue (e.g. block or 15 unstained slides) must be available to be sent for immunophenotyping
STUDY TREATMENT: Tumor tissue from the most recently resected site of disease (preferable) or from the transurethral resection that yielded the initial muscle invasive diagnosis must be provided for biomarker correlative analyses; enrollment is permitted if adequate archived tissue is unavailable
Archival tumor sample available; a minimum of 10 unstained slides; no fine needle aspiration (FNAs) allowed or tumor tissue from bone
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen or leukemic blood sample, only upon written agreement from the study principle investigator (PI)
Participant must consent to repeated biopsy to allow the acquisition of fresh and/or formalin-fixed paraffin-embedded (FFPE) material. Available archived tumor material may be submitted as the pretreatment biopsy provided that minimum requirements are met by local pathology review as defined in the laboratory manual. If archived tumor material is not available or does not meet minimum requirements, then a fresh tumor biopsy must be obtained in accordance with local institutional practice.
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion prior to starting study therapy or from archival tissue of a biopsy that was performed after the most recent systemic therapy
Confirmed availability of representative archival tumor specimens in paraffin blocks (preferred) or >= 10 unstained slides, with an associated pathology report\r\n* Acceptable samples include core needle biopsies for deep tumor tissue or excisional, incisional, or punch biopsies for cutaneous, subcutaneous, or mucosal lesions\r\n* Tumor tissue from bone metastases is not evaluable for PD-L1 expression and is therefore not acceptable\r\n* A subject with insufficient or unavailable archival tissue may be eligible, upon discussion with the principal investigator, if the subject is willing to consent to undergo a pretreatment core, punch, or excisional/incisional biopsy sample collection of the tumor
For breast cancer patients, at least 6 sections of unstained slides should be obtained; if sufficient slides or tissue is unavailable, the patient will be excluded from the trial; for colon cancer patients, confirmation of tissue availability is not required, but documentation that the block is available must be provided to confirm eligibility
Available tissue from prior biopsy (minimum of 10 unstained slides), or willing to undergo core biopsy to obtain tumor material. Biopsy will be mandatory for patients with recurrent disease
Evaluable untreated tumor tissue for biomarker analysis (25 unstained slides or FFPE tissue block); subjects with < 25 slides may be enrolled after discussion with the sponsor-investigator or co-investigator; untreated tumor tissue is defined as no intervening intravesical or systemic therapy since acquisition; subjects without tissue available must be willing and safe to undergo biopsy repeat biopsy (core needle or excisional) prior to enrollment
Willing to undergo a core needle or excisional biopsy on-treatment; subjects will be assessed at the time of biopsy for safety of undergoing the procedure
Confirmed availability of formalin-fixed, paraffin-embedded (FFPE) tumor tissue
Patients with tumor that is felt to be accessible to biopsy must be willing to provide tissue from a newly obtained core biopsy of a tumor lesion at baseline; biopsies will be obtained up to 1 week (7 days) prior to initiation of treatment on cycle 1, day 1; patients who undergo an attempted research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are not required to undergo a repeat biopsy in order to continue on protocol
Patients must have histologically or cytologically confirmed malignant pleural mesothelioma; for phase 2 of this study only, the malignant tissue must show moderate or stronger mesothelin expression in 30% of tumor cells by a companion assay for the patient to be eligible for and registered to the study; for patients in pre-registration for phase 2, submit slides or a tissue block from an archived tissue sample or a fresh tissue sample from biopsy if archived tissue is not available to the central lab for the mesothelin expression assay; central review of pathology will not be performed
Have provided tissue from a newly obtained biopsy obtained from a focus of metastatic disease (an archival tissue sample may be substituted if new biopsy cannot be obtained and by discretion of sponsor investigator)
Consent for use of available archived tissue and tumor obtained during a standard procedure, for research purposes
Subject willing to undergo biopsy prior to treatment with investigational therapy for fresh tissue immune cell analysis and would consider biopsy at disease progression (progression biopsy is not mandated); biopsy should be obtained with core needle; fine needle aspirates are not sufficient; if prior archival tissue is available, it should be submitted
Retroperitoneal soft tissue sarcomas
Tissue Parameters: a. Representative formalin-fixed paraffin-embedded (FFPE) tumor specimens in paraffin blocks (blocks are preferred) or at least 4 unstained slides, with an associated pathology report, for testing of tumor PD-L1 expression (tumor tissue from bone metastases is not evaluable for PD-L1 expression and is therefore not acceptable). b. Tumor tissue should be of good quality based on total and viable tumor content. Fine needle aspiration, brushing, cell pellet from pleural effusion, bone metastases, and lavage samples are not acceptable. For core-needle biopsy specimens, at least three cores should be submitted for evaluation. c. Patients who do not have tissue specimens meeting eligibility requirements must be willing to undergo a biopsy during the screening period
Evaluable tumor tissue (archived or new biopsy) must be available for pre-treatment biomarker analysis and baseline immune monitoring studies
(For Cohort A) - Archived tissue available at pre-screening to confirm FR alpha+ breast cancer
Available archived tissue biopsies will be provided for correlative studies
Inability to obtain Foundation One testing on archival tissue, or, lack of previous next generation sequencing
A formalin-fixed paraffin embedded tumor block (preferred) or unstained slides must be available from a prior biopsy of the primary tumor or lymph node; a minimum of 8 slides must be available
Tissue available for analysis at time of enrollment for biomarker analysis (may be obtained via biopsy prior to initiation of treatment, or submission of available archival tissue: 10-15 slides, or 5 slides with 3 sections per slide
Must agree to a fresh core or excisional biopsy from a metastatic site within a 12-week window prior to enrollment; if such a biopsy is already available, cell blocks must be provided; (Note: fine needle aspiration [FNA] and bone metastases samples are not acceptable for submission); specimens from the nephrectomy and fresh biopsy must be received and assessed for adequacy of tissue by the Data Coordinating Center (DCC) (University of Southern California [USC]) prior to randomization
Phase 2: archival tumor tissue or be willing to provide a pre-treatment biopsy.
Subjects must agree to pre-treament and on-treatment biopsies\r\n* Patients that have available tissue that fulfills the pre-treatment biopsy requirement or other deviations in terms of the tissue requirement, may not need a fresh biopsy at baseline if discussed and approved by the medical monitor
Positivity on CD44 assay as defined by strong (+++) or moderate (++) staining in 20% or more of the tumor tissue/stroma as obtained by biopsy or paracentesis
Available representative tissue (10-15 slides from fresh or formalin fixed paraffin embedded tissue) from the most recent biopsy or archival tumor tissue for clonotype evaluation for minimal residual disease (MRD) testing
Tumor tissue from the core biopsy or resected site of disease must be provided for biomarker analyses
Archival formalin-fixed paraffin-embedded (FFPE) tumor tissue must be available for correlative studies (Note: fine needle aspiration [FNA] and bone metastases samples are not acceptable for submission)
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion after 2 cycles of therapy
Prior local therapy with prostatectomy required, with available tissue from prostatectomy specimen to send for genomic and transcriptomic testing; specifically, either formalin-fixed paraffin-embedded (FFPE) blocks or 35-40 unstained slides from the primary prostatectomy specimen will need to be available for central pathologic review and processing
Agrees to provide available archived tumor tissue specimen; (patients who do not have available archived tumor must agree to have core or excisional biopsy of a tumor lesion obtained up to 42 days prior to the first dose of study drug, if safely accessible; if archived tissue is not available and the tumor is not amenable to safe biopsy, subject is still eligible to participate)
Tumor blocks available from previous surgery/biopsy, or if not available, patients willing to have biopsy
Must have a confirmed diagnosis of metastatic melanoma (cutaneous, acral-lentiginous, uveal and mucosal in origin), based on histological analysis of metastatic tissue and/or cancer cells, archival tissue permitted
Representative formalin-fixed paraffin-embedded (FFPE) tumor specimens in paraffin blocks (blocks are preferred) or at least 5 unstained slides, with an associated pathology report, for central testing of tumor PD-L1 expression \r\n* Tumor tissue should be of good quality based on total and viable tumor content; fine needle aspiration, brushing, cell pellet from pleural effusion, bone metastases, and lavage samples are not acceptable; for core-needle biopsy specimens, at least three cores should be submitted for evaluation\r\n* Patients who do not have tissue specimens meeting eligibility requirements may undergo a biopsy during the screening period; acceptable samples include core needle biopsies for deep tumor tissue (minimum of three cores) or excisional, incisional, punch, or forceps biopsies for cutaneous, subcutaneous, or mucosal lesions\r\n* Tumor tissue from bone metastases is not evaluable for PD-L1 expression and is therefore not acceptable
PRE-SCREENING: Availability of archival or fresh tissue for testing of mesothelin expression level\r\n* Note: archival tissue is preferred and fresh biopsy should only be obtained if no archival tissue is available and if in the investigator’s judgement, there is no additional risk for the patient’s safety; patients with a sarcomatoid histology are not expected to have mesothelin overexpression and should not enter prescreening
Availability of archival or freshly collected tumor tissue before study enrolment
Tissue available from the diagnostic biopsy in the form of blocks, tissue cores, or slides available for submission to central pathology is required for all participants enrolled to this study; formalin-fixed paraffin-embedded tissue from diagnostic tissue is acceptable and recommended; submission of the institutional diagnostic slides is also preferred for all participants enrolled in the study
Agreement to provide mandatory archival tissue or fresh biopsy.
Subject must consent to provide previously collected tumor tissue and a tumor biopsy during screening.
Archived tumor biopsy tissue available from the last relapse and corresponding pathology report available or, if at least one tumor-involved site is deemed accessible at time of screening, willing to undergo pre-treatment biopsy (excisional when possible) for disease confirmation. If a subject has never had a complete response, a sample from the most recent biopsy is acceptable.
Availability of archival tissue for correlative analysis
Able to provide an archival tumor tissue sample if no anticancer therapy was administered since the sample was collected; otherwise, a fresh tumor tissue sample is required prior to the first dose of study drug.
Availability at the study site of formalin-fixed, paraffin-embedded (FFPE) archival tumor specimens, when available, and willingness of the subject to undergo mandatory fresh tumor biopsy prior to treatment initiation unless determined medically unsafe or not feasible; a prior biopsy cannot take the place of the baseline mandatory biopsy\r\n* The archival specimen must contain adequate viable tumor tissue\r\n* The specimen may consist of a tissue block (preferred and should contain the highest grade of tumor) or at least 20 unstained serial sections; fine-needle aspiration, brushings, cell pellet from pleural effusion, bone marrow aspirate/biopsy are not acceptable\r\n* Fresh tumor biopsy at progression will be optional as detailed in study schema
Agree to undergo a biopsy of at least one metastatic site (fresh biopsy of primary prostate only allowed if there is clear local disease and no other measurable disease site or biopsiable bone lesion) to determine DNA repair defects; however:\r\n* Adequate archival metastatic or primary disease tumor tissue can be used if available in lieu of a new biopsy; these patients will only be eligible for protocol therapy if the biopsy has tumor that is positive for DNA repair defects\r\n* Patients with known DNA damage repair defects based on prior appropriately validated metastatic or prostate tissue analysis may be used in lieu of new biopsy/analysis based on central site evaluation of quality of the biopsy and analysis\r\n* Patients with known germline DNA repair defects are eligible without a biopsy; however it will be highly desirable that they undergo a metastatic (or fresh prostate biopsy if there is clear local disease and no other measurable disease site or biopsiable bone lesion) disease biopsy to better define the scope of the DNA repair defects in the current disease context
Have tumor tissue for PD-L1 expression testing
Participants must have sufficient tissue from most recent surgery revealing glioblastoma or variants for submission following registration. The following amount of tissue is required:\r\n* 1 formalin-fixed paraffin-embedded (FFPE) tumor tissue block (preferred) OR\r\n* 10 FFPE unstained slides (5 um thick)
Archival tumor tissue from diagnosis or, preferably, at relapse
If no archive tissue is available, the subject may elect to have a biopsy performed to obtain tissue.
Subject's tumor (either an archival specimen or a fresh biopsy if archival tissue is unavailable) has been pathologically reviewed by a designated central laboratory confirming MAGE-A10 expression.
Must give valid written consent to provide archival formalin-fixed paraffin-embedded (FFPE) and/or newly acquired tumor tissue for the purpose of establishing baseline PD-L1 status as well as consent to provide on- and/or post-treatment tumor biopsy sample
Willingness to undergo a biopsy ? 6 weeks of the start of study treatment to obtain formalin-fixed paraffin-embedded (FFPE) tumor specimens in paraffin blocks (blocks are preferred) or at least 15 unstained slides, with an associated pathology report, for central testing of tumor PD-L1 expression\r\n• Archival tissue is acceptable if obtained within the protocol specified period and if there is no intervening therapy between the tumor biopsy and the initiation of atezolizumab; tumor tissue should be of good quality based on total and viable tumor content; fine-needle aspiration, brushing, cell pellet from pleural effusion, bone metastases, and lavage samples are not acceptable; for core-needle biopsy specimens, at least three cores should be submitted for evaluation\r\n* Patients who do not have tissue specimens meeting eligibility requirements will be required to undergo a biopsy during the screening period; acceptable samples include core-needle biopsies for deep tumor tissue (minimum of three cores) or excisional, incisional, punch, or forceps biopsies for cutaneous, subcutaneous, or mucosal lesions\r\n* Tumor tissue from bone metastases is not evaluable for PD-L1 expression and is therefore not acceptable
Archival tumor tissue retinoblastoma-associated protein (pRb) positive by immunohistochemistry (IHC)
Available archival tumor tissue for correlative studies; submission of archival transrectal ultrasound (TRUS) prostate biopsy tissue is required if available, in the form of representative formalin-fixed paraffin-embedded (FFPE) tumor specimens in paraffin blocks (preferred) or at least 15 slides, with an associated pathology report; if archival prostate tissue are unavailable or cannot be obtained, a repeat TRUS prostate biopsy is not required for eligibility
Archival tissue (paraffin block[s] or unstained slides from paraffin block[s]) from the primary tumor and/or a metastatic site judged reasonably available prior to initiating treatment, or willingness to undergo fresh pre-treatment tumor biopsy; (prior to initiating treatment, the screening team must have documentation that an archival or fresh tumor specimen has been requested from a local or outside facility; however, physical possession of requested tissue or waiting for histological analysis or confirmation that an acquired specimen contains tumor tissue sufficient for analysis is not a requirement prior to initiating treatment); if no archival tissue is available and patient consents to a fresh biopsy, but the patient’s lesion is deemed inaccessible to safe biopsy, the patient will be allowed to enroll if otherwise eligible
Be willing to provide archival tissue from a tumor lesion or obtain a new biopsy if tissue unavailable
Tumor must have dysregulation of the PI3K/AKT/mTOR pathway; for the purposes of this study, patients must have either PTEN protein or genomic loss, or PIK3CA/PTEN mutation; patients must be willing to provide sufficient archival tissue; if this is not available fresh tumor for biopsy is required; in the event that a patient has had tumor analyzed for PTEN/PIK3CA status through commercial means, their eligibility and need for additional tissue will be determined on a case by case basis by the principal investigator
Subjects must be able to provide tissue from 2-3 separate biopsy procedures that will be completed throughout the course of the study; day 1 biopsy: required only if a pre-study biopsy is not available or if a subject has received prior radiation at a tumor site and will be re-radiated at that tumor site as part of the proposed study; the pre-study biopsy may be obtained up to 6 weeks prior to initiation of treatment on day 1; there should be no intervening treatment in between the pre-study biopsy and day 1; day 22 biopsy: required; day 43 biopsy: required
The patient/legal representative must be willing to provide written consent for collection of formalin fixed paraffin-embedded blocks or slides from archival diagnostic histology samples, where available
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor-investigator
Presence of KRAS or BRAF mutation in tumor tissue
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor
Be willing to provide tissue from a newly obtained or archival tissue, if available
Willing to donate tissue to research from the surgical specimen
Phase II only: participant agrees to provide tumor biopsy tissue before treatment, blood samples at the start of treatment and at multiple times during the study and, a tumor biopsy at the end of the trial or after disease progression
Tumor available for fresh biopsy (two biopsies – pretreatment as regards enzalutamide, and during treatment at 4 weeks); the patient will be asked if they would be willing to provide a third biopsy at time of progression
Must have archival tissue available for PD-L1 assessment
Tumor tissue must be available for review to confirm histological diagnosis
Tumor block or unstained slides must be available for molecular profiling
Having archival paraffin tissue is ideal for the correlative study but it is not mandatory
Availability of a diagnostic or pre-chemotherapy tissue biopsy is required (cytologic specimens or bone biopsies not accepted); this biopsy must be within 6 weeks of starting initial therapy; a minimum of 20 5um slides or block is required
Participants in cohorts B-D must be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen within 4 weeks to initiation of treatment and AFTER the last dose of any prior therapy
Available tissue to perform protein and genomic analysis
Adequate archival tissue (10-15 slides, or 5 slides with 3 sections per slide) for biomarker analysis
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion from a metastatic site; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from Merck; the specimen must be from a biopsy site that would be accessible for at least one subsequent biopsy after initiation on the trial
Archival tissue from diagnostic/core biopsy must be available; patients who had a biopsy at an outside institution are eligible as long as it is confirmed that an archival tumor specimen, with an associated pathology report, is available
Patients must have confirmed availability of archival or freshly biopsied tumor tissue meeting protocol-defined specifications prior to study enrollment
Archival tumor tissue slides must be sent or available
Adequate archival tissue must be available from the prior 3 months to signing consent; if not, an adequate tumor specimen obtained by either excisional biopsy, incisional biopsy or core needle biopsy must be sent to the central pathology lab for evaluation; the material must measure at least 0.8 x 0.1 cm in size or contain at least 100 tumor cells
Have provided tissue for PD-L1 biomarker analysis from a newly obtained formalin fixed tumor tissue from a biopsy of a tumor lesion not previously irradiated; the tissue sample must be received and evaluated by the study site prior to start of treatment; fine needle aspirates are not acceptable; needle or excisional biopsies, or resected tissue is required
Tissue available (archived or fresh tumor biopsy) for the PD-L1 assay
Patients must have a pre-treatment tumor specimen available for correlative studies, either core needle biopsy or equivalent amount or via excisional specimen (cytology specimen not acceptable for this purpose); if an archival specimen is to be used then no interceding anticancer therapy (systemic therapy or radiation to the biopsied lesion) should have been administered since that specimen was obtained; patients with no available archived specimen must be willing to undergo a pre-treatment tumor biopsy
Participant must be willing to undergo core or excisional biopsy of a tumor lesion within 4 weeks (28 days) prior to initiation of treatment on day 1 and, after 3 cycles of study treatment; participants for whom newly obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the principal investigator
Sufficient baseline tumor tissue available to perform tumor infiltrating CD8+ T-cell density assessment; (NOTE: The actual CD8+ T-cell density assessment does not need to be performed prior to registration, however the slides must be reviewed prior to registration to ensure that adequate tissue will be available for the pre-treatment tumor infiltrating CD8+ T-cell density assessment)
Fresh or archived colorectal cancer tissue, preferably from a hepatic metastatic site; archival tissue is acceptable for enrollment into this study; subjects who have no archival tissue available do not need to undergo a new biopsy solely for the purpose of this study
Subjects must provide archived tumor specimens for correlative biomarker studies if sufficient tissue is available; a fresh biopsy is not required
Willing to provide consent for an additional tissue biopsy for research purposes, to allow a part of their surgical tumor tissue to be utilized for research (in case tumor tissue has not already been saved in the tumor tissue bank), and to donate samples of blood and saliva collected weekly through the treatment
Be willing to provide archival or fresh tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 4 weeks (28 days) prior to initiation of treatment on day 1; subjects from whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the principal investigator
Subjects must consent to provide archived tumor specimens for correlative biomarker studies; tumor tissue must be identified and availability confirmed prior to initiation of study therapy; in the setting where archival material is unavailable or unsuitable for use, or there have been multiple intervening therapies subjects must consent and undergo fresh tumor biopsy; a tumor lesion planned for biopsy must not be an irRECIST target lesion unless there are no other lesions suitable for biopsy and lesion used for biopsy is >= 2 cm in longest diameter
Patients must have tissue resected by transurethral resection of bladder tissue (TURBT) at the MD Anderson Cancer Center
Archival sample or fresh biopsy or tumor effusion must be available for confirmation of diagnosis
Have submitted a tumor tissue sample, as follows:
For participants entering the Phase 1a dose escalation: have submitted, if available, the most recent archival tumor tissue sample.
For participants participating ONLY in the Phase 1b expansion: have submitted tissue sample from either a newly obtained core or excisional biopsy of a tumor lesion (preferred) or a recent biopsy since last documented progression of disease.
For those participating ONLY in Phase 1b abemaciclib or merestinib expansions: Have submitted tumor tissue sample from a newly obtained core or excisional biopsy for a tumor lesion (preferred) or a recent biopsy taken with 3 months prior to study enrollment and following the participants most recent prior systemic treatment and be willing to undergo a biopsy procedure during the study treatment period for collection of additional tumor tissue sample.
Archival tumor tissue must be available for enrollment
Must have neuroblastoma lesion(s) amenable to non-significant risk biopsy for next generation sequencing (NGS) profiling at Foundation Medicine; biopsies of the brain; lung/mediastinum; pancreas; endoscopic procedures extending beyond the lung, stomach, or bowel; or other significant risk biopsies will not be performed as part of this study; if a subject has tumor tissue archived from a previous biopsy, that tissue may be sent to Foundation Medicine for NGS and an additional biopsy will not be required
The patient must consent to a research biopsy at baseline, and during week 2 of cisplatin-IMRT; all patients will be evaluated for the feasibility of research biopsy at the time of enrollment, as a condition of eligibility; the performing physician must agree that a cup forceps biopsy or an 18 to 14 gauge core needle biopsy can be safely performed; every effort will be made to couple the baseline research biopsy to a standard of care diagnostic or staging procedure; NOTE: patients who have had research tissue procured under an omnibus tissue consent, who are determined to have sufficient fresh, fresh-frozen, and paraffin tissue for analysis of immune-inflammatory biomarkers per the translational science co-chair, may substitute the archived tissue and do not need to undergo baseline research biopsy; such tissue must have been obtained within the prior 24 weeks and no interval anti-cancer therapy administered
Measurable metastatic cancer that expresses NY ESO-1 as assessed by one of the following methods: reverse transcriptase-polymerase chain reaction (RT-PCR) on tumor tissue, or by immunohistochemistry of resected tissue, or serum antibody reactive with ESO
UROTHELIAL CARCINOMA EXPANSION COHORT: Willingness to release archival tissue sample for research purposes, if available
Be willing to provide tissue from a newly obtained bone marrow aspirate and/or biopsy; newly-obtained is defined as a specimen obtained up to 28 days prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g., inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the principal investigator (PI)
Patients must be willing to undergo a biopsy of the cancerous tissue if one was not taken within the previous year, prior to drug initiation if tumor block is not available; biopsy must be done within 14 days of first planned drug dose
Participant must have archived tumor tissue available from initial diagnosis or subsequent relapse(s) of Grade IV GBM for submission for central review at Investigational sites local laboratories.
Archival tissue samples and/or fresh tumor biopsy samples:
Subjects should agree to provide archival and/or fresh tumor biopsy samples
Archival tumor samples should be collected for all enrolled subjects; if archival tissue samples are not available, a recent core needle biopsy should be collected
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the PI or designee
Be willing to undergo tissue biopsies as mandatory as per protocol for patients with biopsy accessible disease
Dose Escalation: Able and willing to give valid written consent to undergo a new tumour biopsy (prior to study treatment) or to provide an available archival tumour sample if taken <3 years prior to enrolment if a new tumour biopsy is not feasible with an acceptable clinical risk.
Cohort Expansion: Able and willing to give valid written consent to undergo a new tumour biopsy (prior to study treatment). Able and willing to undergo a second tumour biopsy on treatment. Where possible, tumour lesions used for new biopsies should not be the same lesions used as RECIST target lesions, unless there are no other lesions suitable for biopsy. Archival samples may be required if there is inadequate tissue in the biopsy specimen.
Central pathology review to determine evaluability of archived esophagogastroduodenoscopy (EGD)/biopsy sample\r\n* NOTE: If archived sample was collected > 8 weeks prior to pre-registration (reg), is not available in a timely manner, or was collected outside of Mayo Clinic and considered unevaluable, then baseline EGD with primary tumor biopsy at Mayo Clinic must be performed unless clinically contraindicated; patient is allowed to enroll regardless of whether this Mayo Clinic tissue sample is evaluable; (only 1 EGD with primary tumor biopsy performed at Mayo Clinic =< 8 weeks prior to pre-reg is required)\r\n* NOTE: For both archival or newly obtained tissue, only biopsies are adequate (fine needle aspiration [FNA] is not adequate)
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion or ascites or plural effusions via paracentesis or thoracentesis; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement of the investigator
Pre-treatment tumor tissue available for research purposes; this tissue can be collected from preoperative laparoscopy, other diagnostic biopsy, or a research-specific biopsy; this pre-treatment tumor must be amenable to repeat tissue sampling after induction therapy
Be willing to provide archival tissue; if archival tissue is not available, or a newly obtained core or excisional biopsy of a tumor lesion will be obtained; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; in cohort 9: paraganglioma-pheochromocytoma or cohort 10, where there is prominent bony disease, biopsies may not be possible due to the nature of the disease
The subject must be medically capable of providing the necessary tissue sample for sequencing, either by surgical resection or open-surgical or core biopsy sampling of the primary tumor\r\n* This requirement may be satisfied by providing an archival tissue sample in the form of a formalin-fixed paraffin-embedded or frozen tissue block from an earlier resection
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained for up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the Sponsor; an optional core biopsy will be requested from an accessible metastatic site after 2 cycles of treatment
If they have previously undergone a VATS, or they do not have a free pleural space to allow for a VATS procedure, then they must be able to undergo a computed tomography (CT) or ultrasound guided needle biopsy to obtain baseline tissue if it is feasible; if this is not anatomically feasible, then they must be able to provide at least 15 unstained slides or a tumor block from their prior biopsy
Availability of tumor tissue (e.g. formalin-fixed, paraffin-embedded [FFPE]) for genomic profile (typically 12 unstained FFPE 5-10 micron slides, minimum of 10)
Patients must agree to submission of tumor tissue from transurethral resection of the bladder tumor (TURBT) including a paraffin block or 20 formalin-fixed paraffin embedded (FFPE) slides of 5-10 microns in thickness; patients must also agree to submission of tissue from cystectomy
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived sample
PD-L1 expression in tumor tissue from any site is required for patients with NSCLC; tumor tissue can be archival, however if no archival tissue is available then a biopsy must be obtained for PD-L1 testing; PD-L1 expression will be analyzed by a Merck assay; PD-L1 expression is not required for patients with melanoma, but melanoma patients are required to submit an extra-cerebral specimen for analysis, unless it is not feasible to obtain one
Have provided tissue for PD-L1 biomarker analysis from either archived tissue or a newly obtained core or excisional biopsy
Patients must have available tissue (archived formalin-fixed paraffin embedded blocks [FFPB] or fresh frozen tissue from original diagnosis or metastatic setting) for correlative studies; patients will not be able to start study drugs without tumor tissue availability; patients without available tumor tissue can still participate if willing to have a fresh biopsy of a metastatic lesion that is deemed to be medically safe (except for bone metastases)
Sufficient tumor tissue available from original diagnosis or subsequent biopsy for analysis of estrogen receptor and aromatase – tumor block or a minimum of 5 unstained slides
PHASE I AND PHASE II DOSE EXPANSION IN RECURRENT GBM UNDERGOING RESECTION: Be willing to provide tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion
PHASE II DOSE EXPANSION IN NEWLY DIAGNOSED GBM: Be willing to provide tissue from an archival tissue sample
At screening, must have tissue available for NY-ESO-1 testing (if not previously performed) or be willing and able to undergo a fresh tissue biopsy
Have archival tissue where available; those patients enrolled on the phase 1 escalation trial where archival tissue is not available will undergo a fresh biopsy where clinically feasible after discussion with the sponsor
Availability of archival tumor tissue for biomarkers analysis (minimum of 10 unstained slides are optional); specimen from primary site will be allowed
Availability of fresh tumor tissue and/or archival tumor tissue at Screening
Tumor tissue available from original diagnosis and/or recurrence; a minimum of 1 FFPE archival tumor tissue block (preferred) or a minimum of 20 FFPE unstained slides from initial and/or most recent pre-registration biopsy or resection. It is recommended that at least 1 cm^2 of tissue composed primarily (defined as greater than 85%) of tumor is present.
Willingness to provide newly obtained tumor tissue at baseline and on treatment unless contraindicated by medical risk in the opinion of the treating physician.
Patients must have adequate fresh or frozen tissue available; if tissue is needed, then subjects may have had it collected previously under protocol PA15-0176
Be willing to provide tissue from a recently obtained core or excisional biopsy of a tumor lesion. Newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on Day -7. Subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from Sanford Research.
Patient must be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 months (168 days) prior to initiation of treatment on day 1; archived specimen can be used for subjects in whom newly-obtained samples cannot be provided
Patients must be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 12 weeks (84 days) prior to date of signing consent; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor; at least 4 mm of tumor tissue will be needed for programmed cell death-ligand (PD-L1) staining
Biopsy containing ? 10 tissue cores sampled
All patients must be willing to provide research tumor tissue for biomarker studies at baseline (from archival tumor tissue or through endoscopy if sufficient archival tissue is not available); all patients must also allow biomarker studies on the tissue obtained through surgery to remove the primary cancer
Availability of archival tumor material, either as a block or slides (Phase Ia and Ib). If no archival material is available then a fresh biopsy should be taken
Have archival tissue available or undergo a fresh biopsy where clinically feasible after discussion with the sponsor
Submission of formalin-fixed, paraffin-embedded (FFPE) archival tumor specimens from the previous 18 months, if available; if not available, a fresh tumor biopsy prior to treatment initiation is MANDATORY unless determined medically unsafe or not feasible by the site investigator\r\n* The archival specimen must contain adequate viable tumor tissue\r\n* Specimens may consist of a tissue block (preferred and should contain the highest grade of tumor) or a recommended minimum of 20 unstained serial sections; fine-needle aspiration, brushings, cell pellet from pleural effusion, bone marrow aspirate/biopsy are not acceptable\r\n* Distant metastases specimens are preferred but if not available primary nephrectomy specimens are acceptable
Availability of a formalin-fixed, paraffin-embedded (FFPE) tumor tissue block from a de novo tumor biopsy during screening (biopsied tumor lesion should not be a RECIST target lesion). Alternatively, a recently obtained archival FFPE tumor tissue block (not cut slides) from a primary or metastatic tumor resection or biopsy can be provided if the following criteria are met: 1) the biopsy or resection was performed within 1 year of randomization AND 2) the patient has not received any intervening systemic anti-cancer treatment from the time the tissue was obtained and randomization onto the current study. If an FFPE tissue block cannot be provided as per documented regulations then, 15 unstained slides (10 minimum) will be acceptable
Availability of an archival FFPE tumor tissue from primary tumor resection specimen (if not provided per above). If an FFPE tissue block cannot be providedas per documented regulations 15 unstained slides (10 minimum) will be acceptable
Available tissue from a newly obtained core biopsy of a tumor lesion not previously irradiated
Has sufficient tumor tissue (slides or blocks) available for central confirmatory testing of IHC and/or cytogenetics/FISH and/or DNA mutation analysis (required for study entry but enrollment based on local results)
Availability of tissue for correlative studies; patients must have at least 6-8 unstained slides of archived formalin-fixed, paraffin-embedded tumor tissue available; if not enough archived tissue is available, a fresh tumor biopsy prior to study initiation is mandatory; for patients who have undergone a fresh baseline biopsy at baseline, the archived tissue is not mandatory
Tissue submitted for HRG-biomarker testing
Subject has one archived diagnostic formalin-fixed paraffin embedded (FFPE) tumor tissue confirmed available for analyses.
Patient must have an available archival/pre-treatment block or fresh tumor biopsy for molecular profiling to be performed
Archival tissue is mandatory (a tumor biopsy-core or excisional) of a metastatic lesion obtained within 1 year prior to study registration (within 4 weeks preferred); tumor tissue from nephrectomy and site of metastasis will be requested; if archival tissue of a metastatic lesion obtained within the preceding year is not available, patients must have at least one site of disease (not including bone metastases) accessible for core needle or excisional biopsy; if archival tissue of a metastatic lesion is not available and biopsy of a new lesion is not feasible, the subject is not eligible for the study
Patients must have archival tissue, 10-20 slides, available for review and testing
No archival or newly biopsied tissue available for analysis
Subjects must agree to provide archival and/or fresh tissue biopsy samples, if available. Tumor biopsy will be done only if the subject has a lesion for which, in the opinion of the Investigator, a non- or minimally invasive tumor biopsy may be performed.
Phase 1b only: Formalin-fixed paraffin embedded blocks (FFPB) or fresh frozen tissue from the original diagnosis or the metastatic setting should be located; tissue must be submitted with 3 weeks of study initiation
Phase II only: Biopsy of a metastatic lesion in patients with reasonably accessible metastatic lesions (chest wall, skin, subcutaneous tissue, lymph nodes, skin, breast, bones, lung, and liver metastases); if a reasonably accessible metastatic lesion is not available, the patient may go on study provided that archived tissue is available; however, if a reasonably accessible site is available for biopsy, the patient must agree to biopsy; any patients not undergoing biopsy must be approved for study enrollment by the Protocol Chair; biopsies may be done with local anesthesia or intravenous conscious sedation, according to institutional guidelines; if a biopsy requires general anesthesia, then it is only allowed if acquisition of tissue is clinically indicated, and excess tissue may be collected for research purposes; patients without sites available for biopsy must have available tissue (archived formalin-fixed paraffin embedded blocks [FFPB] or fresh frozen tissue from original diagnosis or metastatic setting) for correlative studies; tissue needs to be located and available at the time of registration (tissue needs to be submitted within 3 weeks of study initiation)
Archival tumor sample available, or be willing to undergo a fresh tumor biopsy, prior to study
Subject has appropriate tissue available from the cytoreductive surgery for tumor lysate preparation
Agree to undergo a core biopsy of the pancreatic tumor for both research and diagnosis purposes if a prior core biopsy is not performed or the core biopsy specimen is not available for the research purpose of this study
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion
The subject must be expected to have an adequate amount of tumor burden to yield 2-4 pre-operative research core biopsy (14-gauge needle) specimens or the equivalent amount of tissue (4-6 mm punch biopsy), in addition, to the tissue required for diagnostic purposes
The subject must be expected to have an adequate amount of residual tumor after their pre-operative research tumor tissue collection, such that their operative research tumor collection will also yield at least 4-6 research core biopsy specimens or the equivalent amount of tissue
The subject must be willing to undergo the two paired tumor tissue biopsy procedures to obtain samples for biomarker analysis; tissue obtained must not be previously irradiated
Consented for genome sequencing and database of Genotypes and Phenotypes (dbGAP)-based data sharing and has provided or will provide germline and tumor DNA samples of adequate quality for sequencing; fresh tissue is preferred (from biopsy at the time of port placement) but archival tissue is allowed
Archival tumor sample available; a minimum of 10 unstained slides; no fine needle aspiration (FNAs) allowed or tumor tissue from bone
Fresh or archived tumor specimen should be available for correlative studies as required
Prior to registration, all subjects must have adequate archival tissue available prior (unstained slides are to be submitted as outlined in the study procedures manual); if no acceptable archival tissue is available, the subjects must be willing to consent to providing a mandatory pre-treatment core biopsy for research; phase II subjects must be willing to consent to providing a mandatory post-treatment core biopsy for research; fine needle aspiration and cytology samples will not be acceptable
Tissue available (either initial diagnostic or recurrent tissue specimen) for p16 testing (if p16 status is already known, this criterion may be waived)
Availability of fresh tumor tissue and/or archival tumor tissue (obtained within 5 years of the consent date) at Screening
Adequate archival tissue for determination of EGFR-mutation status and PD-L1 status with a leftover cell block (or equivalent) for additional immune correlates from a tumor lesion biopsied in the last 60 days that has not been previously irradiated occurring: 1) after progression on erlotinib and no intervening systemic treatment between biopsy and initiation of MK-3475 and afatinib or amenable to repeat biopsy
Be willing to consent for biopsy at baseline (if inadequate archival tissue per inclusion criteria above) and an on treatment biopsy; have a tumor in a location that in the opinion of the investigator that is amenable to biopsy or have provided tissue for PD-L1 and other biomarker analysis from a newly obtained (within 60 days) formalin fixed tumor tissue from a recent biopsy of a tumor lesion not previously irradiated; no systemic antineoplastic therapy may be administered between the PD- L1 biopsy and initiating study medication; fine needle aspirates are not acceptable; core needle or excisional biopsies, or resected tissue is required
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion
Patients who have tumor deposit(s) that are easily accessible by ultrasound or computed tomography (CT) guidance will be eligible for study; this is the case even in the event that a qualifying archived tumor sample is already available for a particular patient?qualifying archived tumor tissue is tissue extracted while the patient was in the same untreated state as when screened (usually tissue taken within 8 weeks prior to screening)
Tissue block of initial biopsy specimen is available
Patients must:\r\n* Be scheduled to undergo a standard-of-care resection of tumor tissue as part of treatment plan prior to beginning study therapy OR pre-treatment biopsy; patients may not have intervening systemic anti-cancer therapy between the time of resection/biopsy and treatment with nivolumab\r\n* Have collection of adequate pre-treatment tissue for correlative analysis defined as sufficient material for 1) frozen tissue for deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) extraction, 2) formalin-fixed, paraffin-embedded (FFPE) material for immunohistochemistry (IHC); adequacy of collected material will be determined within 5 business days of each collected case\r\n* Have measurable by Response Evaluation Criteria in Solid Tumors (RECIST) version (v) 1.1 (those undergoing pre-treatment resection must have imaging assessment after resection to determine measurability)\r\n** Previously irradiated sites of tumor may be considered measurable if there is radiographic progression at that site subsequent to the time of completing radiation\r\n* Have a safely biopsiable tumor lesion
Consented for genome sequencing and database of Genotypes and Phenotypes (dbGAP)-based data sharing and has provided or will provide germline and tumor DNA samples of adequate quality for sequencing; fresh tissue is preferred (from biopsy at the time of port placement) but archival tissue is allowed
Have provided tumor tissue from a newly obtained core, punch, incisional or excisional tumor biopsy; patients must undergo biopsy (core, punch) or open incisional/excisional biopsy (if done as part of a clinically indicated baseline diagnostic procedure) within 4 weeks of registration on the study
Tumor blocks available from previous surgery/biopsy, or if not available, patients willing to have biopsy
Provision of tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion\r\n* Tumor tissue may be from a diagnostic biopsy or a portion of a surgical specimen, if surgery is a component of definitive intent therapy\r\n* Formalin fixed paraffin embedded (FFPE) tissue samples are acceptable; a fine needle aspirate, frozen sample, plastic embedded sample, cell block, clot, bone, bone marrow or cytologic specimen will not be acceptable for immunohistochemistry (IHC) analysis\r\n* It is recommended that FFPE blocks be sectioned fresh (within 7 days of sectioning and sending for PD-L1 analysis) onto positively charged slides; slides should be stored and shipped (and stored upon receipt at Qualtek) at 2-8 Celsius (C) in the dark\r\n* Recommended fixation time for samples is 24 hours to 48 hours in 10% neutral buffered formalin
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion
Subject has no tissue from UPCC19809 end of study (EOS) biopsy and unwilling to undergo screening biopsy
Patients must have tumor suitable for biopsy (as assessed by trained specialists in interventional radiology) and medically fit to undergo a biopsy or surgical procedure OR if patients do not have a tumor suitable for biopsy but have another tissue (preferably progressive metastatic site) available for molecular evaluation (biopsy will be performed through Ohio State University [OSU]-13053 study or the University of Michigan [UM] Precision Cancer Study)
Histologically proven non-small-cell lung cancer (core biopsy required)\r\n* Squamous or non-squamous histology\r\n* Diagnostic core biopsy specimens must be reviewed by a faculty pathologist at Sidney Kimmel Comprehensive Cancer Center (SKCCC) or Memorial Sloan Kettering Cancer Center (MSKCC)\r\n* Either a formalin fixed paraffin block that has been confirmed by a pathologist to contain tumor or a minimum of twenty 5-micron tissue sections (slides) of tumor biopsy sample must be available for biomarker evaluation (study pathologist must review for adequacy of sampling); this can be obtained from archived tissues if adequate, or from a new biopsy as needed
Biopsy-proven relapsed (response to last treatment > 6 months duration), refractory (no response to last treatment or response duration < 6 months) or residual Hodgkin lymphoma; NOTE: re-biopsy is necessary unless the patient has had a previous biopsy < 180 days prior to registration on this protocol with no intervening therapy and tissue is available for translational research studies
Tumor specimen (paraffin-embedded block or frozen tissue) from prior resection or biopsy available that is sufficient to perform pharmacodynamic assays (>= 3 slides for immunohistochemistry [IHC]) – mandatory for patients in the dose expansion cohort only; if the specific diagnosis occurs radiologically as standard of care and a diagnostic procedure is too dangerous for any reason, subjects may be enrolled on study without tissue that being available for correlative studies
Patient must consent to the use of their archival tumor tissue for protocol use if available
Availability of archival tumor tissue from the thyroid cancer primary or metastasis (a tissue block or a minimum of 30 unstained slides would be required; patients with less archival tissue available may still be eligible for the study after discussion with the MSK principal investigator)
Archival tissue (10 unstained slides - 5 micron sections) from a core biopsy performed and received within 30 days before signing consent or ability to have a fresh core biopsy performed\r\n* Biopsy cannot be from cytology or bone specimen\r\n* Biopsy site must be amenable to re-biopsy at the end of study\r\n** In the event that the tumor resolves on treatment, another site amenable to biopsy will be selected
Participants must have histologically confirmed neuroblastoma or ganglioneuroblastoma or elevated urinary catecholamine metabolites; if tumor tissue was obtained, pathological review of surgical specimen at the Massachusetts General Hospital or other Dana-Farber (DF)/Harvard Cancer Center (HCC) institution is required, but preliminary report only required prior to enrollment; if no tumor tissue was obtained, urinary catecholamine metabolites are required
Patients must consent to participate in the correlative studies and should have available tumor tissue for tumor biopsies
Paired pre-treatment and post-treatment biopsies are required for all patients on Part 1 and first 15 patients in Part 2; participants must have available archival tumor tissue (at least 20 unstained slides); if archival tissue is not available or is found not to contain tumor tissue, a fresh biopsy is required; if a patient is having a tumor biopsy, less than 20 unstained slides are acceptable with approval of the principal investigator (PI); biopsies will only be performed in a given patient if they are not deemed to involve unacceptable risk based on the sites of disease and other concurrent medical conditions
Paraffin block or slides must be available
>= 5 mm by imaging/pathology of core to ensure enough pre- and post-treatment tissue for analysis
Tumor specimens must be available for immunological studies, either from a previous biopsy or a new biopsy obtained before the initiation day 1 of the study
Measurable metastatic cancer or locally advanced refractory/recurrent malignancy including melanoma that expresses ESO as assessed by one of the following methods: reverse transcriptase-polymerase chain reaction (RT-PCR) on tumor tissue, or by immunohistochemistry of resected tissue, or serum antibody reactive with ESO
For expansion cohort, patients must consent to provide tissue from newly obtained (during screening period) core or excisional biopsy of a tumor lesion.
Archival tumor tissue sample must be requested and available prior to study entry; a copy of the local pathology report must be submitted along with the specimens; patients without available archival tissue are excluded
Patients must have archival tissue sample (if available) or be willing to undergo a repeat biopsy (if feasible)
cMet expression in >= 30% tumor cells as demonstrated on immuno-histochemistry analysis of archival slides; punch biopsy or percutaneous core biopsy may be offered to Cohort 1 patients
At least 1 lesion amenable for an outpatient biopsy; this should be a cutaneous or palpable metastatic site or a deeper site accessible by image-guided biopsy that is deemed safe to access by the treating physicians and interventional radiologists; patients without accessible lesions for biopsy but with prior tissue available from metastatic disease would be eligible at the investigator's discretion
Availability of tumor tissue for mesothelin expression testing and for further biomarker analysis
Available tissue of primary lung tumor
Qualifying HRR mutation in tumor tissue.
Willing to provide mandatory archival tumor tissue (block or minimum of 30 unstained slides from a primary or recurrent/metastatic thyroid cancer) for correlative research purposes; NOTE: patients with less archival tumor tissue available may still be eligible for the study after discussion with Academic and Community Cancer Research United (ACCRU); receipt of archival tumor tissue is not required for study registration and initiation of therapy
Representative baseline tumor tissue sample is available
Agreement to provide mandatory archival tissue or fresh biopsy
Willing to provide tumor tissue for biomarker analysis and/or archival tissue available from original diagnostic block
Sufficient tumor tissue for planned analysis
Archival tumor tissue obtained at any time from the initial diagnosis to study entry. Although a fresh biopsy obtained during screening is preferred, archival tumor specimen is acceptable if it is not feasible to obtain a fresh biopsy. Subjects enrolled in a PK/Pharmacodynamic Cohort must provide a fresh biopsy of a tumor lesion not previously irradiated during the screening period and must agree to provide at least one additional on-treatment biopsy.
Be able to provide formalin fixed, paraffin-embedded (FFPE) tumor tissue obtained from either a core or excisional tumor biopsy;
Existence of archival or fresh biopsy for FGFR testing
Available tissue for PD-L1 staining (archival or new core needle biopsy at baseline if no archival tissue available); a minimum of 10 slides are required (unless approval from the PI is obtained)
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 10 weeks (70 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen (if available from prior biopsy) only upon agreement from the sponsor
Possibility of obtaining sufficient tissue sample, via a biopsy or surgical resection of the primary tumour or metastatic tumour tissue
It is preferable that patients have an adequate tissue sample available for correlative studies evaluating SAG expression, cullin neddylation, and KRAS^G12D mutation, but lack of availability of such a tissue sample is not a requirement for trial enrollment
Consent to provide archival tumor tissue and pre/on-treatment biopsies
Available archived tumor (formalin-fixed, paraffin-embedded tissue block) for genomic and proteomic analysis
Provides an archival or newly obtained tumor tissue sample and blood samples for biomarker analysis.
Be willing to provide tissue from a newly obtained oral biopsy
Subjects must provide samples of tumor tissue
Consent to tumor biopsy from accessible tissue (optional in part 1, mandatory in part 2)
Representative formalin-fixed paraffin-embedded (FFPE) tumor specimens in paraffin blocks (preferred) or in freshly cut and unstained slides (exceptional cases) with an associated pathology report for central testing
Appropriate archival OR current tissue blocks or biopsy specimens to determine ER/PR and APR status.
Fresh or archival biopsy tissue available to determine tumor mutation status
Availability a tumor tissue sample from a diagnostic biopsy/surgery or a metastatic tumor biopsy.
Patients must provide tissue from an archival tumor sample (obtained within 2 years from screening visit) or newly obtained core, punch, or excisional biopsy of a tumor lesion if deemed relatively safe and technically feasible
For patients recruited in the expansion cohort only, provision of archival (block) or fresh tumor tissue samples at baseline is mandatory. If archival tumor tissue is not available, patients should be willing to undergo a biopsy for provision of fresh tumor samples
Provision of an archival tissue block, or 10 formalin-fixed paraffin-embedded (FFPE) slides, if available, and if not available having biopsiable disease and agreeing to pre-treatment biopsies
Be willing to provide tissue
Provided archival tumor tissue sample or newly obtained core or excisional biopsy of a tumor lesion not previously irradiated
Must have archival tissue available, be willing to undergo metastatic biopsy or have a sufficient plasma circulating tumor DNA (ctDNA) concentration in order to perform next-generation DNA sequencing
Provided archival tumor tissue sample or newly obtained (no anti-neoplastic therapy since biopsy) core or excisional biopsy of a tumor lesion not previously irradiated.
Availability of an archival (?5 months) or on-study obtained formalin-fixed, paraffin-embedded tumor tissue sample which has not previously been irradiated
BRAF- or MEK-mutation melanoma tumor status will be established prior to entry based on previous BRAF-gene analysis or MEK pathway mutation reports from a CLIA qualified laboratory. If a report is not available, the mutation analysis will be performed at Screening on archival tissue
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion
Ability to provide adequate tissue from archival tumor specimen; confirmation of adequate tissue is required prior to enrollment
Adequate archived primary or metastatic tumor tissue collected before the prior PARP therapy.
Tissue from an archival tissue sample or fresh tissue obtained from a core or excisional biopsy of a tumor lesion.
Willingness to provide pre- and post-treatment tissue for translational studies. Pre-treatment fresh frozen tissue must be available for research purposes. This tissue can be collected from preoperative laparoscopy, other diagnostic biopsy, or a research-specific biopsy.
Must have diagnostic biopsy tissue (pre-neoadjuvant chemo) available for genetic testing.
Must have surgical tissue (post-neoadjuvant chemo) available for genetic testing.
PRE REGISTRATION – INCLUSION CRITERIA: Patient has disease amenable to biopsy if the archival tissue sample is unavailable; note: Archive sample must not be older than 12 months
Patients must have an archival sample of tumor or metastatic site core biopsy to be eligible
Be willing to provide tissue from a newly obtained transurethral resection of bladder tumor (TURBT) or biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 8 weeks (56 days) prior to initiation of treatment on say 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor
Sufficient archival tissue available for correlative studies; submission of formalin-fixed paraffin-embedded (FFPE) tumor tissue from a previous biopsy or resection is required, and the most recent specimen is preferred; if a FFPE block cannot be provided, then 10 unstained, positively-charged slides of 4-5 um thickness must be submitted; if insufficient archival tissue is available, a repeat biopsy will be necessary
Consent to undergo biopsy from a newly obtained core or excisional biopsy of a tumor lesion before study drug administration, and during treatment; biopsy in case of progressive disease is optional
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; in the opinion of the investigator, the patient must have tumor accessible by CT or ultrasound guided core biopsy; subjects for whom newly-obtained samples cannot be provided may submit an archived specimen provided it was obtained after last systemic treatment, within 6 months of signing consent and that tissue is available for either 2 cell blocks or 20 uncut slides (core or excisional biopsy required, fine needle aspirate is not acceptable)
Confirmed diagnosis of MCL with CD20 and cyclin D1 positivity in tissue biopsy.
FOR TISSUE COLLECTION TO ESTABLISH PDX (PART 1): Confirmed MCL tissue diagnosis.
FOR TISSUE COLLECTION TO ESTABLISH PDX (PART 1): Patients must be willing to allow residual tissue to be collected for both in vitro, in vivo (PDX) testing and molecular profiling.
Tissue block of initial biopsy specimen is available
Patients must have adequate tissue (fresh or frozen) available or planned removal of adequate tissue for analysis; at least 250 mg of tumor are needed for peptide elution; there is no specific time limit on how long the tissue can remain frozen prior to use
Representative tumor tissue specimens (paraffin block preferred)
Archival tumor tissue sample (i.e., representative tumor tissue specimen in paraffin block [preferred] or at least 20 unstained slides) must be requested and available prior to study entry
Patients must have access to archival tumor tissue for proposed correlative studies; these may be derived from transurethral resection of bladder tumors (TURBT), cystectomy, or biopsy; if archival tissue is not available for proposed correlatives, patients may be enrolled at the discretion of the study principal investigator (PI) (SKP)
Patients must have adequate tumor tissue available for PD-L1 testing; adequate tumor tissue is defined as:\r\n* For core-needle biopsy specimens, at least three cores should be submitted for evaluation if feasible; acceptable samples include core-needle biopsies for deep tumor tissue (minimum of three cores) or excisional, incisional, punch, or forceps biopsies for cutaneous, subcutaneous, or mucosal lesions; samples collected from fine-needle aspiration, brushing, cell pellet from pleural effusion, bone metastases without a soft tissue component, and lavage are not acceptable\r\n* For pre-treatment archival tissue, representative urothelial carcinoma formalin-fixed paraffin-embedded (FFPE) tumor specimens (tumor blocks or 30 unstained slides) must be provided; patients with < 30 slides may be enrolled after discussion with the MSK principal investigator\r\n* Primary or metastatic specimens (with the exception of bone because it is not evaluable for PD-L1 expression) may be submitted
Stratum 2: Patients with DIPG who have pre-trial tumor tissue available are requested to submit tissue; however, this is not required for eligibility
Histologically confirmed adenocarcinoma of the prostate: screening and on-treatment biopsy is mandatory. If adequate number of paired biopsy samples are collected (>=20 paired samples for each dose level in each Arm, unless an Arm is closed early), then further biopsy sampling will be considered based on available data; screening biopsy can be waived if patient had a recent biopsy after failure of ADT therapy (within 30 days) and the biopsy sample is secured to be sent as screening biopsy for this study.
Part 1 patients must have a tumor tissue form indicating availability of archived tissue from initial resection at diagnosis of glioblastoma completed and signed by a pathologist
Confirmation of availability of sufficient tissue from a prior surgery for correlative studies is required prior to enrollment; these samples must be sent to the DFCI Coordinating Center within 60 days of registration; Cohort 1 participants must have sufficient formalin fixed paraffin embedded (FFPE) tissue from any surgery; Cohort 2 participants must have tissue from biopsy or resection from the most recent recurrence surgery; the following amount of tissue is required:\r\n* 25 unstained formalin fixed paraffin embedded (FFPE) sections (standard 4-5 micrometer thickness)\r\n* AND 1 H&E stained slide (or 1 additional unstained 4-5 um slide for staining) \r\n* AND one of the following for genomics/nucleic acid extraction:\r\n** At least 10 (preferably 20) unstained FFPE sections of 10 micrometer thickness OR\r\n** At least 8 tissue cores from an FFPE block (200 micrometer total thickness of tissue from a block with a total surface area of 0.5 cm^2) OR\r\n** At least 200 mg of frozen tissue
The subject must be willing to provide necessary samples (example [e.g,] biopsy) for the diagnosis of tissue invasive CMV disease at baseline as determined by the Investigator.
There must be availability of a formalin-fixed, paraffin-embedded tumor specimen
MPM tumor sample for determination of ASS1 status. ASS1-deficiency is not required for study entry at study start, but tumor sample for ASS1 status is required. This study will employ an adaptive biomarker-driven design with an interim analysis to be conducted at the end of the phase 2 portion. The interim analysis will evaluate the treatment effect of ADI PEG 20 in combination with pemetrexed and cisplatin on overall survival (OS) in the overall population (biphasic and sarcomatoid histology patients) and pre-defined subpopulation of biomarker-positive patients (ASS1-deficient subpopulation). Thus ASS1 deficiency may be required for the phase 3 portion of the study, pending the interim analysis. ASS1-deficiency, demonstrated on tissue specimen (cytospin samples are not acceptable), will be defined in the laboratory manual. If archived tissue is not sufficient or not available, then tissue must be obtained by biopsy.
Archival or newly obtained tissue sample of a tumor lesion.
Tumor tissue must be provided for biomarker analysis
Patients must consent to analysis on archival tissue; if archival sample is not available, a sufficient tumor biopsy can be performed a minimum of 28 days prior to start of treatment if felt to be clinically reasonable
Patients must have a tumor tissue form indicating availability of archived tissue from initial resection at diagnosis of GBM, completed and signed by a pathologist
The subject must have tumor tissue that is sufficient quantity and quality for sequencing
Whenever possible, a formalin-fixed, paraffin-embedded (FFPE) tumor tissue block or 10 unstained slides of tumor sample (archival or recent) for biomarker evaluation should be made available and submitted to the central lab for correlative studies
TUMOR BIOPSY SEQUENCING: Patient must have tumor amenable to percutaneous or excisional skin biopsy and be willing to undergo a tumor biopsy or biopsy samples (formalin-fixed paraffin-embedded [FFPE] blocks) collected on another study or from a procedure performed due to medical necessity may be acceptable if collected within 6 months prior to registration on MPACT and providing that the patient has not received any investigational or targeted treatment since that time
Fresh/archived tumor tissue available for molecular marker testing is required for entry; a tumor block or at least 5 unstained slides must be available; as an alternative formalin-fixed paraffin-embedded (FFPE) cell block that is sufficient for histologic analysis is acceptable
Whenever available, archival tissue (block or minimum 10 slides) is requested for molecular characterization, e.g. detection of somatic mutations and/or candidate biomarkers of response; this is not mandatory and lack of available tissue would not be an exclusion criteria
Patients must be willing to provide archival formalin-fixed paraffin-embedded (FFPE) or frozen specimens for central analysis, if available
If no adequate archival tumor biopsy is available, patients must undergo a new biopsy
Archival tumor biospecimen (when available) must be procured for correlative evaluation; if tumor tissue is not available or accessible despite good faith efforts, patient may still be treated on study\r\n* Formalin fixed, paraffin embedded (FFPE) tissue block(s) or at least 12 unbaked, unstained slides are required; tissue samples taken from a metastatic lesion prior to the start of screening are acceptable
MANDATORY archival tumor tissue (prior to treatment with a PD-1 or PD-L1 inhibitor) must be identified during screening and confirmation of acquisition should occur prior to registration. Archival tissue should not be shipped until registration of patient to study. Unavailability of tissue will render the subject ineligible for study. Sample requirement is FFPE block + 2 haemotoxylin and eosin (H&E) stained slides or 17 unstained slides + 1 H&E stained slide.
MANDATORY biopsy after registration and prior to cycle 1 day 1 (C1D1) treatment: Primary tumor or a metastatic lesion must be amenable to biopsy after registration and prior to C1D1 treatment for PD-L1 status and other correlative studies. Biopsy should be excisional, incisional or core needle. Fine needle aspiration is allowed as long as there is sufficient cellularity. Sample requirement is formalin-fixed paraffin-embedded (FFPE) block + 2 H&E stained slides or 17 unstained slides + 1 H&E stained slide.
Participants must have archival tumor tissue available for analysis (minimum 20 5 um slide) or be able to undergo a baseline fresh tumor tissue biopsy
If archival tumor tissue from a metastatic melanoma lesion is unavailable OR designated pathologist from participating site cannot sign-off to ensure that “sufficient” tumor is available from existing archival tumor block for support of tumor imaging studies, patients must be willing to consent to undergo a biopsy to collect metastatic tumor tissue; collection of fresh biopsy tissue does not guarantee enrollment, unless the pathologist from the participating site signs-off that “sufficient” tumor has been collected
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion obtained within 28 days prior to study enrollment
Phase II study: measurable disease by RECIST 1.1 criteria; if archival tumor sample is not available tumor sample from fresh biopsy is acceptable
Must have confirmed viable archival prostate biopsy tissue available (only required for patients going on study after the MTD has been reached)
Archival tissue must be available or newly obtained core or excisional biopsy of a tumor lesion
Patient is agreeable to allow tumor and normal tissue samples to be submitted for complete exome and transcriptome sequencing
Relapsed/refractory primary vitreoretinal diffuse large B cell lymphoma (DLBCL) with a CNS lesion, with CSF relapse with positive CSF cytology, or with ocular relapse with positive ocular tissue biopsy; NOTE: tissue biopsy requirement of the CNS lesion is as outlined in bullet above
PSTAT3 SCREENING: Availability of archival tissue specimen suitable for pStat3 testing; either paraffin-embedded or fresh frozen sample is allowed for screening; testing of either primary or recurrent specimen is allowed for screening
Patients with \easily accessible disease\\r\n* Patients with skin or chest wall disease amenable to a punch biopsy under local anesthesia are required to undergo a baseline and cycle 2 biopsy as part of this protocol\r\n* Patients with a breast mass or axillary lymph node amenable to an image-guided core biopsy are also required to undergo a baseline and cycle 2 biopsy as part of this protocol\r\n* Patients with malignant ascites fluid or a malignant pleural effusion of sufficient volume to be amenable to tap (either in-office or image-guided) are also required to undergo a baseline and cycle 2 biopsy as part of this protocol\r\n* Patients who undergo a research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are still eligible and are not required to undergo a repeat biopsy in order to enter the study\r\n* Patients will be approached at the time of progression about providing an optional tissue sample at that time; however, the time of progression biopsy will be optional
Patients with \accessible disease\\r\n* Patients with sites felt to be accessible to an image-guided or incisional biopsy in the opinion of the patient's treating oncologist and physician performing the procedure, and not meeting the criteria for \easily accessible disease\ are required to undergo a baseline biopsy as part of this protocol; such sites may include, but are not limited to: liver, lymph nodes, soft tissue, lung, chest wall, and bone\r\n* Biopsies may be done with local anesthesia or intravenous conscious sedation, according to standard institutional guidelines\r\n* If a biopsy requires general anesthesia, then it is only allowed if acquisition of tissue is necessary for clinical reasons (i.e. is clinically indicated), and excess tissue that would otherwise have been discarded is then used for research purposes; if a biopsy requires general anesthesia, then a biopsy of that site for research purposes only, without a coexisting clinical indication is not allowed on this protocol\r\n* Patients who undergo a research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are still eligible and are not required to undergo a repeat biopsy in order to enter the study\r\n* Some patients may have had a clinically indicated biopsy upon recent disease progression and agreed to submit tissue to their institution's frozen tumor bank; if the tissue was processed as specified in this protocol, no additional pre-treatment biopsy is required if that specimen can be used for the correlative studies described in this protocol\r\n* Patients will be approached at the time of progression about providing an optional tissue sample at that time; however, the time of progression biopsy will be optional
Must have sufficient archival tissue block material (1.5 x 1.5 x 1.5 cm) and/or newly obtained core or excisional biopsy of tumor tissue; minimum of 2 cores
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 10 weeks (70 days) before initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor or may undergo fine needle aspiration
At the point when tumor biopsies become mandatory (expansion phase only), disease amenable to biopsy and willingness to undergo biopsies or patient will be undergoing a procedure due to medical necessity during which the tissue may be collected, or tumor biopsy tissue from a previous research study or medical care is available for submission at registration; criteria for the submission of tissue are:\r\n* Tissue must have been collected within 3 months prior to registration\r\n* Patient has not received any intervening therapy for their cancer since the collection of the tumor sample\r\n* Tumor tissue must meet the minimum requirements outlined
Be willing to undergo a core or excisional biopsy of a bone metastasis prior to study drug initiation for tumor tissue; newly-obtained is defined as a specimen obtained up to 12 weeks (84 days) prior to initiation of treatment on day 1; bone biopsy can have been done prior to screening; archival specimens of bone metastasis are permitted if done for other purpose and available\r\n* If biopsy is non-diagnostic, patient must undergo repeat biopsy as proof of tumor tissue by pathology review; proof of tumor specimen is required for eligibility
Soft tissue lesions >= 1.0 cm in longest axis\r\n* Soft tissue lesions < 1.0 cm that have been stable for > 6 months (must not have enlarged > 5 mm) are permitted
Central laboratory confirmation of the presence of the T790M mutation in tumor tissue\n             in Cohort A and the presence or absence of the T790M mutation in tumor tissue in\n             Cohort B. Centrally indeterminate, unknown or invalid specimens are not acceptable.\n             Biopsy material obtained from either primary or metastatic tumor tissue and sent to\n             the central laboratory must be within 60 prior to dosing study drug but following\n             disease progression on the first EGFR TKI
Dose expansion cohort: the inclusion and exclusion criteria for the expansion cohort are the same as above, except for the expansion cohort also required to express AR (score 1+ or more) by IHC in archival bladder cancer samples or fresh biopsy specimens (if archival tissue not available)
Patients must have a tumor tissue form indicating availability of archived tissue from initial resection at diagnosis of glioblastoma completed and signed by a pathologist; availability of tissue is not a requirement for study participation
Diagnosis of CD-30 positive GCT; CD30 expression will be tested by immunohistochemistry (IHC) in archival or fresh tumor tissue as is routinely done for diagnosis
Be willing to provide either archived tumor tissue or tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1
Subjects must provide sample of archival tumor tissue (tissue block preferred, at least 5 formalin-fixated, paraffin-embedded [FFPE] slides acceptable) collected any time before the general screening; a fresh biopsy will be collected if archival sample is unavailable or insufficient
Patients who are willing to provide a specimen for genomic sequencing\r\n* Preferred method: tumor cell sample available and of sufficient quantity in the Tumor Tissue Shared Resource or patients who are willing to undergo additional tissue collection for tumor genomic sequencing through FoundationOne; available specimens must have been harvested within two years to be eligible\r\n* •\tAlternative method: patients who are unwilling or unable to provide a tumor tissue sample and who undergo liquid biopsy (Guardant360 or Foundation One) may be considered eligible by the treating physician
Representative tumor specimens in paraffin blocks (preferred) or at least 15 unstained slides, with an associated pathology report, requested at any time prior to study entry; only tissue from core needle, punch, or excisional biopsy sample collection will be accepted; fine-needle aspiration, brushing, and lavage samples are not acceptable; for all biopsy types, submitted blocks should have sufficient tissue to generate at least 15 sections, and tissue for which the pathology report specifies that the overall tumor content is low (e.g., “sparse” or “scant”) is not acceptable; tissue from separate time points (such as time of initial diagnosis and time of metastatic diagnosis) or from the multiple metastatic tumors may also be collected for a given patient, on the basis of availability
If archival tissue is either insufficient or unavailable, the patient may still be eligible if the patient can provide at least five unstained, serial slides or is willing to consent to and undergo a pre-treatment core or excisional biopsy sample collection of the tumor; fine-needle aspiration, brushing, and lavage samples are not acceptable
Diagnostic primary tumor tissue must be available for biomarker correlatives, in both the dose-finding and expansion cohorts
Immunohistochemical staining for p16 must be performed on tissue, and this tissue must be submitted for central review; fine needle aspiration (FNA) biopsy specimens may be used as the sole diagnostic tissue if formalin-fixed paraffin-embedded cell block material is available for p16 immunohistochemistry; FNA specimens prepared with adequate p16 testing in this manner are acceptable to submit for central review; if the p16 preparation is not adequate, additional specimens will be required to establish p16 status; centers are encouraged to contact the pathology chairs for clarification
For stage 2 GBM participants, a block of paraffin embedded tissue or 30 unstained slides at standard 4-5 um thickness from any prior surgery demonstrating GBM pathology must be available for submission
For patients enrolling on Part B: tissue blocks or slides must be sent; if tissue blocks or slides are unavailable, the Study Chair must be notified prior to enrollment
Participants must have measurable melanoma; measurable disease is defined as at least one lesion that can be measured accurately in at least one dimension (longest diameter to be recorded) as >= 20 mm with conventional techniques or as >= 10 mm with spiral computed tomography (CT) scan; cutaneous or subcutaneous lesions may be considered measurable if they can be measured reliably as >= 10 mm by direct physical exam measurement; in addition, participants must also have separate disease, which may or may not be measurable as defined by Response Evaluation Criteria in Solid Tumors (RECIST), but must be readily accessible for core needle biopsy, excisional biopsy, and/or surgical resection; this disease may include one large tumor tissue deposit from which biopsies can be harvested multiple times or may include multiple deposits which can be biopsied, or excised individually, on different dates; please see below for suggested minimum size requirements of tumor tissue to be used for biopsy for research:\r\n* 1 lesion >= 5 cm^3 or\r\n* 2 lesions >= 3 cm^3 each\r\n* 3 lesions >= 2 cm^3each OR\r\n* >= 3 skin lesions, such that the surface area is approximately 1 cm^2 each (or in aggregate for several lesions) and the total volume of tumor is approximately 260-325 mm^3 or greater for each biopsy time point; these subjects will need >= 3 such epidermal/dermal tumor lesions; excisional tumor tissue biopsies will be performed on one or more lesions at each time point; it is acceptable to biopsy more than one lesion, that may be less than 1 cm^2 in surface area, as long as the total tissue removed has a surface area of approximately 1 cm^2 or greater\r\n* A combination of these may be acceptable, as long as there appears to be enough tumor tissue to remove approximately 325 mm^3 or more of tissue at each time point
Unresected disease that meets the following criteria:\r\n* Scheduled to undergo definitive surgery (lumpectomy or mastectomy)\r\n* Tumor size >= 1 cm (radiographically or clinically)\r\n* Grade 2 or 3 tumor or Ki-67 proliferation index of >= 10% (or both)\r\n* Any estrogen receptor (ER), progesterone receptor (PR) or human epidermal growth factor receptor 2 (HER2) status; however, receptors must have been tested on a diagnostic specimen\r\n* NOTE: bilateral cancers are eligible as long as at least 1 tumor meets the eligibility criteria above; if possible, tissue should be collected from both cancers at the time of tissue collection\r\n* A patient planning to initiate preoperative therapy who would like to take part in the study may do so if she agrees to undergo a study biopsy at the completion of digoxin dosing and prior to start of treatment, or at any time prior to start of treatment in those patients randomized to receive no drug; in these patients, tissue from the definitive surgery may still be collected for study correlates at the discretion of the protocol chair and pathologist
As GvHD is a clinical diagnosis, and patients will have already been initiated on steroid therapy at the discretion of the attending physician, tissue confirmation of refractory GvHD by biopsy is not required for entry to this study; it is anticipated that most, but not all, patients will have undergone tissue confirmation of the initial diagnosis of GvHD; however lack of tissue confirmation for this clinical syndrome is not exclusionary
Tumor tissue must be sent; if tumor tissue is unavailable, the study chair must be notified prior to enrollment
Patient has diagnostic tissue available for correlative studies
Intent to submit tissue for central HER2 testing
Patients must have tissue available and must agree to submission of tissue and blood; one to two paraffin-embedded tissue blocks or 15-20 unstained slides are requested (a minimum of 12 slides is required); cytology (i.e. fine-needle aspirations, pleural effusion specimens) is acceptable if a cell block or sufficient unstained slides are available; tumor material must be reviewed by a local pathologist who must confirm that at least 100 viable tumor cells are present in the sample and sign the S1403 Pathology Review Form prior to registration; patients must also be willing to submit blood samples for correlative research at baseline, during treatment and at progression
Patients enrolled at sites participating in the Repeat Biopsy Study must agree to submission of tissue obtained by a repeat biopsy performed at the time of disease progression
Participant has one of the following available for PD analyses including somatic BRCA testing: Archived diagnostic formalin-fixed paraffin embedded (FFPE) tumor tissue; or tumor tissue biopsy collected prior to Cycle 1 Day 1.
Has sufficient tumor tissue (slides or blocks) available for central confirmatory testing of immunohistochemistry and/or cytogenetics/fluorescence in situ hybridization (FISH) and/or deoxyribonucleic acid mutation analysis (required for study entry but enrollment based on local results) For Dose Escalation Only:
Available representative tissue from the most recent biopsy after the last therapy; if such tissue is not available, a fresh biopsy must be obtained
Must have tumor tissue available for biomarker analysis. Biopsy should be excisional, incisional, punch, or core needle
Tumor tissue need be received by the central vendor (block or unstained slides). Note: Fine Needle Aspiration (FNA)and bone metastases samples are not acceptable for submission.
NSCLC and gastric adenocarcinoma subjects must have tissue available for HA-selection and PD-L1 testing.
Participant must consent to provide archived tissue or cytology sample of NSCLC lesion for analysis.
Patients must have tumor tissue from transurethral resection of the bladder tumor (TURBT) available for submission that is sufficient for COXEN testing and must agree to submission of 20 (10 micron) slides of formal-fixed paraffin embedded (FFPE) tissue, with 2 (5 micron) slides at the start and end of the 20 slides, for a total of 22 unstained slides; the diagnostic TURBT sample must have been obtained within 56 days prior to registration; all sections should be placed on \plus\ slides, as is the standard procedure in most pathology units
Is able to provide tumor tissue from a site not previously irradiated as follows: Cohort A must provide a core or excisional biopsy from soft tissue or bone biopsy within 1 year of screening and after developing mCRPC; Cohort B: must provide an archival tumor tissue sample or tumor tissue from a newly obtained core or excisional biopsy from soft tissue if the lesion is clinically accessible; and Cohort C with soft tissue disease must provide a core or excisional biopsy from a soft tissue lesion if clinically accessible within 1 year of screening and after developing mCRPC and an archival specimen if available. Participants with bone metastasis only must provide an archival tumor tissue specimen
Tumor tissue must be available for prospective determination of FGFR2b overexpression
Subject must consent to provide previously collected tumor tissue
Has provided tissue for biomarker analysis from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion not previously irradiated from a muscle invasive urothelial carcinoma or a metastatic biopsy, originally from the original tumor.
Available archival tumor tissue should be submitted to MSKCC for integrated mutation profiling of actionable cancer targets (IMPACT) analysis, but will not be required prior to registration; note: if tissue is depleted, patient will still be eligible after discussion with the principal investigator (PI)
Availability of an archival formalin fixed, paraffin embedded (FFPE) tumor tissue block or a minimum of 15 slides
adequate tumor tissue available prior to randomization
Archival tumor tissue available or a fresh biopsy must be obtained prior to study treatment initiation
Patients must have available and be willing to submit a minimum of five unstained slides from primary, lymph node, or metastatic site to determine PD-L1 expression; the tumor tissue must be adequate for PD-L1 testing (defined as >= 100 tumor cells as confirmed by the treating institution’s local pathologist); this must be documented by having a pathologist sign the S1404 Local Pathology Review form prior to step 1 registration; the specimens may come from an archived block but must be submitted within 20 days from cutting the slides
Patients must have formalin-fixed, paraffin-embedded tumor samples available from the primary or recurrent cancer or agree to undergo fresh biopsy prior to study treatment initiation.
Patients must have archived tumor specimens available unless pre-treatment biopsy is being performed; if pre-treatment biopsy is being performed, availability of archived specimen must still be assessed and collected if available
Archival tumor tissue specimen meeting protocol specifications or the participant will be offered the option of a pre-treatment biopsy to obtain adequate tissue sample.
Subject has measurable disease according to RECIST 1.1. 4. Archival formalin-fixed, paraffin-embedded tumor sample collected within 90 days prior to subject consent available or subject has biopsiable metastatic lesion and is willing to undergo biopsy .
Available pretreatment biopsy, either fresh (optimal) or archival (acceptable)
Baseline tumor tissue, either fresh (preferred) or from paraffin block/unstained slides if contemporary biopsy is unsafe or not otherwise obtainable from the primary tumor site or metastatic site to be available for use on correlative studies
Group 2 patients should have archived or fresh tumor tissue available from the non-craniotomy site and will have fresh tumor tissue available from the planned craniotomy
Adequate archival tissue from a biopsy performed after progression of disease on previous EGFR-TKI or willing to consent for a fresh tumor biopsy; (mandatory for Cohorts A, B, C; optional for dose escalation and Cohort D)
Available archival tumor tissue for the proposed correlative studies
KRAS or NRAS mutation detected in tumor tissue specimen
Participants must agree to undergo a research biopsy, if tumor is safely accessible, at baseline; previously collected archival tissue will also be obtained on all participants; for participants for whom newly-obtained samples cannot be provided (e.g. inaccessible or participant safety concern) the archival tissue alone will be acceptable; tissue needs to be located and availability confirmed at time of registration; participants must agree to a mandatory repeat biopsy 3-6 weeks after starting treatment, if tumor is safely accessible; for patients randomized to carboplatin alone who decide to crossover to nivolumab monotherapy at time of progression, a mandatory biopsy will be required, if tumor is safely accessible, prior to initiating nivolumab; participants must also agree to undergo this biopsy, if applicable
Able to provide biopsy tissue for biomarker analysis
Available archival tumor specimen of the soft tissue sarcoma that meets inclusion criterion #1, #2 or #3.
Willingness and ability to provide archived formalin fixed paraffin embedded tissue block or a partial block from surgery after neoadjuvant chemotherapy and from core-biopsy before start of neoadjuvant chemotherapy, which will be used for centralized retrospective confirmation of hormone- and HER2-status and to evaluate correlation between genes, proteins, and mRNAs relevant to the endocrine and cell cycle pathways and sensitivity/resistance to the investigational agents. In case of bilateral breast cancer, tumor tissue of both sides needs to be assessable.
Willingness to undergo a pretreatment and on-treatment tumor biopsy to obtain tumor tissue.
Must provide adequate tissue for biomarker analysis for Cohorts A and B from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion not previously irradiated.
Availability of formalin-fixed paraffin-embedded tumor tissue diagnostic of glioblastoma.
Can provide tumor tissue.
Available archived tumor tissue for central analysis
Availability of paraffin embedded or formalin fixed tumor tissue; OR, a minimum of 10 and up to 20 slides of archived tumor tissue or new biopsy, if archived tissue is unavailable for central laboratory confirmation of AR status and molecular subtyping. Metastatic tumor tissue is preferred when possible.
Can provide tissue for PD-L1 and mesothelin biomarker analysis
Patients must be willing and able to undergo a biopsy after signed consent and prior to registration; patients must have tumor tissue and blood samples available and be willing to submit tumor and blood samples; NOTE: core biopsy required; fine needle aspiration (FNA) is not an acceptable substitute for core biopsy
Has provided archival tumor tissue sample or newly obtained core or excisional biopsy of a tumor lesion not previously irradiated.
Availability of recent tumor tissue with 3 months prior to enrollment, when feasible.
Tumor tissue sections must be available for biomarker evaluation
Archival tumor tissue block or 15 freshly cut, unstained, serial slides available for submission, or willingness to undergo a core or excisional biopsy prior to enrollment (fine-needle aspiration, brush biopsy, and lavage samples are not acceptable). Participants with fewer than 15 slides available may be eligible for study entry following discussion with Medical Monitor
Formalin fixed, paraffin embedded tumour sample from the primary or recurrent cancer must be available for central testing.
Archival tumor tissue
Fresh Biopsy or Archival Tumor Tissue
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the study principle investigator (PI)
A paraffin-embedded tumor tissue specimen from the initial diagnostic biopsy has been located and ready to ship to the Mayo Clinic Lymphoma Laboratory following pre-registration; Note: excisional tumor biopsy is preferred; core needle biopsies will be considered adequate if there is enough tissue for the mandatory central pathology review immunohistochemistry and Genomics Education Partnership (GEP); submission of a tumor block is preferred, but if unavailable submit alternative materials
For Parts B, C, D, E and F: Have available tumor tissue.
Availability of an archival or freshly biopsied tumor tissue sample must be confirmed for study enrollment
Agreement to mandatory archival tissue or fresh biopsy
Subjects must be willing and able to have a fresh tumor biopsy prior to start of study treatment for research evaluations and cohort categorizing; Note: if insufficient fresh tissue is obtained to provide sub-classification for cohorts, then tissue material from a previous relapse biopsy and/or original diagnostic block may be requested to meet this criterion
For participants who will undergo serial biopsy in dose-escalation cohort, baseline tumor tissue samples should be of core needle biopsies for deep tumor tissue or organs or excisional or punch biopsies for cutaneous or subcutaneous lesions (>/=5 millimeter [mm] in diameter amenable to serial biopsy)
All patients must provide archival tissue block or paraffin sample from archival tissue block (approximately 10 sections) for use in pharmacodynamic correlative studies (NOT required for patients enrolled on the dose escalation for intermittent ABT-888 portion of the study)
Available TNBC diagnostic tumor tissue (archived tissue allowed)
Has sufficient archival tumor tissue (a minimum of 10 slides or tumor block) available for central retrospective testing of BAP1 status
Tumor tissue available from most recent biopsy to determine cell of origin
Must have available tumor tissue for TIM-1 expression testing
Willing to submit an evaluable tumor tissue sample, preferably from a liver metastasis, unless tumor is considered inaccessible or biopsy is otherwise considered not in the subject's best interest
Have consented to undergo mandatory serial peripheral whole blood and tumor tissue sampling.
An archived tumor block or punches instead block must be available for submission for PD-L1 analysis. If an archived tumor block sample cannot be shipped for this study, then two 3mm punches from the core needle biopsy blocks may be provided for analysis. NOTE: core or excisional biopsy is required for this study. Fine needle aspirates (FNA) and cytology specimens are not adequate for PD-L1 analysis.
Have sufficient tumor tissue available for central analysis.
Lung cancer confirmed to express gpNMB, as assessed by immunohistochemistry at a central lab (using expression in ? 5% of tumor epithelial cells as a cut-off for positivity). This can be tested on archived tissue if available, although preferred tumor specimen is a biopsy after the most recent therapy.
Availability of formalin-fixed paraffin-embedded (FFPE) tumor tissue block.
Available evaluable archival tumor tissue for correlative studies including assessment of immune infiltration and Btk expression is required; if archival tissue is unavailable, patients must be willing to undergo repeat prostate biopsy; tissue is considered sufficient for correlative endpoint analyses if they are obtained from at least 2 prostate cores and consist of at least 15 unstained slides from the largest tumor volume and/or highest Gleason score; the availability of archival tissue or consent for repeat prostate biopsy is required for study eligibility; determination of tissue sufficiency is not required for study eligibility
Subject's tumor (either an archival specimen or a fresh biopsy if archival tissue is unavailable) has been pathologically reviewed by a designated central laboratory confirming NY-ESO-1 and/or LAGE-1a expression.
Availability of a tumor tissue specimen (ie, archived formalin fixed paraffin embedded tissue [block preferred, or 15 unstained slides]), which will be used for centralized, retrospective biomarker analysis. If archived tumor tissue is not available, then a de novo biopsy will be required for patient participation.
Availability of tumor tissue for biomarker analysis from a newly obtained core or excisional biopsy or willing to undergo a tumor biopsy. For first line NSCLC participants only, PD-L1 expression should be 1% or higher.
Archival tissue of carcinoid biopsy must be available
Tumour tissue for central pathology review and correlative studies must be provided.
A formalin fixed paraffin embedded lymph node or tumor biopsy specimen must be submitted during the Screening Period. The specimen must have been acquired by a surgical or core needle biopsy (? 2 cores at baseline); material from a fine needle aspiration is not acceptable.
Fresh core biopsy, frozen, must be performed before start of therapy and submitted for storage. This is optional only for the subjects who have a biopsy-accessible site and consent to the procedure. In case no prior fixed formalin paraffin embedded (FFPE) biopsy is available, this specimen can also be used for diagnostic confirmation.
Consent to provide a formalin-fixed, paraffin-embedded (FFPE) tumor tissue block (preferred) or a minimum of 20 (25 preferred) freshly cut unstained tumor slides from the most recently collected, available tumor tissue for PIK3CA-mutation testing
Subjects with archival tumor tissue suitable for proteasome activity and genetic testing must give permission to access and test the tissue; subjects without archival tumor tissue are eligible.
FFPE tumor tissue either fresh core needle biopsied or archived (two FFPE cores preferred whenever possible) is required for participation in the study. If fresh tissue is obtained, the core biopsy must be done at least ?7 days prior to Day 0.
Sufficient tissue available for central pathology review and MGMT methylation status evaluation
The subject has available at the site a representative, formalin-fixed, paraffin-embedded, tumor specimen that enabled the definitive diagnosis of breast cancer with adequate viable tumor cells in a tissue block (preferred) or ? 10 (20 preferred) freshly cut, unstained, serial slides and the associated pathology report
If the patient is enrolled at Memorial Sloan-Kettering (MSK) he/she must consent to a pre and post treatment biopsy (or have archived tissue available for the pretreatment analysis); pretreatment archival tissue for patients enrolled outside of MSK should be submitted to MSK; if there is no archival tissue available, a repeat biopsy is not required for non-MSK patients
Tumor tissue for correlative studies is mandatory
Availability of adequate Formalin-fixed, paraffin embedded (FFPE) archival tumor material.
Biopsies (DLBLC, MM): Diagnostic archival FFPE (either in tumor blocks or sectioned/mounted specimens) may be submitted in lieu of a pre-study research biopsy if it has been obtained no more than 1 year prior to enrollment and only after discussion with the Celgene Medical Monitor
Have provided an archival tumor tissue sample or newly obtained core or excisional biopsy of a tumor lesion not previously irradiated for PD-L1 analysis.
Have provided tissue for PD-L1 analysis from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion not previously irradiated.
Archival tumor tissue sample or newly obtained core or excisional biopsy of a tumor lesion as required.
A formalin-fixed, paraffin-embedded tumor block (or 16 unstained sections [charged, 4 um]) of the biopsy or curettage must be submitted along with the corresponding pathology report; patients without such material, but willing to undergo repeat biopsy or curettage, are eligible; repeat biopsy must occur after consent but prior to randomization
Patients for whom a formalin-fixed, paraffin-embedded tumor block (or 16 unstained sections [charged, 4 um]) of the biopsy or curettage are unavailable and patient is unwilling to undergo repeat biopsy or curettage
Newly obtained core or excisional biopsy of a tumor lesion for part 2A and if they qualify, one pre-randomization biopsy for part 2B
Archival tumor tissue, preferably obtained from the most recent available biopsy; there must be adequate tissue for a PD-L1 stratification test, as assessed by central pathologist
Subjects must provide samples of archival tumor tissue collected and submitted anytime during the study
provide a newly obtained tumor tissue sample. Tumor tissue biopsies may be taken by surgical resection, core needle biopsy, or fine needle biopsy
Has provided a tumor tissue sample either collected from prior cytoreductive surgery or fresh newly obtained tumor tissue at screening
Patients with diffuse intrinsic brain stem glioma (DIPG) can be enrolled without the need for available tumor tissue for RB protein status confirmation.
Mandatory tumor tissue available
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion
Has agreed to the collection of archival tumour tissue or recent tumour biopsy tissue, it taken for routine clinical purposes at baseline if archival tissue is not available, for molecular biomarker analyses. Inclusion Criteria Specific for Part B:
Availability of archival or freshly collected tumor tissue before study enrollment
Have availability of adequate formalin-fixed paraffin-embedded (FFPE) tumor derived material.
Neuroendocrine archival tissue from a previous biopsy will be required
Archived tumor tissue (minimum of 8 slides for paraffin-embedded tumor tissue) for assessment of tumor-based biomarkers and immune score is required for eligibility
Have tumor tissue available for biomarker analysis.
Previously obtained archival tumor tissue or tissue obtained from biopsy at screening
Have an archived tissue sample to be submitted either as a formalin fixed paraffin-embedded (FFPE) tumor block, or 5 to 15 unstained slides
The formalin-fixed, paraffin-embedded (FFPE) tumor tissue block must be available to be sent for retrospective central pathology review after registration
Patient must agree to provide tumor tissue
Patients must have a formalin-fixed, paraffin-embedded (FFPE) tumor block OR 1 representative hematoxylin and eosin (H&E) and 20 unstained myxoid liposarcoma tissue slides available for submission to central pathology review; this review is mandatory prior to registration to confirm eligibility
Availability of tumor tissue sufficient for confirmatory testing of FGFR1 and 11q amplification status
Patients must to have tumor tissue collected prior to enrolling on this trial; up to 10 patients will be accepted with no pre-treatment research tissue collection or tissue collection from an outside institution\r\n* If the tissue is from an outside institution, it must be reviewed at Indiana University Health Pathology Department
Patients must have additional tumor available and be willing to submit tissue and blood samples
Availability of a representative formalin-fixed, paraffin-embedded (FFPE) tumor specimen, required prior to randomization
Provided newly obtained formalin fixed tumor tissue from a biopsy of a tumor at the time of or AFTER the diagnosis of metastatic disease has been made AND from a site not previously irradiated
Paraffin-embedded tumor block(s) or 15 to 20 unstained slides available for centralized assessment of ER, PR, and HER2.
Confirmed availability of archival or freshly biopsied tumor tissue prior to study enrollment
Have sufficient archival tumor tissue for analysis.
Patient must agree to provide tumor tissue from metastatic tissue at baseline
Patients must have provided consent for tissue collection for the molecular testing through participation on study UPCC 22210 entitled; “PROTOCOL TO PERMIT THE ACQUISITION OF SAMPLES OF TUMOR AND NORMAL TISSUE FOR BIOLOGICAL ENDPOINTS IN PANCREATIC CANCER”
Patient must agree to provide tumor tissue
Patient must be able to provide either archival tumor samples (hematoxylin and eosin [H&E] slides and one paraffin block or 10 unstained slides) or undergo tumor biopsy
Tumor tissue is positive for EBV
Must consent to allow submission of archived tumor tissue sample from definitive surgery.
Tissue available for PD-L1 testing and for correlative science testing
Representative formalin-fixed paraffin-embedded (FFPE) tumor specimens in paraffin blocks or at least 4 unstained slides, with an associated pathology report, for central testing of tumor PD-L1 expression.
If an archived tumor block exists, then either the block or at least 4 unstained slides from the block should be submitted. Tumor tissue should be of good quality based on total and viable tumor content, i.e. at least 50 viable tumor cells and intact tissue architecture. Fine needle aspiration, brushing,and lavage samples are not acceptable. If the block is tissue from a core-needle biopsy, then the block should contain tissue from at least three cores to be sufficient for evaluation.
Patients who do not have existing (archived) tissue specimens meeting eligibility requirements may undergo a biopsy during the screening period. Acceptable samples include core needle biopsies for deep tumor tissue (minimum of three cores) or excisional, or forceps biopsies for endobronchial or nodal lesions. The tissue should be fixed in formalin and embedded on site and sent as a block.
Archival tumor specimens must be submitted prior to enrollment; samples collected from fine-needle aspiration, brushing, cell pellet from pleural effusion, bone metastases, and lavage are not acceptable; acceptable samples include core-needle biopsies for deep tumor tissue (minimum of three cores) or excisional, incisional, punch, or forceps biopsies for cutaneous, subcutaneous, or mucosal lesions; if archival tissue is being used, representative urothelial carcinoma formalin-fixed paraffin-embedded (FFPE) tumor specimens (tumor blocks or 30 unstained slides) must be provided; patients with < 30 slides may be enrolled after discussion with the principal investigator; primary or metastatic specimens may be submitted
Willing to provide a sample from a recently obtained (within 42 days prior to initiation of day 1) biopsy of a tumor lesion;\r\n* If recently-obtained samples are unavailable an archived metastatic specimen not previously irradiated may be submitted upon agreement from the study principal investigator (PI)
Tumor tissue (a minimum of 10 and up to 15 unstained slides, or paraffin block, ideally from the patient's most recent biopsy, must be available at the patient's local institution prior to the first dose of study therapy.
At least one site of disease must be accessible to provide repeat biopsies for tumor tissue for sequence and immunological analysis.
Must agree to provide tumor tissue sample, either from a previous surgery or biopsy within 6 months or fresh, prior to the start of treatment in this study
Willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up-to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the study principal investigator (PI)
Patient must consent to allow for a baseline tumor biopsy. Tumor material from biopsies done before the screening period are acceptable if the biopsy was performed within 3 months prior to the planned treatment start and no other systemic cancer therapy was administered in the interim. If a biopsy is performed and the specimen is considered non-diagnostic or does not have enough tissue, this does not prevent the patient from proceeding with the treatment.
An archival tumor sample from either a prior core needle biopsy or surgical specimen must be available to be submitted for correlative studies as an eligibility requirement prior to registration. The sample must be shipped within 6 weeks of enrollment. Participants without an available archival tumor sample are considered ineligible.
Availability of archival (diagnostic) specimens and willing to undergo a pre-treatment biopsy.
Participants must have biopsiable disease and be willing to undergo pre-treatment biopsy, or have an archival tumor sample obtained < 20 months prior to study entry
Have confirmation of available tissue from an archived specimen of ovarian cancer; if there is no archival tissue available, the participant will be required to undergo a biopsy to obtain a fresh tumor sample
Patients must have available an archival paraffin tumor block (from surgery on any meningioma or schwannoma) sufficient to generate at least 5 unstained slides; or, if a paraffin tumor block is unavailable, at least 5 unstained slides; Note: tumor block from the target meningioma is not required
Patients must have archival tissue from the primary tumor or metastases available for correlative studies; either a paraffin block or twenty unstained slides are acceptable; (if less than twenty unstained slides are available, the patient may be able to participate at the discretion of the investigator)
Consent for the use of any residual material from biopsy (archival tissue) and serial blood draws will be required for enrollment; fresh biopsy (pre and post dose) of tumor tissue will be optional; NOTE: Patients without adequate tissue for bio correlates will not be excluded or required to have a repeat biopsy
If an archived tumor tissue is available, be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1 of RT
Consent for use of available archived tissue for research purposes
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen
Availability of tumor tissue for biomarker analysis
Participant has provided a formalin fixed tumor tissue sample from a biopsy of a tumor lesion either at the time of or after the diagnosis of metastatic disease has been made and from a site not previously irradiated to assess for a protein known as Programmed death-ligand 1( PD-L1) status. Fine needle aspirates, endobronchial ultrasound (EBUS) or cell blocks are not acceptable. Needle or excisional biopsies, or resected tissue is required. Archival tissue may be acceptable. Submission of formalin-fixed paraffin embedded tumor tissue sample blocks are preferred; if submitting unstained slides, the slides should be freshly cut and submitted to the testing laboratory within 14 days from site slide sectioning date otherwise a new specimen will be requested.
Subject has available formalin-fixed, paraffin-embedded tumor specimen with adequate viable tumor cells in a tissue block or unstained serial slides accompanied by an associated pathology report prior to enrollment. Archival or fresh biopsy tissue is required.
Representative tumor specimens in paraffin blocks (preferred) or at least 10 unstained slides, with an associated pathology report, requested at any time prior to study entry; only tissue from core needle, punch, or excisional biopsy sample collection will be accepted; fine-needle aspiration, brushing, and lavage samples are not acceptable; for all biopsy types, submitted blocks should have sufficient tissue to generate at least 10 sections, and tissue for which the pathology report specifies that the overall tumor content is low (e.g., \sparse\ or \scant\) is not acceptable; if archival tissue is either insufficient or unavailable, the patient will need to consent to and undergo a pre treatment core or excisional biopsy sample collection of the tumor; fine needle aspiration, brushing, and lavage samples are not acceptable; the immediate unavailability of tissue blocks or unstained slides aside from the slides needed for diagnostic confirmation of lung cancer does not exclude patients from this trial; if the patient chooses to not undergo a repeat biopsy aside from biopsy for diagnostic purposes, the patient will still be eligible to enroll on 2014-0722; however, availability of core or excisional biopsy samples must be ascertained prior to enrollment
Tissue for correlative studies must be available (paraffinized or frozen), but confirmation at screening is not needed; archival tissue may be used instead of a fresh biopsy at baseline if it already exists
Patients must all have available tumor tissue for biopsy and not have any bleeding diathesis and/or chronic anticoagulation that cannot be stopped for the biopsy
Availability of a recent formalin-fixed, paraffin-embedded (FFPE) tumor tissue block from a de novo tumor biopsy during screening (biopsied tumor lesion should not be a RECIST target lesion). Alternatively, a recently obtained archival FFPE tumor tissue block (not cut slides) from a primary or metastatic tumor resection or biopsy can be provided if the following criteria are met: 1) the biopsy or resection was performed within 1 year of enrollment AND 2) the patient has not received any intervening systemic anti-cancer treatment from the time the tissue was obtained and enrollment onto the current study. If an FFPE tissue block cannot be provided as per documented regulations,, 15 unstained slides (10 minimum) will be acceptable.
Availability of an archival FFPE tumor tissue block from primary diagnosis specimen (if available and not provided per above). If an FFPE tissue block cannot be provided, 15 unstained slides (10 minimum) will be acceptable
PART A: Patient has agreed to two newly obtained tumor biopsies and as required re-biopsies (that can be biopsied on investigator’s assessment) and to providing the acquired tissue for biomarker analysis; analysis of one of the fresh biopsy samples for PD-1hiCD8+CTLA4hi in the CD8+CD45+ gate based on flow cytometry will be done; a second fresh biopsy sample is required for further biomarker analysis and confirmation at a later date of low PD-L1 expression using an immunohistochemistry (IHC) assay for PD-L1 expression; a valid flow cytometry result is not required for study participation, but repeated biopsy for reanalysis is strongly recommended for patient with insufficient TILs in the first tissue sample
Have available tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion
Mandatory diagnostic biopsy and whole blood sample are required. The tumor biopsy tissue will be analyzed for the presence of immune cells and will also undergo genomic, transcriptomic, and proteomic profiling.
Patients unwilling to consent to analysis of their tumor tissue.
Provides an archival or newly obtained (?60 days prior to first dose of study treatment) tumor tissue sample (Cohort B).
Active connective tissue disease
Availability of tumor tissue is required for study eligibility. The participant must have consented to provide archived formalin-fixed paraffin embedded (FFPE) tumor tissue or be subject to a pre-treatment re-biopsy of primary or metastatic tumor tissue for future central pathology review and translational research (if archived tissue is unavailable).
The participant has evaluable tumor tissue available for biomarker analyses.
Willingness to undergo research biopsy under the following circumstances:\r\n* Patients with “easily accessible disease”\r\n** Patients with skin or chest wall disease amenable to a punch biopsy under local anesthesia are required to undergo a baseline biopsy and a biopsy at the time of disease progression as part of this protocol\r\n** Patients with a breast mass or axillary lymph node amenable to an image-guided core biopsy are also required to undergo a baseline biopsy and a biopsy at the time of disease progression as part of this protocol\r\n** Patients with malignant ascites fluid or a malignant pleural effusion of sufficient volume to be amenable to tap (either in-office or image-guided) are also required to undergo a baseline tap and a tap at the time of disease progression as part of this protocol\r\n** Patients who undergo a research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are still eligible and are not required to undergo a repeat biopsy in order to enter the study\r\n** Patients will be approached during cycle 1 about providing an optional tissue sample at that time; however, this biopsy will be optional\r\n* Patients with “accessible disease”\r\n** Patients with sites felt to be accessible to an image-guided or incisional biopsy in the opinion of the patient’s treating oncologist and physician performing the procedure, and not meeting the criteria for “easily accessible disease”, are required to undergo a baseline biopsy as part of this protocol; such sites may include, but are not limited to: liver, lymph nodes, soft tissue, lung, chest wall, and bone; cycle 1 biopsy and biopsy at time of disease progression are optional\r\n** Biopsies may be done with local anesthesia or intravenous conscious sedation, according to standard institutional guidelines\r\n** If a biopsy requires general anesthesia, then it is only allowed if acquisition of tissue is necessary for clinical reasons (i.e. is clinically indicated), and excess tissue that would otherwise have been discarded is then used for research purposes; if a biopsy requires general anesthesia, then a biopsy of that site for research purposes only, without a coexisting clinical indication is not allowed on this protocol\r\n** Patients who undergo a research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are still eligible and are not required to undergo a repeat biopsy in order to enter the study\r\n** Some patients may have had a clinically indicated biopsy upon recent disease progression; no additional pre-treatment biopsy is required if that specimen can be used for the correlative studies described in this protocol\r\n** Patients will be approached at the time of progression about providing an optional tissue sample at that time; however, the time of progression biopsy will be optional\r\n* Other patients\r\n** Patients who do not have biopsy-accessible disease are not required to undergo a biopsy as part of study participation\r\n** In addition, patients who are being treated with therapeutic doses of anticoagulant(s), are not required to undergo a biopsy as part of study participation; if it is felt clinically appropriate despite anticoagulation (i.e. a skin punch biopsy, etc) by the treating physician, a biopsy is allowed, it is simply not required\r\n** The sites of metastatic disease and reason that the disease is not biopsy-accessible should be documented in the medical record and case report form(s)\r\n** Patients who do not undergo baseline biopsy must have their study participation approved by the overall principal investigator (PI) before start of protocol therapy; only patients who have biopsy inaccessible disease may enter the study without the requirement for baseline biopsy
Have tissue from an archival tissue sample that has been identified and confirmed as available for study, or newly obtained core or excisional biopsy of a tumor lesion
Consent for use of available archived tissue for research purposes
Subjects in Phase 2 must have disease amenable to biopsy and must be willing to undergo pre- and post-treatment tumor biopsies. Optional for Phase 1. Note: archival tissue will be requested for all subjects preferably from primary tumor site prior to cancer treatment; however, archival tissue is not a requirement for study entry.
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion; while 20 unstained slides or a tumor block are preferred, at least 14 unstained slides are requested for analysis; principal investigator (PI) approval for a lower number of slides is acceptable
Patient must have sufficient tumor tissue available for submission.
Have identified tissue from an archival tissue sample (preferably from a metastasis, but sample from primary tumor allowable) or newly obtained core or excisional biopsy of a tumor lesion.
Tumor tissue available for evaluation of PD-L1 expression
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion
Can provide tissue for PD-L1 biomarker analysis from a core or excisional biopsy (fine needle aspirate is not sufficient): A newly obtained biopsy (within 90 days prior to start of study treatment) is preferred but an archival sample is acceptable.
Availability of tissue if applicable (from the primary tumor or metastases) for correlative studies.
Willingness to release and confirmed availability of archival tissue sample for research purposes
Archived or fresh tumor sample available; willingness to donate blood and tissue for mandatory correlative research studies
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion
Available tissue from a newly obtained core or excisional biopsy of a tumor lesion not previously irradiated
Written consent to provide newly acquired tumor tissue (preferred) or archival tissue for the purpose of establishing PD-L1 status.
Have provided tissue from an archival tissue sample (< 6 months old) or newly obtained core biopsy of a tumor lesion before radiation therapy
Have permission to access tissue from an archival tissue sample; (absence of archival tissue will not preclude trial participation)
Availability of archived tumor tissue for correlative studies (5 unstained slides)
Participates must be able to submit 20 unstained slides from the initial tissue diagnosis for confirmation of diagnosis and correlative studies
Mandatory provision of an unstained, archived tumour tissue sample in a quantity sufficient to allow for central analysis of EGFR mutation status.
Patients must consent to a research biopsy of tumor tissue at baseline, for conduct of correlative studies; archived biopsy material may not be substituted
Patients must be willing to provide and have available formalin fixed paraffin embedded tissue sample from archival tissue or newly obtained core or excisional biopsy of a tumor lesion for central analysis; Note: fine needle aspiration’s (FNA), frozen samples, plastic embedded samples, cell blocks, clots, bone, bone marrow, or cytologic specimens are exclusionary
Must have tissue available from the pre-treatment diagnostic biopsy (tissue blocks if possible; if not possible, 10 unstained slides from each positive core sample for a total of 30 slides whenever possible)
Patients must provide tissue from an archival tumor sample or newly obtained core, punch or excisional biopsy of a tumor lesion if deemed relatively safe and technically feasible\r\n* Note: newly obtained biopsy is preferable
Able to provide tissue for biomarker analysis from an archival tissue sample or newly obtained core or excisional biopsy of a tumor lesion not previously irradiated
Available tissue for biomarker analysis
Tumor tissue available for PD-L1 biomarker analysis
At least 15 unstained slides or at least 1 tissue blocks must be collected from at least one prior surgery; frozen tissue is also requested if available
Histological confirmation of node positive (any T stage N1-3) proximal esophageal, distal esophagus or gastroesophageal (GE) junction adenocarcinoma (Siewert I, II, or III) after completing preoperative chemoradiation and surgery; supporting pathology report sufficient for registration; available tumor tissue from endoscopic biopsies prior to preoperative chemotherapy (chemo)/radiation therapy (RT), and tumor from surgical specimens will be submitted to Academic and Community Cancer Research United (ACCRU), but not be required prior registration; Note: if tissue is depleted, patient will still be eligible after discussion with the physician
Tumor tissue [formalin-fixed paraffin-embedded (FFPE) archival or recent acquisition] must be received by the central vendor (block or unstained slides) in order to randomize a subject to study treatment. (Note: Fine Needle Aspiration [FNA] and bone metastases samples are not acceptable for submission)
Written consent to provide newly acquired tumor tissue (preferred) or archival tissue for the purpose of establishing PD-L1 status.
Patients must have histopathological documentation of adenocarcinoma of the prostate prior to starting this study and evaluable biopsy tissue (e.g., unstained slides or blocks) available for analysis; if evaluable tissue is not available, the patient must agree to undergo a pre-vaccination prostate biopsy on study as an alternative to having available tissue available
Availability of archival tumor tissue from the thyroid cancer primary or metastasis (a tissue block or a minimum of 30 unstained slides would be required; patients with less archival tissue available may still be eligible for the study after discussion with the Memorial Sloan-Kettering [MSK] Principal Investigator)
Availability of tumor tissue specimen
Availability of an archival tumor sample or a pre-treatment fresh tumor sample for confirmation of PRCC by a central laboratory and other biomarker
Patients must have archival tissue from the primary tumor or metastases available for correlative studies; either a paraffin block or twenty unstained slides are acceptable; if twenty slides are not available, a lesser amount may be acceptable after discussion with the principal investigator
Patients must agree to undergo biopsy of a malignant lesion; biopsies do not need to be done if either the investigator or person performing the biopsy judges that no tumor is accessible for biopsy or that biopsy poses too great of a risk to the patient; patients may also be exempt if frozen tumor tissue has been collected within 12 months of study enrollment that the principal investigator deems is appropriate/sufficient for analysis on this protocol
Have documented ALK positivity by a different test and tissue available for the Vysis® FISH test. Tissue should be derived preferably from a biopsy taken after progression with crizotinib. If such a sample is not available, testing may be performed with archived tumor tissue.
HER2-overexpression in the patient's tumor tissue
Availability of tumor tissue sample that can be used for assessment of PrR levels with the use of immunohistochemistry;
Agree to undergo a biopsy of at least one metastatic site for RB status evaluation; adequate metastatic tissue from prior biopsy/resection can be used if available in lieu of a biopsy
Collection of archival tissue specimens – outside institution biopsies need to be reviewed by Brigham and Women’s Hospital (BWH) pathology department for confirmation of MCC; available slides and blocks from outside institutions will be requested by the patient coordinator and sent to the BWH pathology department for review; if unavailable, new tumor biopsy will be required prior entering in the study
ASS1 deficiency (defined as ?50% ASS expression) demonstrated on tissue specimen (cytospin samples are acceptable) by immunohistochemistry (IHC). For subjects previously treated with chemotherapy, this specimen may have been obtained before that chemotherapy. A new tissue specimen obtained after most recent chemotherapy is not required. Thus ASS1 deficiency is required for entrance into the study. If tissue is not available to determine ASS1 deficiency, then tissue must be obtained by biopsy to determine ASS1 status.
The availability of archival tissue to evaluate retrospectively the participant’s retinoblastoma protein (Rb) status as well as to perform next generation (NextGen) sequencing for tumor protein p53 (TP53) and liver kinase B1 (LKB1) status; the requirement is a minimum of 5 unstained slides with each tissue cut measuring 4 microns in width; ideally 15 slides will be requested; patients without available archival tissue may be enrolled at the discretion of the principal investigator
Tissue is required prior to enrollment. If patient was diagnosed outside and tumor tissue is not available, a pleural biopsy for frozen tissue collection is required.
Histological tumor tissue specimen
Patients must consent to both a pretreatment and a post-treatment mandatory research biopsy prior to enrolling on trial, and therefore, must have tissue (excluding bone or brain) that is amenable to biopsy
Availability of a formalin fixed paraffin embedded (FFPE) block of cancer tissue from the original or most recent biopsy for mutational analysis; availability must be confirmed prior to enrollment
Must be willing to provide and have available archival tissue for PD-L1 testing.
Must consent to allow submission of adequate archived tumor tissue sample from definitive surgery for genomic assessment of tumor.
Willingness to provide blood and urine samples, and biopsy samples if on the expansion phase of the study, for research purposes; for the expansion cohort, patients must have tumor amenable to biopsy (excisional or incision biopsies of skin or head and neck [H & N] lesions under visualization) and willingness to undergo a tumor biopsy or patient will be undergoing a procedure due to medical necessity during which the tissue may be collected, or archival tumor biopsy tissue from a previous research study or medical care is available for submission at registration; criteria for the submission of archival tissue are:\r\n* Tissue must have been collected within 3 months prior to registration\r\n* Patient has not received any intervening therapy for their cancer since the collection of the tumor sample\r\n* Tumor tissue must meet the minimum requirements
Patients who are unwilling to consent to mandatory tumor biopsy; patients with archival tissue permitted to enroll on study per Memorial Sloan-Kettering (MSK) principal investigator discretion
Adequate archival tissue to perform molecular analysis through Memorial Sloan Kettering (MSK)-Integrated Mutation Profiling of Actionable Cancer Targets (IMPACT) if MSK-IMPACT has not been performed previously on the participant's tumor; if MSK-IMACT has not been previously performed and adequate archival tissue is not available, a participant should be agreeable to a pre-treatment biopsy
Mandatory primary or metastatic tumor biopsy. If archival tumor tissue is available from a biopsy/surgery the tumor tissue may be submitted without repeating a tumor biopsy during the screening period.
Patients must have measurable disease according to the modified Response Evaluation Criteria in Solid Tumors (RECIST) criteria for pleural mesothelioma, or standard RECIST for peritoneal mesothelioma; patients must have adequate tissue sample available for molecular profiling with Memorial Sloan-Kettering (MSK)-IMPACT (archived tissue block or 15-20 unstained slides); patients will sign a separate informed document (Institutional Review Board [IRB] #12-245) to allow this to be performed
Participants must agree to undergo a research biopsy of a reasonably accessible metastatic lesion (chest wall, skin, subcutaneous tissue, lymph nodes, skin, breast, bones, lung, and liver metastases); if a reasonably accessible metastatic lesion is not available, the patient may go on study provided that archived tissue is available; however, if a reasonably accessible site is available for biopsy, the patient must agree to biopsy; any patients not undergoing biopsy must be approved for study enrollment by the overall principal investigator at Dana-Farber Cancer Institute (DFCI); biopsies may be done with local anesthesia or intravenous conscious sedation, according to institutional guideline; if a biopsy requires general anesthesia, then it is only allowed if acquisition of tissue is clinically indicated, and excess tissue may be collected for research purposes; patients without sites available for biopsy must have available tissue (archived formalin-fixed paraffin embedded blocks [FFPB], blocks from which slides can be created, or fresh frozen tissue from original diagnosis or metastatic setting) for correlative studies; tissue needs to be located and available at the time of registration
Available archival tumor tissue or patient is willing to undergo new biopsy
Availability of fresh and archive tumor in formalin fixed paraffin embedded tissue
Archived tumor tissue must be available for all subjects for biomarker analysis and confirmation of the diagnosis before or during treatment; samples must be provided within 4 weeks of enrollment
For the phase 2 portion of the study; patients must have willingness to undergo research biopsy under the following circumstances:\r\n* Patients with “easily accessible disease”\r\n** Patients with skin or chest wall disease amenable to a punch biopsy under local anesthesia are required to undergo a baseline biopsy as part of this protocol\r\n** Patients with a breast mass or axillary lymph node amenable to an image-guided core biopsy are also required to undergo a baseline biopsy as part of this protocol\r\n** Patients with malignant ascites fluid or a malignant pleural effusion of sufficient volume to be amenable to tap (either in-office or image-guided) are also required to undergo a baseline biopsy as part of this protocol\r\n** Patients who undergo a research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are still eligible and are not required to undergo a repeat biopsy in order to enter the study\r\n** Patients will be approached at the time of progression about providing an optional tissue sample at that time; however, the time of progression biopsy is optional\r\n* Patients with “accessible disease”\r\n** Patients with sites felt to be accessible to an image-guided or incisional biopsy in the opinion of the patient’s treating oncologist and physician performing the procedure, and not meeting the criteria for “easily accessible disease” are required to undergo a baseline biopsy as part of this protocol; such sites may include, but are not limited to: liver, lymph nodes, soft tissue, lung, chest wall, and bone; biopsies may be done with local anesthesia or intravenous conscious sedation, according to standard institutional guidelines\r\n** If a biopsy requires general anesthesia, then it is only allowed if acquisition of tissue is necessary for clinical reasons (i.e. is clinically indicated), and excess tissue that would otherwise have been discarded is then used for research purposes; if a biopsy requires general anesthesia, then a biopsy of that site for research purposes only, without a coexisting clinical indication is not allowed on this protocol\r\n** Patients who undergo a research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are still eligible and are not required to undergo a repeat biopsy in order to enter the study\r\n** Some patients may have had a clinically indicated biopsy upon recent disease progression and agreed to submit tissue to their institution’s frozen tumor bank; if the tissue was processed as specified in this protocol, no additional pre-treatment biopsy is required, particularly if that specimen can be used for the correlative studies described in this protocol\r\n** Patients will be approached at the time of progression about providing an optional tissue sample at that time; however, the time of progression biopsy will be optional\r\n* Other patients\r\n** Patients who do not have biopsy-accessible disease according to above are not required to undergo a biopsy as part of study participation\r\n** In addition, patients who are being treated with therapeutic doses of anticoagulant(s), are not required to undergo a biopsy as part of study participation; if it is felt clinically appropriate despite anticoagulation (i.e. a skin punch biopsy, etc) by the treating physician, a biopsy is allowed, it is simply not required\r\n** The sites of metastatic disease and reason that the disease is not biopsy accessible should be documented in the medical record and case report form(s)\r\n** Patients who do not undergo baseline biopsy must have their study participation approved by the overall principal investigator (PI) before start of protocol therapy
Patients must have available and be willing to submit baseline tissue taken at the time of disease progression to prior BRAF inhibitor-based therapy (either fresh frozen [preferred], or paraffin-embedded tumor blocks) OR must have a site of disease that can be biopsied within this study for translational medicine studies; tissue may be from an archival biopsy or a new biopsy after the patient has been registered to the protocol; since patients are referred to this protocol after progression on prior BRAF inhibitor-based therapy, the biopsy taken at the time of progression will be used as the baseline biopsy for this study; patients must be willing to submit plasma and whole blood for translational medicine studies
Patients must have a block of banked tumor tissue and/or fresh tumor tissue or at least 10 unstained slides available to be sent to the central laboratory
Patients should have tumor tissue available, and a tissue block of sufficient size to make 15 slides, which must be sent to Dana-Farber Cancer Institute (DFCI) for correlative research; if a tissue block is unavailable, sites may send one H&E stained slide and 15 unstained sections of paraffin-embedded tissue on uncharged slides; slide sections should be 4-5 microns in thickness; it is also acceptable to submit 2 cores from a block of invasive tissue using a 1.2 mm diameter coring tool; if tumor is not available, the investigator must document why tissue is not available in the patient medical record, and that efforts have been made to obtain tissue
Available archival tumor sample (excisional or core biopsy) for confirmation of LGS carcinoma diagnosis. If adequate archival tumor sample is not available, willingness to consent to tissue biopsy.
Agree to the evaluation of already collected core biopsy, as well as surgical resection tissue, for predictive biomarkers; the biopsy prior to taxol #1 is optional
Tumor tissue from an unresectable or metastatic site of disease for biomarker analyses
Histologically confirmed Stage IV pancreatic ductal adenocarcinoma w/ documented disseminated neoplasm to liver and /or lung. Must have archival or fresh tissue (block /slides) available pre-dose.
All patients must have adequate tumor tissue for the correlative analyses on study, or must undergo a biopsy to obtain adequate tissue; cases with limited tissue available should be reviewed with the primary investigator prior to enrollment
Mandatory tumor biopsy/biopsies in accessible tumors; the determination of accessibility for biopsy is to be done by the ear, nose and throat (ENT) surgeon on examination and/or review of trans-sectional imaging: mandatory tumor biopsies (1st and 2nd biopsy; 3rd biopsy is optional)\r\n* For inaccessible tumors availability of tissue is required: >= 10 tumor containing formalin-fixed paraffin-embedded (FFPE) slides/sections; 12-18 ideal
Willingness to undergo a research biopsy of the affected breast\r\n* Biopsies may be done with local anesthesia or intravenous conscious sedation, according to standard institutional guidelines\r\n* If a biopsy requires general anesthesia, then it is not allowed on this protocol\r\n* Patients who undergo a research biopsy procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are still eligible and are not required to undergo a repeat biopsy in order to enter the study\r\n* Some patients may have had a clinically indicated biopsy upon recent disease progression and agreed to submit tissue to their institution’s frozen tumor bank; if the tissue was processed as specified in this protocol, no additional pre-treatment biopsy is required as that specimen can be used for the purposes of participation in this clinical trial
Patients must have available tissue (archived formalin-fixed paraffin embedded blocks [FFPB] or fresh frozen tissue from original diagnosis or metastatic setting) for correlative studies; tissue needs to be located and available at the time of registration (tissue needs to be submitted within 3 weeks of study initiation); patients will not be able to start study drugs without tissue availability
Ability to provide a formalin-fixed, paraffin-embedded (FFPE) tumor tissue sample containing representative tumor tissue from a previously obtained biopsy/resection that meets specific tissue sample requirements at screening
Archival and/or fresh biopsy tissue samples must be available prior to the first dose of the study drug
Candidate for and willingness to have a surgically placed intraperitoneal catheter and tissue acquisition at the time of port placement; note: if an intraperitoneal catheter is already in place, a tumor biopsy will still be required; a guided core-needle biopsy is sufficient in these cases
Patient has consented for tissue banking and a research biopsy after the lead-in treatment of trametinib (required to enroll on this study); patient also consents to another pre-treatment biopsy if insufficient archival tissue is available (minimum of 5 unstained slides) for cohorts 2a, 3, and expansion exists
If archived tissue is unavailable for KRAS, NRAS, or BRAF mutation testing, or patient refuses a fresh biopsy for mutation analysis
Patients must have histologically confirmed metastatic breast cancer; if available, tissue (a minimum of 3 slides) from the most recent biopsy should be submitted for review and confirmation of eligibility; NOTE: Material should ideally be from the metastatic disease, however material from the primary tumor is acceptable if that is all that is available; availability of tissue is not mandatory for confirmation of eligibility or enrollment to the study
Archival Formalin-fixed paraffin-embedded (FFPE) tumor material if available
Available archived tumor tissue sample.
A formalin fixed, paraffin-embedded (FFPE) tumor tissue block or unstained slides of tumor sample (archival or recent) must be available for biomarker evaluation. Specimens must be received by the central lab prior to randomization. Biopsy should be excisional, incisional or core needle. Fine needle aspiration is insufficient
Ability to provide a formalin-fixed, paraffin-embedded (FFPE) tumor tissue sample containing representative tumor tissue from a previously obtained biopsy/resection that meets specific tissue sample requirements at screening
Patients should have archival tumor tissue (either unstained slides or tumor blocks) available for retrieval
Consent to provide fresh tumor tissue during screening
Availability of archival tumor tissue
Availability of adequate tumor tissue for exploratory analysis and plan to obtain the material
The mutational analysis (SNaPSHOT panel) requires a paraffin-embedded block or ten unstained slides from the untreated biopsy specimen obtained at the time of upper endoscopy or initial diagnostic biopsy; patients without sufficient material for SNaPSHOT will NOT be excluded from the study
Tumor GANQ, GNA11, and BAP1 mutational status must be determined on all patients; if initial testing is performed locally or not available, MSKCC or Columbia University Medical Center (CUMC) patients must consent to provide a tumor block or unstained slides to MSKCC or CUMC for central review of mutational status; if tissue is not available, a pre-treatment biopsy will be necessary for eligibility \r\n* Patients enrolled at Vanderbilt University Medical Center may have GNAQ and GNA11 mutational status determined on a Clinical Laboratory Improvement Act (CLIA)-approved assay at Vanderbilt University Medical Center, CUMC, or MSKCC; tissue must be sent to MSKCC for BAP1 mutational status determination\r\n* The determination of mutational status may be performed retrospectively and will not delay patient treatment on study as long as tissue is available for molecular analysis
Agree to undergo a biopsy of at least 1 metastatic site for gene-fusion status analysis; adequate archival metastatic tissue can be used if available in lieu of a biopsy; patients will only be eligible for protocol therapy if the biopsy has tumor and the tissue is evaluable for ETS fusion status
Availability of a tissue block from initial breast cancer diagnosis and/or metastatic recurrence; if a tissue block is not available, 10-20 unstained slides may be provided as an alternative; if unstained slides will be provided, they should not be sent until specifically requested by the Dana-Farber Cancer Institute (DFCI) study coordinator
For patients with biopsy-accessible disease, patients must be willing to undergo a required on-treatment research biopsy; this biopsy will occur on cycle 2 day 9;\r\n* Biopsies may be done with local anesthesia or intravenous conscious sedation, according to standard institutional guidelines\r\n* Research biopsies requiring general anesthesia are not allowed on this protocol unless a biopsy is being obtained simultaneously for clinical reasons, in the judgment of the patients’ treating physician\r\n* Patients who undergo an attempted on-treatment research biopsy and in whom inadequate tissue is obtained are still eligible to continue protocol therapy; they will not be required to undergo a repeat biopsy attempt
Patient must have archival prostate tumor block available for analysis of correlatives
Baseline paraffin embedded tissue from the patient’s primary diagnosis is requested before study enrollment and should be forwarded to the designated central laboratory where central assessment of Rb and p16 expression will be performed by using immunohistochemistry; in patients with measurable disease a tissue biopsy may be obtained by core biopsy and submitted to the designated central laboratory
Histologically documented mantle cell lymphoma with co-expression of CD20 and CD5 and lack of CD23 expression by immunophenotyping and at least one of the following confirmatory tests: 1) positive immunostaining for cyclin D1; 2) the presence of t(11;14) on cytogenetic analysis; OR 3) molecular evidence of B-cell leukemia/lymphoma 1 (bcl-1)/immunoglobulin heavy locus (IgH) rearrangement\r\n* Cases that are CD5-negative and/or CD23-positive will be eligible provided that the histopathology is consistent with mantle cell lymphoma AND positive for cyclin D1, t(11;14), or bcl-1/IgH rearrangement\r\n* A tissue block or unstained slides (10 – 20 slides) will be submitted to the Roswell Park Cancer Institute (RPCI) Pathology Department for central pathology review\r\n* A diagnosis based on peripheral blood or bone marrow aspirate is allowed; if the diagnosis is based only on blood, in addition to the immunophenotype and molecular confirmation above, a peripheral blood smear must be available for central pathology review; if the diagnosis is based on a bone marrow, the bone marrow core biopsy or aspirate clot tissue block will be submitted to the RPCI Pathology Department: if the tissue block is not available please submit the diagnostic smears for review
Paraffin-embedded and/or snap-frozen tumor tissue samples (from primary tumor or metastasis) taken as part of routine clinical care must be available for study related correlative studies; if paraffin-embedded and/or snap-frozen tumor tissue samples are not available, at least 15 unstained tumor slides will be requested
Availability of 10 unstained slides or paraffin-embedded tissue block from archived tumor specimen
Have sufficient archival FFPE tumor tissue available for planned analyses. Archival tissue from the most recently collected biopsy or debulking surgery should be provided, if available.
Available tumor tissue (archival or recent acquisition)
Availability of archival diagnostic tissue (paraffin tissue block of resected tumor, core biopsy, fine needle aspirate cell block, or if block cannot be submitted 20-25 [5 micron] unstained slides cut from a block representative of tumor, is required)
Either a formalin fixed tissue block or a minimum of 10 slides of tumor sample (archived or fresh) must be available for biomarker evaluation (a local pathologist must review for adequacy of sampling)
Adequate tissue sample from either archival formalin-fixed paraffin-embedded (FFPE) tumor tissue or new biopsy of tumor
Archival and screening tumor biopsy
For patients enrolled in Part 2 (surgical substudy), patients must be willing to undergo surgical resection and have pre-treatment archival tumor tissue (15 unstained paraffin slides) available for molecular analysis
Presence of a BRAF V600E mutation in lung cancer tissue. Mutation must be locally confirmed in a CLIA-certified laboratory (or equivalent). An adequate amount of tumor tissue (archived tumor tissue, or fresh biopsy if archived tissue is not available) must be available at the time of enrolment for central validation of BRAF mutation;
Archived, paraffin-embedded tissue block (primary or metastatic) available for genomic studies is required
Archived, paraffin-embedded tissue block (primary or metastatic) available for genomic studies required
Adequate tumor tissue available for KRAS mutational analysis or known KRAS wild-type status
EXPANSION COHORT ONLY: Patients must have pre-treatment archival tumor tissue; one paraffin block, frozen curls, or at least 10 freshly-prepared unstained slides from the most representative single paraffin-embedded tumor tissue block should be submitted; slides from the primary tumor are preferred; if both the primary and metastatic tumor blocks are available, at least 10 slides from each of the sites should be submitted, if possible; if tissue from the primary tumor is not available, a paraffin block or unstained slides from a metastatic site are acceptable; fine needle aspirates (FNAs) have insufficient tumor tissue and are not permitted
Archival paraffin-embedded invasive tumor tissue or newly obtained biopsy must be available prior to the first dose of study drug for biomarker analysis; patients must be offered sequential biopsies at baseline and 6 weeks unless in the opinion of the trial principal investigator (PI) this would be hazardous
Patients with pathologically proven diagnosis of grade 2-3 (intermediate or high grade) soft tissue sarcoma with size >= 5 cm are eligible to enroll if the intention to treat is curative; they must have sufficient tissue to submit to central laboratory for review as well as for NGS sequencing (see submission requirement); availability of tumor tissue is mandatory for study eligibility; the patient must have consented to provide archived formalin-fixed paraffin-embedded tumor tissue for future central pathology review, NGS sequencing and/or translational research
Can provide either a newly obtained or archival tissue sample for PD-L1 by immunohistochemistry analysis
Patients must have tissue from the primary tumor or metastases available for correlative studies; either a paraffin block or at least 20 unstained slides are acceptable (30 unstained slides would be ideal); (if less than twenty unstained slides are available and a paraffin block is not available, the patient may be able to participate at the discretion of the investigator)
Patients must agree to undergo two research biopsies of (a) malignant lesion(s); tumor tissue obtained prior to study consent or treatment as part of standard care can also be submitted in lieu of performance of the first pre-treatment biopsy, if the principal investigator deems it to be of sufficient quantity/quality/timeliness; patients may be exempt from biopsy if 1) the investigator or person performing the biopsy judges that no tumor is accessible for biopsy, 2) the investigator or person performing the biopsy feels that the biopsy poses too great of a risk to the patient, or 3) the patient's platelet count is < 100,000/mcl or he/she cannot be safely removed from anti-coagulation therapy (if the anti-coagulation therapy needs to be temporarily held for the biopsy procedure); if the only tumor accessible for biopsy is also the only lesion that can be used for RECIST v1.1 response evaluation, then the patient may be exempt from biopsy; if the investigator deems a second research biopsy to be high risk after a patient has completed the first research biopsy, the patient may be exempt from the second biopsy
Tumor tissue material available (archival or recent tumor biopsy)
Ki67 index by central analysis of ?20% on untreated breast tissue
Participants must be willing to undergo an incisional or excisional lymph node or tissue biopsy or provide a lymph node or tissue biopsy from the most recent available archival tissue.
Availability of a formalin-fixed paraffin-embedded block containing tumor tissue or 7 unstained tumor slides suitable for PD-L1 expression assessment.
Availability of tissue for HPV testing (paraffin block or one 7-µm section on a slide).
Must have undergone biopsy after development of acquired resistance to erlotinib with available archived tissue (equivalent of >= 10 unstained slides)
Has a documented new diagnosis of SCLC by histology or cytology from brushing, washing, or needle aspiration of a defined lesion. Participants who do not have histology samples (defined as core or excisional biopsy, or resections) will need to undergo a new biopsy to provide a tissue sample.
Has provided archival tumor tissue sample or newly obtained core or excisional biopsy of a tumor lesion not previously irradiated
Formalin fixed, paraffin embedded tumor sample (either archival or fresh sample) from the primary or recurrent cancer must be available for central testing. If there is not written confirmation of the availability of an archived or fresh tumor sample prior to enrollment, the subject is not eligible for the study.
Be willing to consider providing fresh tissue for biomarker analysis, and, based on the adequacy of the tissue sample quality, for assessment of biomarker status. Repeat samples may be required if adequate tissue is not provided. Newly obtained biopsy specimens are preferred to archived samples and formalin-fixed, paraffin-embedded block specimens are preferred to slides. Note: Information on 1 tumor biopsy sample is mandatory and is as follows: (1) To determine eligibility, historical (diagnostic) tumor biopsy official pathology report +/- an archival sample. Additional biopsy samples, preferably obtained from the same localized region, are highly desirable when feasible at the following time points: (2) Sample before the first dose of study treatment, (3) Sample after completion of Cycle 2 but before the start of Cycle 3 dosing, and (4) Sample either at the time of response or at the End of Study Visit (if no response).
Additional available archival tumor tissue in the form of 15-20 unstained slides should be submitted to MSKCC for future correlative analysis, but will not be required prior registration; Note: if tissue is depleted, patient will still be eligible after discussion with the MSK principal investigator (PI)
(For expansion cohort only): Tissue must be available to confirm positive expression of AG7 antigen, defined as proportional score ?2, via slides or tumor block from either original diagnostic biopsy material or biopsy of relapsed disease
Tumor tissue from surgery or biopsy must be available to determine MAGE-A3 expression for correlative studies.
At least 15 unstained slides or 1 tissue block (frozen or paraffin embedded) available from the most recent biopsy or surgery (archival tumor material); Exception: Arm C patients may be allowed to enroll without minimum number of requested unstained slides available, however consultation and approval by overall principal investigator (PI) is required
Availability of tumor tissue for HER2 status confirmation
Tumor tissue available and adequate for analysis at screening
All patients must provide a baseline tumor sample at registration. If an archival sample is not available, patients must have a metastatic biopsy collected at the screening visit.
Must have available tumor tissue and consent to biopsy while on study.
Must submit unstained slides from archival tumor tissue for PD-L1 and exploratory analysis; sites must verify that a tumor block is available to obtain unstained slides from prior to registration to the trial
Availability of paraffin embedded or formalin fixed tumor tissue; OR, a minimum of 10 and up to 20 slides of archived tumor tissue for central laboratory confirmation of AR status and molecular subtyping. Metastatic tumor tissue is preferred when possible
Has an archived, diagnostic tumor tissue available for analysis.
Must consent to provide an archival tumor biopsy sample at any time point from screening to study exit
Must consent to allow the acquisition of new tissue biopsy samples during the study
Availability of formalin-fixed paraffin-embedded (FFPE) tumor tissue block or unstained slides to demonstrate HER2 expression.
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor
Satisfactory archival tumor biopsy tissue is retrieved, or new tumor biopsy is performed, prior to starting Cycle 1
Have undergone a biopsy or surgical resection of either primary or metastatic tumor tissue within 60 days of the first day of study treatment, C1D1, and have tissue available to send to sponsor laboratories or are able to undergo a biopsy during screening and provide tissue to sponsor laboratories
Tumor tissue requirements: Availability of archival tissue, or willingness to undergo fresh biopsy at baseline; Enrollment in PK/PD cohort may be limited to subjects with disease amenable to pre- and post-dose biopsies, and willingness to undergo biopsy.
Subjects must have archival tumor tissue available for mutational analysis. A study specific biopsy can be performed if archival tissue is not available.
Tumor tissue available at time of screening for molecular profiling.
Must submit tumor tissue for correlative analyses
Representative tumor specimens in paraffin blocks (preferred) or at least 10 unstained slides, with an associated pathology report, requested at any time prior to study entry. Tissue from core needle, punch, or excisional biopsy sample collection is preferred but slides from fine needle aspiration, brushing, and lavage samples are acceptable.
Have provided tissue from a newly obtained core or excisional biopsy of a tumor lesion or a recent biopsy defined by ?3 years since last documented progression of disease
The participant is willing to consent to provide a tumor tissue sample (fresh biopsy) before (Parts 2 and 3) and after (Part 2 only) receiving the study drug
Archival tumor tissue available for immunohistochemistry (IHC) (1 paraffin-embedded block)
Extended RAS and BRAF wild type status documented on archival tumor tissue or on fresh biopsy if no archival tissue present
Availability of fresh tumor tissue at screening
Known KRAS and NRAS mutation status (if unknown status for either of these genes, and no archival tissues is available, a fresh tumor biopsy will be made)
Availability of tumor tissue for central laboratory analyses.
Have tissues from a biopsy, or have up to 20 unstained slides available from archived metastatic tissue block for biomarker evaluation
Must have available tumor tissue and consent to biopsy while on study.
Availability of fresh or archived tumor tissue.
Must have archival tumor tissue available for biomarker analysis. A study-specific tumor core biopsy, pleural effusion or ascites sample must be obtained prior to treatment if archival tissue is not available.
Cohort Expansion: Available archival tumor tissue block or 5-10 unstained, consecutive core biopsy slides from one archival tumor block that meet specific tissue requirements.
Patients must have agreed to a new biopsy of tumor (deemed accessible and safe for biopsy by the investigator's assessment) and allowing acquired tissue to be used for biomarker analysis. If the biopsied lesions were previously irradiated, they must demonstrate either radiographic or pathological evidence of recurrent or residual disease.
Archival sample or fresh biopsy or tumor effusion must be available for retrospective mesothelin analysis Inclusion Criteria Part A: MAD and Extension Phase (Group 1 and Group 2)
Availability of an original diagnostic tumor tissue or the most recent metastatic tumor biopsies (archival biopsy or de novo biopsy) and a peripheral blood sample for Notch receptors genomic profiling
Tumor specimens must be available for immunological studies either from a previous biopsy or a new biopsy obtained before the initiation of the study
Availability of a representative formalin fixed paraffin embedded tumor tissue sample. If archival tumor sample is not available, a newly obtained tumor sample needs to be submitted instead.
Baseline tumor tissue to conduct molecular and / or genetic studies should be available from all study patients enrolled in this study. (optional in Phase 1b)
Must have available recent (before treatment start) or archival tumor specimen.
Availability of archival diagnostic tissue (paraffin tissue block, cytospin block from a fine needle aspirate, or unstained slides from resected tumor, core biopsy, or fine needle aspirate) is required
Archival tumor block (or 20 unstained slides) for biomarker testing. Patients without archived tumor block material will be allowed to participate in the study.
Mandatory availability of tumour tissue (archival or fresh if archival is not available) for TP53 determination.
For all subjects: Availability of archival tissue, or willingness to undergo fresh biopsy if archival tissue is not available.
Lymphoma subjects will be required to undergo EZH2 mutation testing. This will require availability of archival tissue, or willingness to undergo fresh biopsy, for central testing of EZH2 mutation status.
Measurable metastatic melanoma that expresses ESO as assessed by one of the following methods: reverse transcription polymerase chain reaction (RT-PCR) on tumor tissue, or by immunohistochemistry of resected tissue, or serum antibody reactive with ESO
Histologic documentation of invasive breast cancer by core needle or incisional biopsy; excess baseline biopsy tumor tissue sufficient to make three 5-micron sections must be available for molecular analyses as part of this study
Patients must have histologically or cytologically proven non-small cell lung cancer; tumor tissue must be available from all patients prior to initiation of protocol therapy, either from original diagnostic biopsy, or biopsy performed prior to initiation of protocol therapy
Representative archival tumor sample from glioblastoma (formalin-fixed paraffine embedded tissue) must be available.
2. Histologically proven diagnosis of MPM. All subjects must have biopsy material (archival tissue is acceptable) available for immunohistochemistry determination of Merlin status prior to enrollment.
Adequate tumour tissue (greater than 0.5cm3 preferred, 3 X core biopsy acceptable) available and agreement from subjects that this tissue from their primary and/or metastatic tumour be made available for assessment of potential biomarkers.
Patient has archival or fresh tumor tissue for the analysis of PI3K-related biomarkers. One tumor block (preferred) or a minimum of 12 unstained slides to be provided. Enrollment in the study is contingent on confirmation of an adequate amount of tumor tissue.
Adequate amount and quality of tumor tissue from first surgical resection available for genetic profiling
LUNG ADENOCARCINOMA COHORT (COHORT 3 ONLY): Mesothelin expression in at least 5% of cells as assessed in archival tumor tissue samples, determined by the immunohistochemistry (IHC) assay performed at Laboratory of Pathology/CCR/NCI; archival samples must be available for eligibility
Tumor tissue biopsy within 60 days prior to study entry or availability of an archival specimen obtained within 60 days of study screening
Availability of archival tumor tissues (formalin-fixed paraffin-embedded [FFPE] tissue block or 10-15 unstained slides)
Representative formalin-fixed paraffin-embedded (FFPE) tumor specimens in paraffin blocks (blocks are preferred) or at least 10 unstained slides, with an associated pathology report, for central testing of tumor PD-L1 expression\r\n* Tumor tissue should be of good quality based on total and viable tumor content; fine-needle aspiration, brushing, cell pellet from pleural effusion, and lavage samples are not acceptable; for core-needle biopsy specimens, at least three cores should be submitted for evaluation\r\n* Patients who do not have tissue specimens meeting eligibility requirements may undergo a biopsy during the screening period; acceptable samples include core-needle biopsies for deep tumor tissue (minimum of three cores) or excisional, incisional, punch, or forceps biopsies for cutaneous, subcutaneous, or mucosal lesions
A formalin fixed, paraffin-embedded (FFPE) tumor tissue block or minimum of 3 unstained slides of tumor sample obtained via excisional, incisional, or core needle biopsy from a metastatic or loco-regionally recurrent lesion; a new baseline biopsy does not need to be obtained for study purposes; if 3 unstained are unavailable from a metastatic or loco-regionally recurrent lesion, with permission of the principal investigator (PI), FFPE tumor tissue from the primary disease site at the time of original diagnosis is acceptable
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor
Has a core or excisional baseline tumor biopsy specimen available or willingness to undergo a pre study treatment tumor biopsy to obtain the specimen.
Patients must have archival tissue sample available, collected either at the time of diagnosis or any time since; if archival tissue is unavailable, patient must be eligible and willing to undergo a fresh tissue biopsy
Available tissue for AR testing for research purposes
Have provided tissue from an archival tissue sample or newly obtained core or excisional biopsy of tumor lesion.
Archived tissue sample or new biopsy sample.
For Part 1, willing to provide archived tumor tissue (if available) and willing to undergo pre- and on-treatment tumor biopsy (if considered safe and medically feasible by the treating investigator)
Tissue availability for programmed cell death ligand 1 (PD-L1) expression is mandatory for enrollment; however if archived tissue is unavailable the patient will be given the option to consent to pre and post treatment tissue biopsies; tissue biopsies will be collected pretreatment (prior to the first dose of therapy) and post treatment (after at least 1 dose, preferably 2 doses of nivolumab)
Patient willing to comply to provide tumor tissue (archival or fresh biopsy specimen)
-  Availability of tumor tissue from any time since diagnosis of prostate cancer disease. If no tumor samples are available the participant might still be eligible following discussion between the investigator and the medical monitor.
Availability of FFPE tumor tissue, either archival or obtained at study entry through fresh biopsy o Tumor tissue from fine needle aspiration is not acceptable.
Must have available archival or recently acquired bone marrow biopsy/aspiration or tumor tissue for central review to be eligible.
Have provided tumor tissue from a newly obtained core, punch, incisional or excisional tumor biopsy; patients must undergo biopsy (core, punch) or open incisional/excisional biopsy (if done as part of a clinically indicated baseline diagnostic procedure) within 4 weeks of registration on the study
Availability of tumor tissue from formalin-fixed, paraffin-embedded (FFPE) core biopsy of breast primary tumor
Availability of FFPE tumor tissue, either fresh core-needle-biopsied or archived
Confirmed positive CD70 expression on tumor tissue
Documented MUC16 expression from archival or fresh tissue by IHC central review
Sufficient tissue (block or slides) from diagnostic biopsy to undergo testing for FRa
Patient must have archival tumor specimen available for submission
Tumor programmed death-ligand 1 (PD-L1) expression, as determined by immunohistochemistry (IHC) assay of archival tumor tissue or tissue obtained at screening
Availability of an archival or newly obtained tumor sample (collected at diagnosis or progression) with accompanying pathology report
Tumor tissue from formalin-fixed paraffin-embedded cores (FFPE) core biopsy of breast primary tumor that is confirmed as evaluable for phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) mutation status by central histopathology laboratory
Availability of FFPE tumor tissue, either archival or obtained at study entry through fresh biopsy
Tumor tissue from fine needle aspiration is not acceptable.
Availability of tumor tissue, either archival FFPE or obtained at study entry through fresh biopsy
Patient must have access to archival tumor tissue sample or agree to undergo biopsy after study eligibility has been confirmed to obtain fresh sample for evaluation of WT1 expression. In place of archival tumor tissue samples, subjects with AML should have available a bone marrow aspirate and/or, bone marrow biopsy, with PCR for WT1 transcript performed before the first dose of study drug. Note: The archived tumor tissue sample does not need to be delivered to the clinical site prior to enrollment of the patient, however its availability should be confirmed through provision of the accession number or other identification number. Patient Inclusion Criteria - Part 2:
Patient must have access to archival tumor tissue sample or agree to undergo biopsy after study eligibility has been confirmed to obtain fresh sample for evaluation of WT1 expression. In place of archival tumor tissue samples, patients with AML should have available a bone marrow aspirate and/or bone marrow biopsy with PCR for WT1 transcript performed before the first dose of study drug.
Tumor tissue (archived acceptable) available for biomarker studies. For Phase 2 Part 2
Availability of a representative formalin-fixed paraffin-embedded tumor specimen
Tumor tissue from the resected site of disease must be provided for biomarker analyses
Availability of formalin-fixed paraffin-embedded (FFPE) tumor tissue, either fresh core-needle-biopsied or archived
Patients must have a site of disease that is amenable to pretreatment and on-treatment core biopsies; at least 3 formalin fixed, paraffin embedded (FFPE) slides at five microns each may be collected at each biopsy; determination of tissue accessibility and quantity will be made by the consenting clinician; patients must consent to the two study-required biopsy procedures
HER2 Positive disease documented as FISH-positive and/or 3+ by IHC on previously collected tumor tissue.
Available archived tissue to perform molecular analysis\r\n* Patients without available archived tissue can have repeat biopsies to determine EGFR status as per standard clinical care guidelines
Sufficient archived tumor samples (if taken within 6 months prior to treatment may be submitted) available for PD assessments, or willingness to undergo a pre-treatment core needle biopsy, preferably of the primary tumor, in order to obtain such tissue;
Available archival tumor tissue or willingness to undergo repeat biopsy is required at trial initiation
Availability of FFPE tumor tissue (from either the primary tumor, locoregional disease or a metastatic site), either fresh core-needle-biopsied or archived (two FFPE cores preferred whenever possible). If fresh tissue is obtained, the core biopsy must be done at least 7 days prior to randomization.
Availability of a representative tumor specimen (primary or metastatic, archival or newly obtained)
Patients with confirmed p53 mutation by molecular analysis and/or evidence of p53 overexpression by immunohistochemistry (>= 10% of cells within the tumor staining positive) will be eligible; this will be assessed semi-quantitatively by a Clinical Laboratory Improvement Amendments (CLIA) approved pathology core pathologist, using CLIA approved mutational analysis or immunohistochemistry techniques on formalin-fixed paraffin-embedded tissue; in the case of equivocal immunohistochemistry (IHC) results, p53 involvement may be confirmed by detection of p53 molecular analysis on tumor deoxyribonucleic acid (DNA); patients on whom molecular analysis of p53 mutations is already available, will not require IHC analysis; molecular analysis may be performed as an additional research procedure at the end of the study (distinct from eligibility determination) if the principal investigator (PI) deems it of scientific value and research funding is available to cover the cost
Availability of archival tumour tissue sample. If archival sample is not available, a fresh tumour biopsy must be provided.
Patients must provide tissue from a punch biopsy of the skin at baseline, at the time of a clinical event (at the time of response, progression or appearance of a new lesion) and at the end of treatment; additional punch biopsies every 3 cycles are optional; an archival tissue sample is optional
Tumor tissue submitted for molecular and genetic analysis through the companion Stand-up 2 Cancer (SU2C) radiologically guided biopsy of abiraterone and/or enzalutamide refractory mCRPC protocol\r\n* Patients who consent to participate in the companion biopsy protocol and are subsequently determined to be ineligible for biopsy are eligible to participate in the current protocol
Must have adequate fresh or archival tumour tissue at the late disease progression immediately prior to the study entry
Confirmed availability of archival or freshly biopsied tumor tissue meeting protocol-defined specifications prior to study enrollment
Patient must consent to provision of a representative formalin fixed paraffin block of tumor tissue, if available, in order that the specific correlative marker assays may be conducted.
Must have undergone biopsy after development of acquired resistance to erlotinib (which is performed as standard of care) with adequate tissue to determine EGFR T790M and tumor histology; slides from an outside institution may be used
Availability of a pretreatment tumor biopsy (excluding fine needle aspiration and cytology samples) taken after the subject has discontinued sorafenib and within 28 days before the day of first dosing with MSC2156119J. From the pretreatment biopsy either a formalin-fixed (formalin fixation is mandatory) paraffin-embedded block with tumor tissue (preferred) or at least 15 unstained slides must be sent to the central laboratory prior to enrollment. An associated pathology report must also be sent with the sample
Availability of tumor tissue sample suitable for the central confirmation of the genetic alteration and exploratory analyses
HCC tissue either from an archived specimen or from a new biopsy of sufficient amount and quality should be available for IHC determination of ASS status, and other biomarkers, to be performed retrospectively. Subjects with no tissue available would require a biopsy.
If available, patient must agree to provide archival tissue for research purposes (either archival paraffin tissue block or 10 unstained slides of a primary or metastatic melanoma lesion) prior to enrollment; samples should be shipped within 1 month after enrollment
A tumor tissue sample is provided for immunohistochemical analysis of relevant antigens, immune markers and potential prognostic factors. Preferably a paraffin block or 10-12 unstained slides will be submitted prior to study entry. Patients for whom tumor samples are unavailable or inadequate are permitted to participate in the study; however, the absence of available/adequate tumor specimen must be documented.
Availability of FFPE tumor tissue, either archival or obtained at study entry through fresh biopsy o Tumor tissue from fine needle aspiration is not acceptable.
Must have submitted a diagnostic FFPE tumor tissue sample to confirm tumor GR positivity. Tumor tissue may be from primary or metastatic lesion. In the absence of sufficient tissue to complete IHC, a tumor biopsy will be required.
Consent to provide archival tumor tissue for biomarker testing
Availability of tumor tissue, either archival FFPE or obtained at study entry through fresh biopsy
Sufficient archival tumor specimen is available for HER3 immunohistochemistry (IHC) analysis, or subject is willing to undergo a fresh tumor biopsy for HER3 IHC analysis.
Needle biopsy or incisional biopsy
Excisional biopsy
Availability of tissue from the initial diagnosis and the recurrent tumor that is estimated to be of sufficient quality and quantity for both genomic deoxyribonucleic acid (DNA) and total ribonucleic acid (RNA) isolation; preferably some of the tissue would be snap frozen for high quality RNA preparation
Molecular characterization of the tumor demonstrating a KRAS mutation by a CLIA-certified assay. Adequate archival tissue, tissue core biopsy specimen, or DNA samples must be available for central testing of INK4a/Arf and p53 if not previously performed by a CLIA certified lab.
The pathologic tissue is available to determine FGFR1 amplification status
Archival tumor tissue to conduct molecular and / or genetic studies must be collected from all study subjects enrolled in this study.
Patient has tumor tissues available (archival or fresh).
Consent to provide archival tumor tissue for biomarker testing
Availability of archival tumor tissue required for assessment of deregulated FGF pathway signalling, but not limited to, FGFR1 amplification or FGF2 or FGFR1 expression. If archival tissue is not available, a fresh biopsy is required. In Arms A and B, subjects will be prospectively screened for FGFR1 gene amplification using a Fluorescence in situ hybridization (FISH) assay for the dose expansion and the MTD/MFD cohorts only. For inclusion in this study, based on the central laboratory testing, FGFR1 gene amplification must meet one of the following criteria: a ratio of FGFR1/CEN 8 of >=2; or average number of FGFR1 signals per tumor nucleus of >=6; or the percentage of tumor nuclei containing >=5 FGFR1 signals is >=50%. In Arm C, FGF2 expression by IHC will be evaluated retrospectively in tissue samples by a central laboratory and is not a requirement for study entry.
Availability of fixed tumor specimen (block or slides) for exploratory biomarker analysis. If no slides or block are available, fresh tumor biopsies should be obtained and used for these assessments
A representative FFPE tumor sample must be available for molecular testing along with a corresponding pathology report. An archival tumor sample may be submitted. However, if not available, a new tumor biopsy obtained for the purpose of this study must be submitted instead.
Patients who do not have an archival or fresh tumor sample (or sections of it) available or readily obtainable.
Availability of fresh or archival FFPE tumor specimens for analysis of LHRH receptor expression.
MET Diagnostic-High tissue reported by the central authorized laboratory using archival or recent biopsy tumor samples
Subjects have available tumor tissue
Available archival tumor sample (excisional or core biopsy) that can be acquired and provide consent to biomarker testing of the tumor.
Availability of archival tumor tissue (core biopsy or surgical tumor blocks) for analysis. Sites will be asked to submit archival tissue (subjects may start the study if tissue is available at an outside hospital, but not yet requested or received).
At least one soft tissue site that meets criteria for a TARGET lesion defined by:
Confirmed availability of archival or freshly collected tumor tissue
PTEN deficient tumor as documented from archival or fresh (from biopsy) tumor tissue analyzed by GlaxoSmithKline selected laboratory
All subjects must provide a tumor tissue sample from [Formalin Fixed Paraffin Embedded (FFPE) slides] archival tissue or fresh biopsy collected before Cycle 1, Day 1
Tumor tissue (archived or fresh) is required and must be available to be shipped to GSK or site specific laboratory.
Availability of an existing tumor biopsy sample (or consent to allow pre-treatment tumor biopsy if sample not available)
Patients must have a tumor tissue form indicating availability of archived tissue from initial resection at diagnosis of glioblastoma completed and signed by a pathologist
The patient must have at least 1 block of tissue available or 15 unstained slides at a minimum, for central pathology review and molecular profiling of the tissue sample
Patient must consent to provision of, and investigator(s) must confirm access to and agree to submit to the Canadian Cancer Trials Group (CCTG) Central Tumour Bank, a representative formalin fixed paraffin block of tumor tissue in order that the specific correlative marker assays described in the protocol may be conducted; where tissue exists but local center regulations prohibit submission of blocks of tumor tissue, the approval of the CCTG must be sought prior to randomization of the first patient to allow cores (two 2 mm cores of tumor from the block) and slides (20 x 5 micro thick unstained slides) of representative tumor tissue to be substituted; where tumor tissue is available, failure to submit any tissue samples will result in the patient being considered ineligible
Consent to submit a formalin-fixed, paraffin-embedded tumor (FFPE) tissue block or freshly cut unstained, serial tumor slides from the most recently collected tumor tissue for central molecular analysis:
Patient must agree to undergo tumor HRD testing at screening. The tumor sample must be submitted for HRD testing during the Screening Period. Patients do not have to wait for the HRD test result to be enrolled. If archival tumor tissue is not available for testing, the patient must agree to undergo a fresh biopsy.
Provision of (archival or fresh) FFPE tumor tissue. (For Cohort 3 only: if diagnosis was made by cytology and archival tissue is not available, patient will not need to provide tumor tissue)
Participants with confirmed availability of representative tumor specimens in formalin-fixed, paraffin-embedded (FFPE) blocks (preferred), or sectioned tissue
Participants must have accessible lesion(s) that permit a total of two to three biopsies (pretreatment and on-treatment) or one biopsy (on-treatment, if archival tissue can be submitted in place of a pre-treatment biopsy) without unacceptable risk of a significant procedural complication. RECIST lesions should not be biopsied.
Patients who do not have an archival tumor sample (or sections of it) available or readily obtainable.
EGFR-mutation negative tumor tissue as determined by sequencing; if an individual tissue test result is inconclusive (unable to be determined), it will be considered negative for study eligibility purposes
Consent to provide archival tumor tissue for biomarker testing
Consent to the collection of an archival formalin-fixed paraffin-embedded (FFPE) block or freshly cut unstained tumor slides from archival tumor tissue or a newly collected tumor sample
Available paraffin-embedded tissue should have been collected no longer than 6 months prior to first administration of SAR3419. Cryo-preserved tissue cannot be used. If archival material is not available, a Fine Needle Aspiration (FNA) must be obtained.
availability of tissue sample for diagnostic testing is required
Availability and willingness to provide an adequate archival sample of tumor
Willingness to provide archival tissue from the primary diagnosis (original lymphoma lymph node tissue biopsy)
Tumor verified to be CD20+ (based on local evaluation), from a current or previous tissue biopsy. Tissue biopsy should be repeated if no report or specimen is available, CD20 staining was not previously performed, or there is clinical suspicion that the indolent lymphoma has transformed to aggressive lymphoma/higher malignancy grade.
For participants in Part B, C, D, E, and F, a tumor tissue sample is mandatory, when safe and feasible, for biomarker analysis
The participant has archived tumor tissue available for analysis (can be either primary tumor or metastases).
Availability and willingness to provide sufficient tumor tissue sample for testing
Measurable soft tissue plasmacytoma
Consent to research use of their BCC tissue
Patients must have a signed tissue acquisition consent and have at minimum, adequate samples of primary fresh tissue or blood available for use in this study.
Histopathologic confirmation of one of the following cluster of differentiation antigen 20 positive (CD20+) B-cell non-Hodgkin's lymphomas (tissue diagnostic procedures must be performed within 6 months of study entry and with biopsy material available for review):
Histologically-confirmed CD30-positive disease; tissue from the most recent post diagnostic biopsy of relapsed/refractory disease must be available for confirmation of CD30 expression via slides or tumor block.
Paraffin-embedded sections of tissue acquired from surgery at the time of suspected recurrence must be available for analysis
Documentation of disease: \r\n* Histologic documentation: histologically proven mucosal melanoma by local pathology\r\n* Tumor tissue: tumor tissue from the primary site of disease must be available for PD-L1 testing (stratification factor)
Consent to collection of a pre-treatment tumor sample, on-treatment biopsy, and, if applicable, a tumor tissue sample at the time of progressive disease (PD) Inclusion Criteria Specific to Obinutuzumab-Containing Cohorts
Sufficient tumor tissue must be available for histologic assessment of PD-L1 expression and whole exome sequencing
Patients only: must have a tumor in extremity muscle tissue or in the pelvis
Have pre-resection tissue (esophagogastroduodenoscopy [EGD] or EUS biopsy from the diagnosis) available
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor
Tumor tissue available and deemed adequate for genomic studies
Archival tissue available for Foundation One analysis
There must be availability of a formalin-fixed, paraffin-embedded tumor specimen with adequate viable tumor tissue
Unresectable thyroid cancer expressing TG as assessed by one of the following methods: real-time (RT)-polymerase chain reaction (PCR) on tumor tissue, or by immunohistochemistry of resected tissue
Subjects must have existing tissue available for correlative studies; if availability of tissue has been confirmed the study drug can be started prior to the tissue being obtained
Presence of BRAF V600E mutation in tumor tissue
Tumor tissue must be available for submission for central pathology review
Local pathology review for histological confirmation; A formalin-fixed, paraffin-embedded (FFPE) tumor block or appropriately stained slides from a fresh biopsy is required.
Availability of archived tumor tissue sample that can be used for assessment of PrR status by the central laboratory;
Participants must have an archival tumor sample available (1 block or 20 unstained slides); if no archival tissue is available, participants must be willing to undergo a research biopsy of their disease if it is safely accessible
Has provided tissue for Programmed Cell Death Receptor Ligand 1 (PD-L1) biomarker analysis from a core or excisional biopsy. If an excisional or incisional biopsy has been performed, participants remain eligible for the study provided the residual disease meets the staging criteria required for the trial (e.g., excisional biopsy of a lymph node with residual T4 primary). Prior surgical debulking, including tonsillectomy, for the head and neck cancer under study is not allowed.
All participants must provide tumor tissue from the primary or metastatic tumor site obtained from a prior or new biopsy or surgical procedure for detection of PIK3CA mutation by central laboratory test. Confirmation of adequate tissue is required prior to enrollment. For participants enrolled to biopsy cohorts or who consent to optional tumor biopsies, the pretreatment tumor biopsy may be used
Availability of archived tumor tissue for banking
Availability of a formalin fixed paraffin embedded (FFPE) block of cancer tissue from the original surgery or biopsy or from a biopsy of recurrent disease
Availability of tumor tissue (>= 10 slides) for PD-L1, gene expression profiling (GEP), and additional testing
Request for formalin-fixed, paraffin-embedded (FFPE) archival tumor specimens if available and willingness of the participant to undergo mandatory fresh tumor biopsy unless determined medically unsafe or not feasible; a note from the study team should be provided documenting availability of tissue; if a target lesion is biopsied at screening, this lesion must be followed as non-target lesion after the biopsy unless it is the patient’s only target lesion; if there is only one target lesion, it should be followed as a target lesion regardless\r\n* The archival specimen should contain adequate viable tumor tissue\r\n* The specimen may consist of a tissue block (preferred and should contain the highest grade of tumor) or at least 30 unstained serial sections; fine-needle aspiration, brushings, cell pellet from pleural effusion, bone marrow aspirate/biopsy are not acceptable\r\n* Fresh tumor biopsy at progression will be required in cases where patients experience relapse after an initial response if medically safe
Primary breast reconstruction in women at least 18 years old with surgically absent breast tissue (two-stage reconstruction [tissue expanders utilized with or without the use of human acellular dermal matrices (ADM), limited to AlloDerm® and FlexHD® PLIABLE, utilized in a prior surgery to expand tissue for study device placement] to replace breast tissue post-mastectomy)
Demonstrates tissue characteristics that are clinically incompatible with successful use of a breast implant (e.g. inadequate tissue or compromised vascularity)
Archival tumor tissue obtained at any time from the initial diagnosis to study entry; a fresh tumor biopsy using a procedure that is safe for the subject on a lesion not previously irradiated unless lesion progressed will be required if archival tissue is unavailable.
Patients receiving osseocutaneous free tissue transfer regardless of the indication for free tissue transfer; this includes osseocutaneous tissue from fibula and scapula
No use will be made of fetal tissue
Previously cryopreserved and stored cortical ovarian tissue available for autologous transplantation
Passage through non-aerated lung or tissue
Willing to undergo fresh liver biopsy if provided archival tissue was taken greater than (>) 6 months from Cycle 1 Day 1
Willing to undergo biopsy if archival tissue is not available or if archival tissue was taken >6 months from Cycle 1, Day 1
Willing to undergo biopsy if archival tissue is not available or if archival tissue was taken >6 months from Cycle 1 Day 1
Tissue available for the evaluation of AR by IHC on pretreatment HCC samples; if tissue is not available, a pretreatment biopsy will not be necessary for eligibility
Availability of tumor tissue at study enrollment
Adequate archival or fresh tumor tissue (from biopsy, bone marrow, or peripheral blood) for analysis of potential predictive biomarkers.
All participants must consent to provide archived diagnostic formalin-fixed paraffin embedded (FFPE) tumor tissue and on study biopsies.
Tissue from an archival tissue sample or fresh tissue obtained from a core or excisional biopsy of a tumor lesion
Pre-treatment fresh frozen tissue available for research purposes; this tissue can be collected from preoperative laparoscopy, other diagnostic biopsy, or a research-specific biopsy
Group 2: Patients must have a confirmed diagnosis of unresectable GIST with a D842V mutation in the PDGFR? gene. The PDGFR? mutation will be identified by local or central assessment, either in an archival tissue sample or a new tumor biopsy obtained prior to treatment with avapritinib.
Groups 1 and 2: A tumor sample (archival tissue or a new tumor biopsy) has been submitted for mutational testing.
Adequate archival tissue from a biopsy performed after progression of disease on previous EGFR-TKI or willing to consent to a fresh tumor biopsy (mandatory for dose expansion cohort only; optional for dose escalation)
Patient must have an accessible non-bone tumor lesion from which serial core biopsy specimen can be obtained; NOTE: if baseline biopsy is attempted and is unsuccessful (e.g., patient intolerance, inadequate tissue), the patient will still be considered eligible for the study; if core biopsy is not possible, other methods may be approved in advance by the protocol chair/designee
Tumor PD-L1 expression as determined by immunohistochemistry (IHC) assay of archival tumor tissue or tissue obtained at screening
Available tissue that was obtained at or after the time the usbject was found to have muscle invasive disease and is of suitable quality and quantity and to assess the FGFR3 status by genetic testing. For subjects participating in the Randomized Phase only, if suitable archival tissue is unavailable, then a core biopsy of tumor tissue (metastatic or primary) must be obtained prior to randomization even if a blood sample sample was used to determine FGFR3 genetic status
Participants should be able to submit 20 unstained formalin-fixed, paraffin-embedded (FFPE) slides from the initial tissue diagnosis prior to study registration for confirmation of diagnosis and correlative studies
Tissue available for the required analyses (either clinical tissue block or slides and scrolls)
Non-surgical cohort only: positive phospho-EGFR assessment (>= 100 stained pixels) from tissue obtained from previous clinical liver biopsy
Pre-intervention biopsy tissue (most proximal to enrollment) with sufficient tumor tissue to cut 5-10 unstained slides confirmed to be available upon request
Must be willing to undergo fine needle aspiration of breast adipose tissue at 0 and 3 months of the study
Biopsy of tumor tissue for central evaluation, within 60 days prior to the first day of study treatment
Agree to undergo a biopsy of at least one metastatic site or primary prostate for determination of the RB status; adequate archival metastatic tissue can be used if available in lieu of a biopsy if done when patient had CRPC (within 6 months of treatment start)
Patients enrolled in Part 2 must have at least 20 (preferably 40) slides of archival tumor tissue from a prior surgery demonstrating GBM; patients enrolled in Part 1 will not be required to have archival tissue
The availability of formalin-fixed paraffin embedded archival tissue from core biopsy of tumors is recommended for exploratory analysis
HER2-overexpression in the patient's tumor tissue
All patients must agree to provide an archival tissue block or paraffin sample from archival tissue block (approximately 10 sections) for use in pharmacodynamic correlative studies; however, patients are not considered ineligible if archival tumor is not available
Tumor tissue EBV positive
Confirmation of availability of sufficient tissue from a prior surgery for correlative studies is required prior to enrollment; patients must have representative non-transitional cell carcinoma (non-TCC) or the urothelial tract formalin-fixed paraffin-embedded (FFPE) archival tumor specimens (tumor blocks or 30 unstained slides; preference for tumor blocks); these samples may be submitted between the time of consent and the start of treatment; patients with < 30 slides may be enrolled after discussion with the principal or co-principal investigators
Provision of formalin-fixed paraffin embedded tissue sample from primary or metastatic disease
Availability of formalin-fixed, paraffin-embedded (FFPE) archival tumor specimens, when available, and willingness of the subject to undergo mandatory fresh tumor biopsy prior to treatment initiation unless determined medically unsafe or not feasible; given that fresh tumor tissue is required for correlative assessments, a prior biopsy cannot take the place of the pre-treatment mandatory biopsy\r\n* The archival specimen, when available, must contain adequate viable tumor tissue\r\n* The specimen may consist of a tissue block (preferred and should contain the highest grade of tumor) or at least 20 unstained serial sections; fine-needle aspiration, brushings, cell pellet from pleural effusion, bone marrow aspirate/biopsy are not acceptable\r\n* A mandatory biopsy at the time of radiographic progression will be requested from patients who have an initial response to treatment and then subsequently progress as determined by RECIST version 1.1
Patients must be willing to provide a core tissue biopsy at baseline and with repeat tissue collection after 12 cycles of protocol therapy
The pathology report and either (1) tissue (blocks or an unstained slides) or (2) a photomicrograph of the ER IHC slides from at least one site of metastatic disease and/or from primary breast cancer must be available for central review and analysis\r\n* NOTE: if photomicrographs are submitted, the submission of hematoxylin and eosin (H&E), PR and Ki67 IHC’s, if performed, are also to be submitted
Patients must document their willingness to be followed for up to 24 months after recruitment by signing informed consent documenting their agreement to have clinical endpoints and the results of histopathologic tissue analysis (when tissue becomes available from routine care) entered into a research database
Archived tissue from the CRC primary tumor in sufficient amounts to allow advanced quantitative real time-polymerase chain reaction (qRT-PCR) analysis; specimen from metastatic sites are not required but highly preferred
Be willing to undergo fresh tumor tissue biopsy of an accessible tumor lesion prior to pembrolizumab; a mandatory fresh biopsy will be collected following C11-AMT PET imaging; subjects for whom fresh samples cannot be provided (e.g. inaccessible or subject safety concern) or do not agree to this fresh tumor research biopsy of accessible tumor will be deemed ineligible for study participation; exception to the mandatory tumor tissue collection are patients with metastatic lung lesions as the only site of metastatic disease; fresh biopsy collection from these subjects will be optional, due to high risk of pneumothorax
Be willing to allow for investigators to collect archival tumor tissues from surgical procedures that may have been performed before or after enrollment into this trial for research purposes (in-house cases and/or outside cases). These samples will be obtained by study staff as long as subject continues on follow-up. Blocks of tissue will be requested, and if blocks are not able to be obtained, 5 micron slides (10-15) will be sufficient
Willing to allow use or collection of pathology tissue for the purposes of research from either clinical biopsy or surgical procedure (if adequate tissue is available) or research only biopsy
Archival tumor tissue from biopsy or resection will be required for all patients; archival tissue should be of good quality based on total and viable tumor contents; fine needle aspiration, brushing, and cytologic cell pellets are not acceptable
The patients will be asked to consent to provide access to data obtained from molecular analysis that has been done on archived tumor tissue that will be correlated with 89Zr-DFO-trastuzumab imaging results
Patients must document their willingness to be followed for at least 24 months after recruitment by signing informed consent documenting their agreement to have clinical endpoints and the results of histopathologic tissue analysis (when tissue becomes available from routine care) entered into a research database
Expected to undergo tumor tissue biopsy for known or suspected prostate cancer (in the primary, recurrent or metastatic disease setting)
Prostate biopsy within 6 weeks (unless biopsy is planned from extraprostatic tissue)
Sufficient fresh or frozen tissue remaining from pre-treatment core biopsy/incisional biopsy or willing to undergo biopsy (at University of North Carolina [UNC] via LCCC9819) for research purposes only (approximately 10 mg or one core's worth of tissue needed)
Is willing to provide archival tumor tissue from a biopsy performed within 6 months of progression during treatment with erlotinib, gefitinib, afatinib, or osimertinib OR has at least one lesion, not previously irradiated, amenable to core biopsy and is willing to undergo screening tumor biopsy
Willingness to undergo a tumor biopsy prior to starting treatment (or if biopsy is not feasible, provide archival tissue).
Is willing to provide tissue from a tumor lesion at baseline and at time of surgery.
Subjects must have adequate fresh or paraffin embedded tissue
Patients must have available an archival paraffin tumor block sufficient to generate at least 10 unstained slides of 8 micron thickness; or, if a paraffin tumor block is unavailable, at least 10 unstained slides of 8 micron thickness
Be willing to provide tissue from a newly obtained biopsy of a tumor lesion, most commonly an esophagogastroduodenoscopy (EGD) biopsy from the esophagus; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor; please note, patients may not initiate therapy until the biopsy specimen is received at the Dana-Farber Cancer Institute
Availability of a paraffin-embedded or frozen tumor-tissue block with a minimum of 1 cm^2 of tumor surface area from a tissue specimen that demonstrates pathological transformation to glioblastoma (WHO grade IV) or a progressive specimen that harbors one of the genetic alterations\r\n* If a tumor block cannot be submitted, then 20 unstained slides (preferably 10 slides from two different tumor blocks from the same surgery) from the tumor specimen must be submitted
Has provided a tumor tissue sample (archival or newly obtained core or excisional biopsy of a tumor lesion)
Tissue analysis demonstrating pathology other than glioblastoma
Subjects, for whom tissue is not available, must have a soft tissue or metastatic bone lesion that can be biopsied and be willing to undergo percutaneous biopsy to obtain tissue for OATP1B3 expression
Tissue specimen is inadequate for sampling and analysis
Have tissue block available from core biopsy for correlative biomarkers and genomic assay
Patients younger than 18 years of age with a histologically or cytologically confirmed diagnosis of cancer who are being treated for cancer at the NIH Clinical Center and who will already be undergoing a clinically necessary medical procedure during which tumor tissue will be resected or needle biopsy tissue collected
Tumor tissue:
Part 1, Dose Escalation: tumor tissue
Part 2, Expansion: tumor tissue
Paraffin-embedded and/or snap-frozen tumor tissue samples from the diagnostic procedure must be available for study-related correlative studies; if paraffin-embedded and/or snap-frozen tumor tissue samples are not available, at least 15 unstained tumor slides will be requested
Tumor tissue blocks or at least 20 unstained slides from a prior diagnosis will be requested; hematoxylin and eosin (H&E) to confirm diagnosis must be available; the 20 unstained slides is preferred, but not required
Patients must be agreeable to provide tissue prior to enrollment
Soft tissue progression
Tissue confirmation.
Sufficient fresh or frozen tissue remaining from pre-treatment core biopsy/incisional biopsy or willing to undergo biopsy for research purposes only (approximately 10mg or one core’s worth of tissue needed)
Willing to undergo two mandatory core biopsies after diagnosis to obtain tissue for correlative studies; the third biopsy time point is optional
Archive tumor tissue (obtained from a biopsy or surgical resection of a metastatic lesion done within 4 months from study enrollment) availability is required for patient participation. If the available tissue is insufficient for the required baseline analysis, the patients are given the option to repeat the biopsy for the purpose of study participation as long as they have not already started palbociclib or ribociclib.
Lack of archive tumor tissue from a biopsy or surgical resection of a metastatic lesion done within 4 months of study enrollment. Patients will be given an option to have a repeated biopsy of a metastatic lesion if they had a diagnostic tumor biopsy intended for use in the current study that was performed more than 4 months prior to analysis, or there is insufficient tissue from the initial biopsy to complete the analysis, as long as they have not started treatment with a CDK 4/6 inhibitor. Otherwise, the patient will be excluded from the study participation.
Patients without either fresh or archival tumor tissue accessible.
Consent to provide archival tissue
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor
Patients with archival tumor tissue suitable for measurement of proteasome activity and biomarker status must give permission to access and test the tissue. Patients without archival tumor tissue are eligible for the Dose-Escalation stage, but not the Dose-Expansion stage of the study
Representative formalin-fixed paraffin-embedded (FFPE) tumor specimens in paraffin blocks (blocks preferred) or at least 15 unstained slides, with an associated pathology report, for central testing and determined to be evaluable for tumor PD-L1 expression prior to study enrollment; participants who have fewer than 15 unstained slides available at baseline (but no less than [<] 10) may be eligible following discussion with the Medical Monitor
Are amenable to provide tumor tissue prior to treatment and provide tumor tissue after treatment initiation (both mandatory).
Patient must be able to provide a formalin-fixed and paraffin-embedded (FFPE) tumor tissue specimen prior to treatment. The specimen may have been taken at any time during the course of the disease and may be from the primary tumor or from a metastasis
Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor lesion; newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) prior to initiation of treatment on day 1; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may submit an archived specimen only upon agreement from the sponsor and primary investigator
Histologically confirmed muscle-invasive urothelial cancer of the bladder within 60 days of study enrollment\r\n* Patients must be willing to provide a TURBT specimen during screening and prior to enrollment if adequate specimen (formalin-fixed paraffin-embedded [FFPE] tissue block or 20 unstained slides) from initial TURBT documenting muscle-invasive urothelial bladder cancer is not available
Consent for the use of any residual material from biopsy (archival tissue) and serial blood draws will be required for enrollment; patients without adequate tissue for bio-correlates will not be excluded or required to have a repeat biopsy