Patients with newly diagnosed higher risk RCC of any histology including sarcomatoid or (if preoperative biopsy was uninformative) - “unknown” histology; RCC must have been confirmed by biopsy within 4 months prior to randomization; if the biopsy clearly demonstrated a benign condition or a different type of cancer, the patient is not eligible to be randomized
Patients must have tumors determined to be easily accessible for biopsy and must be willing to have serial biopsies (with a third biopsy upon evidence of disease progression)
Patients must have a site of disease amenable to biopsy, and be a candidate for tumor biopsy. Patient must be willing to undergo a new tumor biopsy at baseline or at molecular pre-screening if applicable, and during therapy on this study. For patients in the phase II part of the study, exceptions may be granted after documented discussion with Novartis. After a sufficient number of paired biopsies are collected, the decision may be taken to stop the collection of biopsies.
Subjects must have measurable disease as demonstrated by residual abnormal tissue at a primary or metastatic site (measurable on CT or MRI) at the time of biopsy; tumor must be accessible for biopsy. In addition, subjects with bone or bone marrow only disease expected to be >75% tumor are eligible to enroll.
7. Willingness to provide consent for biopsy samples;
Participants enrolled must have disease that is accessible for tumor biopsies and must agree to a pre-treatment tumor biopsy
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
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 agree to have a biopsy of 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 may undergo an additional biopsy attempt (at the same or a different site, determined by the investigator)\r\n* For patients with an intact primary and no metastatic site that can be safely biopsied, biopsy of the primary is acceptable, but must be approved by the principal investigator\r\n* Baseline tumor biopsy may be omitted if the tumor is inaccessible and/or a biopsy is not thought to post exceptionally high procedural risk due to location or other factors
Patients with pancreatic adenocarcinoma; patients must have histologic diagnosis and either locally advanced unresectable or metastatic disease that has failed at least one standard regimen; eight patients will participate in the paired biopsy studies; patient selected for biopsy must have a primary or metastatic non-bone site that is amenable to safe biopsy; bone only lesions are not suitable for biopsy; these patients will provide informed consent for the paired biopsy study (dose expansion phase, arm A)
Patients with colorectal adenocarcinoma; patients must have histologic diagnosis and either locally advanced unresectable or metastatic disease and have previously received oxaliplatin, irinotecan, and a fluoropyrimidine; eight patients will participate in the paired biopsy studies; patient selected for biopsy must have a primary or metastatic non-bone site that is amenable to safe biopsy; bone only lesions are not suitable for biopsy; these patients will provide informed consent for the paired biopsy study (dose expansion phase, arm B)
Availability of a cancerous lesion amenable to biopsy and willing to undergo a pre-treatment biopsy
Patients must have an accessible metastatic lesion for pretreatment core biopsy.
Phase 2 only: Willing to consent to 1 mandatory pre-treatment and 1 on-treatment tumor biopsy
Patient must have a site of disease amenable to biopsy, and be a candidate for tumor biopsy according to the treating institution's guidelines. Patient must be willing to undergo a new tumor biopsy at baseline, and again during therapy on this study.
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 patients enrolled on Phase 2 of study at UCSF, tumor biopsy is required in the subset of patients who have a metastatic lesion amenable to biopsy in the judgment of study investigator and Interventional Radiology
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
For Arm A, patients must have disease that is amenable to biopsy and must be willing to provide consent for a tumor biopsy at baseline (within 30 days of beginning ONC201) and at least 1 on-treatment tumor biopsy.
Mandatory biopsy is required during screening
Limited disturbance of tumor during biopsy.
Suitable for a new tumour biopsy.
Part B: subjects must have at least 1 lesion amenable to the mandatory fresh tumor biopsy at study entry and provide a biopsy suitable for the NGS required for this study.
Unwilling or unable to undergo research biopsy during the baseline (pre-surgical) clinic visit, or inadequate research biopsy obtained during the baseline (pre-surgical) clinic visit (determined by the gynecologic oncologist at the time of the subject’s pelvic exam)
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
Subject must appropriately be able to complete Screening assessments before beginning treatment for DLBCL, in the judgement of the Investigator. For subjects with bulky disease, B-symptoms, compressive disease, elevated bilirubin due to lymphoma, rapidly progressing adenopathies, or worsening performance status, pre-phase treatment with up to 100 mg/day prednisone, or equivalent, for a maximum of 10 days is permitted prior to beginning the treatment period, at the discretion of the Investigator. A washout period is not required, however, the Screening positron emission tomography (PET), CT, tumor biopsy (if needed), and bone marrow biopsy (if needed) should be completed before initiating corticosteroids.
Women with surgical breast biopsy(s) performed within 3 years or core biopsy(s) performed within 1 year prior to the screening mammogram.
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
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
Has ?1 distant, discrete non-injected lesion which is amenable to biopsy.
Available biopsy of primary tumor with adequate samples
Invasive features on colposcopy and the biopsy specimen
Patient must have a site of disease amenable to biopsy and be a candidate for tumor biopsy according to the treating institution's guidelines. Patient must be willing to undergo a new tumor biopsy at screening/ baseline or at molecular pre-screening if applicable, and during therapy on this study.
The participant’s primary tumor is accessible to biopsy in the outpatient clinic setting and the participant is willing to have baseline and end of study (day 15-26) 4 mm punch biopsies of tumor and adjacent visually normal appearing tissue for biomarker analysis\r\n* If the participant has a biopsy-confirmed cancer, the baseline biopsy to collect tissue for biomarker analysis will be in addition to the pre-study diagnostic biopsy\r\n* If the participant is having surgical treatment, the end of study biopsies may be collected at the time of surgery unless surgery is delayed beyond day 26\r\n* If the participant is not having surgical treatment, the end of study biopsies will be collected prior to initiation of non-surgical treatment
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.
Participant’s core biopsy slides suggest that later re-sectioning will not contain sufficient tumor to allow for an adequate evaluation of Ki67 and TUNEL assays, at a minimum
Participants enrolling to the HR or replicative stress cohorts during stage 1 must have disease that is amenable to biopsy and be willing to undergo a pre-treatment tumor biopsy.
Participants enrolling to the HR or replicative stress cohort during stage 1 may not be on anticoagulant therapy unless the treating investigator has deemed it safe to temporarily hold to facilitate the pre-treatment tumor biopsy.
Phase I: Patients with a site of disease amenable to biopsy, and willing to undergo a new tumor biopsy at screening, and during treatment.
Must have measurable disease by RECIST v1.1, a successful pre-treatment tumor biopsy, and be willing to undergo tumor biopsy during treatment
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
Patients in the Phase 1a dose escalation combination cohorts must have at least 1 tumour lesion amenable to biopsy and must be medically fit and willing to undergo a biopsy during screening and, unless clinically contraindicated, after 2 weeks on monotherapy.
A minimum of 10 patients with mCRPC, CRC and 'other' tumors will be required to have a site of disease that is safely accessible for biopsy (paired) upon enrollment. Accessible lesions are defined as those which are biopsiable (at screening) and amenable to repeat biopsy (after 2 weeks of monotherapy), unless clinically contraindicated. In the case that the second sample is not taken, the patient will remain in the study and there will be no penalty or loss of benefit to the patient and they will not be excluded from other aspects of the study. The tumor-specific cohorts will be closely monitored to ensure the desired number of biopsiable patients are enrolled. The requirement for biopsies must be made clear to each patient at the time of initial approach by the Investigator.
Presence of >= 1 tumor lesion not included as a RECIST 1.1 target lesion which is assessed by investigator and/or radiologist as likely to be amenable to percutaneous biopsy by punch, computed tomography (CT)-, or ultrasound-guided core needle biopsy for serial sampling on treatment
Neg pregnancy test Part A extension only: • Has a primary tumor or a metastatic site that is accessible for pre- and post-dose biopsy without subjecting patient to high level of risk Part B only:
Subjects are willing to undergo a biopsy to confirm lower GI aGVHD. Biopsy results are not needed to initiate treatment. However, if aGVHD is not confirmed histologically, treatment with F-652 will be discontinued.
Consent for a tumor biopsy at screening
All patients except cohort 6 must have at least one lesion deemed safe to biopsy and be willing to undergo a mandatory baseline biopsy; for cohort 5, the second biopsy at progression is mandatory for the responders (PR/CR/stable disease [SD]) >= 4 months
Patient must agree, as part of the informed consent, to provide blood and archived tumor samples for molecular correlates, pharmacokinetics and pharmacodynamics; patients in the expansion cohort A must have tumor sites that are accessible for tumor biopsy and must agree to undergo a pre-treatment and post-treatment biopsy; patients in cohort B group 3 and 4 must have tumor sites that are accessible for tumor biopsy and must agree to undergo a pre-treatment and post-treatment biopsy; this requirement may be waived after discussion with the principal investigator as long as a minimum of 5 patients in cohort B group 3 and 10 patients in cohort B group 4 are able to undergo the required biopsies
COHORT A: Patients must have accessible tumor sites for biopsy and must agree to pre-treatment and post-treatment biopsies
Patients enrolled at Dose Level 6 or higher in the phase I portion of the trial must have at least one tumor mass suitable and easily accessible for excisional biopsy, or alternatively, accessible for CT or ultrasound guided core needle biopsy. The procedure must be able to be performed with minimum morbidity.
Patients must have an accessible primary tumor or metastasis, and be willing to have a pre-treatment and post-treatment tumor biopsy (at 6 to 8 weeks after beginning)
Participants must be willing to undergo one mandatory on-study tumor biopsy following a 4 week, single cycle induction treatment of olaparib. A second on-study biopsy at time of disease progression is optional, but not mandatory.
Must have at least one tumor site accessible for a biopsy
Patients must agree to have a biopsy of metastatic tissue at baseline and on-treatment, 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 may undergo an additional biopsy attempt (at the same or a different site, determined by the investigator)\r\n* For patients with an intact primary and no metastatic site that can be safely biopsied, biopsy of the primary is acceptable, but must be approved by the principal investigator
Have at least 2 tumor lesions accessible for biopsy
For biopsy identified participants: be willing to undergo repeat biopsy of a tumor lesion before and after treatment; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may be exempted from this requirement after consultation with the principal investigator; note: enforcement of biopsy requirement may come into effect for all participants depending on the state of accrual compared with number of obtained biopsies at any point in the study
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)
All subjects must agree to pre-treatment tumor biopsy; 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
Hepatic metastases present which are amenable to biopsy
At least 1 lesion accessible for biopsy
STUDY ENTRY: Confirmation of diagnosis (by surgical excisional/incisional biopsy or imaging-guided core biopsy), and patients for whom the plan of management will include NACT followed by ICS. The decision to proceed with NACT will be at the treating physician’s discretion and include patients with advanced stage disease considered at low likelihood for optimal cytoreduction with primary debulking surgery.
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
Pathologic confirmation of respective malignancies; biopsy of metastatic disease is preferred but not mandatory
Biopsy with less than 20% of tumor removed
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)
At least 30 days from any major surgeries including brain biopsy and have complete resolution of its effects
Consent to participate in the correlative studies and should have available tumor tissue for tumor biopsies; acceptable biopsies include surgical biopsy, core biopsy or punch/surgical tumor biopsies (of accessible lesions)
Tumor accessible for biopsy
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.
At least 30 days from any major surgeries including brain biopsy and have complete resolution of its effects
Patients who have had a multiparametric MRI of the prostate performed and have undergone transrectal systematic biopsy plus biopsy of any volumes considered suspicious per the MRI (PIRADS version 2 score of 4 or 5) within 6 months before signing consent.
No features supporting an alternative diagnosis by transbronchial biopsy, bronchoalveolar lavage (BAL), surgical lung biopsy, culture and non-culture based data, if performed
Subjects must have disease that can be safely biopsied (for RP2D biopsy expansion cohort only), and agree to undergo a pretreatment and on-treatment biopsy.
Tolerated previous transrectal ultrasound guided biopsy procedure under local anesthetic\r\n* Uncomplicated previous transrectal ultrasound (TRUS) biopsy procedure (i.e., no prior hospitalization due to sepsis, prostatic abscess or severe hemorrhage following TRUS prostate biopsy)
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.
Core biopsy, including bone marrow biopsy within 2 days prior to study drug administration.
The subject has biopsy accessible tumor and is willing to undergo biopsy prior to planned protocol treatment
For biopsy identified patients: be willing to undergo repeat biopsy of a target lesion before treatment and after radiation; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may be exempted from this requirement after consultation with the principal investigator
Patients must agree to undergo two research biopsies of (a) malignant lesion(s); the investigator must also judge that the patient has tumor(s) safely accessible for biopsy; patients may be exempt from the second biopsy if after the performance of the first biopsy it is felt that a second biopsy would be unsafe for the patient; if the patient has only one Response Evaluation Criteria in Solid Tumors (RECIST) measurable target lesion for response assessment, research biopsies must not be performed on that target lesion
Patient willingness and disease accessible to pre-treatment, on-treatment tumor, and progression biopsies (core biopsies); a cell block from a pleural effusion may be substituted for a core biopsy; in select cases, patients may be allowed to enroll without a pre-treatment biopsy and/or continue treatment without an on-treatment biopsy (even if a pre-treatment biopsy is obtained) after speaking with the sponsor if performing the biopsy is technically challenging, poses significant risk to the patient, or may result in significant discomfort
Tumor deemed amenable to biopsy by core for metastatic site or endoscopic biopsy for primary tumor (for both before and on-treatment biopsies)
Pre-treatment biopsy must establish the diagnosis AND have enough remaining tissues to satisfy the mandatory research studies
Lymphoma that is amenable to safe pre-treatment and post-treatment biopsy; the safety of the procedures will be determined by the treating physician and the surgeon or other proceduralist, in consultation with the principal investigator (PI), and in accordance with standard clinical practice; acceptable sites of disease include, for example: (1) palpable tumor mass that is accessible under direct visualization or sonogram, (2) non-palpable tumor tissue that is accessible for biopsy under computed tomography (CT) or sonogram guidance, (3) bone marrow
Additional criteria for expansion cohorts: A) patients must have histologically-confirmed advanced or recurrent ovarian cancer with RPA or that had progression during prior PARP inhibitor treatment, endometrial cancer with RPA, or other solid tumor types with RPA; B) measurable and biopsy-accessible disease; C) patient must be willing to undergo biopsy procedure; D) prior treatment with PARP inhibitors is allowed
At least two sites of measurable disease as defined by Response Evaluation Criteria in Solid Tumors (RECIST) 1.1; one of which must be amenable to treatment with SAR and accessible for a mandatory pre-treatment biopsy and a post-treatment biopsy at physician discretion; if a pulmonary nodule is being considered for SAR it must range in size from 1-5 cm
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
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
However, if the treating physician and diagnostic radiologist strongly suspect PET positivity, the patient should not be enrolled even if the biopsy is negative (to exclude patients with false-negative biopsy)
Prior surgical therapy other than incisional/excisional biopsy or organ-sparing procedures such as debulking of airway-compromising tumors; residual measurable tumor is required for enrollment on study as outlined above
Patients with > 10% blasts on a day +14 bone marrow biopsy following 7+3 may either be enrolled or may be treated with a course of standard re-induction (e.g. 5+2 or similar) and then re-evaluated for response; eligible patients will meet any of the above criteria on a subsequent biopsy
Positive serum anti-poliovirus titer >= 1:8 prior to biopsy
Must be willing to undergo an incisional or excisional lymph node biopsy of accessible adenopathy or provide the most recent, available archived tumor biopsy.
Tumor blocks available from previous surgery/biopsy, or if not available, patients willing to have biopsy
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.
Biopsy is not required, though if biopsy of the retroperitoneal node(s) was obtained, pathology must be consistent with pure seminoma
Patient must have disease amenable to biopsy and must agree to have one baseline biopsy
Patient must provide a tumor biopsy as the time of progression on Arm B; if a patient does not have a tumor lesion amenable of biopsy or it has been unsafe for a biopsy to be performed, cross-over will be allowed
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
Stereotactic biopsy will not be allowed unless there is plans for second surgery to remove >= 80% of the tumor
Subject that underwent excisional biopsy of the primary tumor.
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
Hemoglobin >= 9 prior to biopsy
Positive serum anti-poliovirus titer prior to biopsy
Patient must consent to two mandatory biopsies and have tumor amenable to biopsy
Willing to undergo tumor biopsy at baseline and during treatment (during week 6 or 7); please note that tumor biopsy is not needed in subjects where the tumor is not accessible or if tumor biopsy is considered not in patient’s best interest
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
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
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
At least one lesion (metastasis or primary tumor) being considered accessible by non-high-risk collection procedures for biopsy.
Willing to provide tumor tissue amenable to ultrasound or computed tomography (CT)-guided biopsy for biomarker analyses\r\n* Patients with malignant ascites are permitted to participate and provide ascites samples for biomarker analyses\r\n* Patents receiving radiation to a single metastatic site in which only the primary tumor is accessible for biopsy by endoscopy will also be eligible
An image-guided biopsy (via Artemis Ultrasound with MRI co-registration) is encouraged but not required if not performed as standard of care biopsy
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
Tumor amenable to biopsy will be mandatory for this study
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
At least 1 lesion amenable for outpatient biopsies; 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
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
Paired tumor biopsy is mandatory for all subjects enrolled in the Expanded cohort; subjects should agree to and be eligible for paired tumor biopsy
Patients must have disease that is amenable to biopsy and be willing to provide the same; NOTE: Patients in whom a baseline biopsy is attempted, but is not successful, will still be considered eligible for the study; in addition, if the primary oncologist has a concern regarding the feasibility of a biopsy, it may be omitted after consulting with the protocol chair
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.
Dose Expansion Cohort Group 1 and 2: At least one tumor lesion amenable to repeat core needle biopsy or punch biopsy without unacceptable risk of a major procedural complication
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
For biopsy identified patients: be willing to undergo repeat biopsy of a tumor lesion before treatment and after radiation; subjects for whom newly-obtained samples cannot be provided (e.g. inaccessible or subject safety concern) may be exempted from this requirement after consultation with the principal investigator\r\n* Note: enforcement of biopsy requirement may come into effect for all patients depending on the state of accrual compared with number of obtained biopsies at any point in the study
Biopsy confirming metastatic breast cancer and retinoblastoma protein (Rb) positivity by immunohistochemistry prior to enrolling on this protocol is required; biopsy must be obtained immediately before study enrollment; no intervening treatments are allowed
If an accessible lesion is present, a biopsy will be performed within 6 weeks of the start of study intervention; the results of the biopsy must be obtained prior to initiation of study intervention
Patients acceptance to have a tumor biopsy
The presence of metastatic disease amenable to computed tomography (CT) or ultrasound guided biopsy; this may include thoracolumbar vertebral bodies, pelvis, femur or humerus or soft tissue or nodal metastasis amenable to biopsy (excluding lung or pleural lesions)
Patients with documented HER2-positive metastatic disease based on most recent biopsy
At least 2 anatomically distinct lesions accessible for biopsy.
Ability to have a skin and tumor biopsy from any site; patients without accessible tumor for biopsy will be considered on a case by case basis\r\n* Patients who cannot be biopsied will not be replaced (although up to 5 ineligible/inevaluable patients can be replaced)\r\n* Patients without accessible tumor for biopsy must provide archived tumor from the most recent biopsy available
Consent to provide archived tumor biopsy material (all patients)
Patients who had excisional biopsy for diagnosis of their cancer (i.e., instead of a core biopsy)
Must be able to provide biopsy specimens obtained ?3 months for biomarker analysis. If bone marrow biopsy was performed 3 months before screening but subject had anti-cancer treatment after biopsy, the bone marrow biopsy and aspiration should be repeated CLL Participants:
Tumor that is accessible for mandatory biopsy
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
The subject must agree to undergo the pre- and post-treatment research biopsies if a non-osseous metastatic site is available for biopsy; the pre-treatment biopsy will be standard of care, and used for diagnostic purposes to assess ER/ progesterone receptor (PgR) / HER2 status and confirm the presence of breast tumor cells; the post-treatment (day 11) biopsy will be performed for research purposes; both the pre- and post-treatment biopsies will be assessed on-site by a pathologist by touch-prep to ensure that the biopsied tissue contains tumor cells
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
Tumor blocks available from previous surgery/biopsy, or if not available, patients willing to have biopsy
Patients in the dose expansion part must have tumor that is amenable for biopsy
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
Patients must agree to undergo two separate biopsies of a malignant lesion; biopsies do not need to be done if one of the following apply:\r\n* If either the site 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 (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 after discussion with the MSK principal investigator)\r\n* The goal will be to have a minimum of 6 patients from Cohort A and 3 patients from Cohort B attempt to have one or both of these research biopsies done (for a total of 9 patients total); accrual may be limited only to subjects for whom tumor is accessible for biopsy and attempt at biopsy is considered safe if continued enrollment of those who are not candidates for biopsy make it impossible to reach the accrual goals for research biopsies described above (e.g., if 19 [of 25] patients are accrued to Cohort A without any biopsies having been obtained within the cohort, then all further subjects who are registered to that cohort must qualify for attempted research biopsy in order to be enrolled into the study [i.e., subjects who would have been excluded from having biopsies done due to the above reasons would be excluded from participating in the study; these conditions also apply to Cohort B])
Patient amenable to liver tumor biopsy
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
Subjects meeting the American Association for the Study of Liver Disease (AASLD) criteria may be randomized without a biopsy, but will undergo a biopsy during the RFA procedure unless contraindicated or unattainable.
If prior standard-of-care pre-treatment biopsy is inadequate for analysis by immunohistochemistry, and the patient is unwilling to undergo an additional biopsy procedure
Prior treatment (e.g., open surgical biopsy, lumpectomy) of index cancer
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
Patients must agree to have a biopsy at baseline and on treatment
Pre-SBRT prostate volume > 120 cc as estimated by trans-rectal ultrasound at time of prostate biopsy (TRUS biopsy)
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
Patients whose tumor is not accessible for a core biopsy
Phase II cohorts only: Patients must have a site of disease amenable to biopsy, and be a candidate for tumor biopsy according to the treating institution's guidelines. Phase Ib patients need not have disease accessible to biopsy
Histologic confirmation of cancer will be required by biopsy, prior surgery, and re-biopsy at the discretion of the treating physician
Must be willing to provide a tumor biopsy specimen 9 weeks after the start of treatment for exploratory analyses, if considered safe by the Investigator.
Core biopsy, including bone marrow biopsy, within 2 days prior to study drug administration
Consent to undergo on treatment biopsy if tumor is accessible and safe to biopsy
Baseline tumor biopsy must be adequate
Patients must have measurable metastatic disease amenable to biopsy; patients who decline to undergo a biopsy for this trial will be ineligible
Treatment with any of the following medications within 4 weeks before the baseline diagnostic biopsy is taken:
Consent to tumor biopsy from accessible tissue (optional in part 1, mandatory in part 2)
All patients must have tumor specimens adequate for analysis of EGFR mutations and have tumor accessible to biopsy and must consent to biopsy.
DCIS diagnosed with core biopsy
At least one lesion (metastasis or primary tumor) being considered accessible for a biopsy
Patients must have at least ONE of the following: 1) Recurrent/progressive disease at any time (biopsy not required, even if partial response to intervening therapy); 2) Refractory disease (i.e., less than a partial response to frontline therapy, including a minimum of 4 cycles of chemotherapy) (no biopsy is required for eligibility for this study); 3) Persistent disease after at least a partial response to frontline therapy (i.e., patient has had at least a partial response to frontline therapy but still has residual disease by MIBG scan, CT/MRI, or bone marrow) (patients in this category are REQUIRED to have a biopsy [bone marrow biopsy included] of at least one residual site demonstrating viable neuroblastoma)
RENAL COHORT: Patients with an outside biopsy within 12 months is allowed for entry requirements; during the screening phase, patients without a tissue diagnosis may undergo a renal biopsy for histologic confirmation on PA13-0291
All patients must consent to pre-treatment biopsy of the tumor if it can be done safely (as judged by the investigator) during screening. Week 10 on-treatment biopsies will be required for a minimum 10 patients. After 10 paired biopsies have been obtained then week 10 on-treatment biopsy will be made optional.
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
Patients must have biopsiable tumor and agree to study biopsy
The patient must have measurable disease according to RECIST v1.1 and must have one site amenable to biopsy that, in the opinion of the investigator and/or interventional radiologist, is likely to yield acceptable tumor sample for a core biopsy per the below pathology criteria
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.
For the expansion patients must provide a fresh tumor biopsy at enrolment
Phase 2 only: Willing to consent to 1 mandatory pre-treatment and 1 on-treatment tumor biopsy
Must have two biopsy accessible lesions:
Patient must agree to provide fresh biopsy specimens and peripheral blood samples at the time of screening and during the study
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
TREATMENT: Patient must have predefined targeted mutation in tumor biopsy
Patients must have tumors determined to be easily accessible for biopsy and must be willing to have serial biopsies (with a third biopsy upon evidence of disease progression); tumor biopsies will be performed on the most accessible biopsable site of disease; all possible precautions to avoid complications will be taken, including discussions in multidisciplinary meetings, if needed; patients affected by glioma will not be considered for study biopsies
If no adequate archival tumor biopsy is available, patients must undergo a new biopsy
For enrollment in the first stage of Cohort B, patients must have accessible pre-treatment and post-treatment (4-6 weeks) tumor for biopsy
Inability to test core biopsy for study markers
For lymphoblastic lymphoma: diagnosis may be made by i) biopsy of involved site (e.g., node, mediastinal mass), or ii) by cytology from pleural fluid or other fluid collection or iii) by marrow aspirate/biopsy demonstrating < 30% involvement by lymphoblasts (confirmed by flow cytometry, immunohistochemistry, cytogenetics and/or FISH studies) in a patient with evidence of lymphomatous masses by radiographic studies; note: marrow aspirate and/or biopsy must be performed in patients with lymphoblastic lymphoma prior to study entry to confirm that patient does not meet definition of ALL; in rare circumstances, lymphoblastic lymphoma patients may be registered prior to marrow aspirate/biopsy if it is felt that the procedure cannot be safely performed; permission in advance by principal investigator or designee is required
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
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 primary investigator (PI) before start of protocol therapy; only patients who have biopsy inaccessible disease may enter the study without the requirement for baseline biopsy
Cohort II (MTD): willing to provide the biologic specimens as required by the protocol; note: this is part of the mandatory translational research component; note: patients with the only tumor accessible for biopsy in the pancreas will not be eligible as core biopsies are associated with significant increase in risk for the patient
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
Biopsy accessible tumor deposits
Transrectal ultrasound-guided biopsy with >= 10 systematic biopsy cores and >= 2 MRI-ultrasound fusion targeted biopsy cores from above MRI-derived ROI\r\n* Histologically-confirmed adenocarcinoma from targeted biopsy cores \r\n* Overall Gleason score not to exceed 3 + 4
Pre-enrollment biopsy parameters (as per H.L. Moffitt C.C. review)\r\n* Minimum of 10 biopsy cores\r\n* Gleason score 6 or 7\r\n* Unilateral cancer (only right-sided or left-sided, not bilateral)
COHORT EXPANSION PHASE: At least one tumor lesion amenable to core needle biopsy without unacceptable risk of a major procedural complication (one pretreatment and at least one on-treatment biopsy will be performed)
Osteosarcoma, neuroblastoma and melanoma that have been treated with standard frontline therapy and are judged to be incurable with standard therapy, based upon the fact that they are unresectable, metastatic, progressive/persistent or recurrent; evaluable disease must be present\r\n* For all histologies except osteosarcoma and neuroblastoma, pathologic review of frozen tissue must document GD2+ expression; positive expression is defined as at least 2+ expression (0-4+ scale) in > 50% of the tumor cells using anti-GD2 monoclonal antibody (mAb) 14G2a; if adequate archived frozen tissue is available, this may be utilized, or if not, patients may undergo biopsy following enrollment to obtain tissue to assess GD2 expression, with the following restrictions\r\n* Patients with histologies other than osteosarcoma or neuroblastoma must have adequate accessible tumor for biopsy (at least 1 cm diameter)\r\n* Procedures employed to acquire biopsies for tumor lysates will be limited to percutaneous needle or core biopsies, thoracoscopic excision or open biopsies of readily accessible lesions; pulmonary lesions may be biopsied but extensive surgery such as thoracotomy or laparotomy should not be employed\r\n* Patients who will require biopsy should not be enrolled if in the opinion of the principal investigator, the tumor site places the patient at substantial risk from the biopsy procedure
Pre-surgery tumor deemed amenable to core biopsy (with at least 100 mm^3 tumor volume per biopsy)
Patients must be willing and able to undergo a pre-surgery biopsy and wait 2 weeks before their debulking surgery; NOTE: consented patients with subsequent inadequate biopsy material will not receive INCB024360 or be analyzed and will be replaced; the study will be stopped if adequate tissue is not obtained in more than 2/3 of paired samples with a maximum accrual of 18 patients
Patient must agree to allow 3 separate biopsies of any malignant lesion; biopsies do not need to be done if:\r\n* Tumor is not considered accessible by either the investigator or the person performing the biopsy (it is determined the risk is too high due to location near vital organs or too great of a risk of an adverse event)\r\n* Patient is on anticoagulation and it would be unsafe to temporarily hold the anticoagulation\r\n* Consent of the principal investigator (PI) not to have a biopsy done\r\n* A minimum of 8 subjects must participate in the biopsy part of the study
Presence of appropriate size and site of viable tumor tissue for safe tumor biopsy collection (the biopsy is optional and requirement is only applicable to subjects considered for the expansion cohort stage of the study)
Pathologic confirmation of DCIS of the female breast without invasive cancer, with diagnosis rendered on core biopsy only, completed within 60 days before registration; patients diagnosed with DCIS on the basis of surgical biopsy are not eligible for this study\r\n* Patients with microinvasion on diagnostic core biopsy, defined as tumor =< 1mm in greatest dimension, will be allowed to participate\r\n* All patients must have a clip placed, either at the time of the diagnostic biopsy or at the time of the baseline MRI prior to the start of treatment
Endoscopy with biopsy
Diagnosis of liver confined hepatocellular carcinoma (HCC) confirmed by histology or American Association for the Study of Liver Diseases (AASLD) guidelines\r\n* Lesions < 1 cm in diameter have a low likelihood of being malignant and should be followed; lack of growth over 1-2 years suggests it is not HCC\r\n* Alpha-fetoprotein (AFP) > 200 and radiological evidence (arterial hypervascularity) of lesion > 2 cm does not require biopsy\r\n* Two imaging modalities (triphasic computed tomography [CT], MRI, ultrasound, angiography) demonstrating “arterial hypervascularity” in the background of cirrhosis does not require biopsy\r\n* One imaging modality with a lesion with arterial hypervascularity with wash out in early or delayed venous phase, does not require a biopsy\r\n* Atypical appearances on imaging requires a biopsy\r\n* Non-conclusive biopsy requires closer monitoring \r\n* For non-cirrhotics (by biopsy or imaging findings), diagnosis of HCC requires biopsy
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
Tumors that are amenable to serial biopsy
Fresh baseline tumor biopsies (defined as a biopsy specimen taken since completion of the most recent prior chemotherapy regimen) are required for all cohorts except glioblastoma
Biopsy confirmation of GVHD is not required. Enrollment should not be delayed for biopsy or pathology results unless local institutional practice mandates biopsy confirmation to make a GVHD treatment decision.
Provide a baseline tumor biopsy
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
For certain subjects, willing and able to provide pre-treatment and on-treatment fresh tumor biopsy
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
Tumor accessible for biopsy
Biopsy-confirmed adenocarcinoma of the prostate. Biopsy (minimum 10 cores) obtained ? 6 weeks and ? 6 months before treatment, or at the discretion of PI.
The subject is willing to undergo tumor biopsy during the Screening period, or if the tumor is inaccessible for biopsy, archived tumor material must be available for submission;
Willing and able to provide pre-treatment and on-treatment fresh tumor biopsy
Patients must have disease amenable to biopsy and must be willing to undergo a paired biopsy for correlative analyses (the first biopsy within 28 days prior to start of treatment and the second biopsy while on treatment)
All subjects in Cohort 3 or Phase 2 dose (P2D) must have a lesion accessible for FNA or core or open biopsy on day 8 of the first treatment cycle.
A tumor accessible for biopsies and consent to undergo tumor biopsies before and during MSC2363318A treatment. Subjects who do not have a tumor suitable for biopsy (such as, but not limited to, high procedural risk, inaccessible site for needle biopsy, etc.) but are otherwise eligible for this study may be considered for enrollment on a case-by-case basis after discussion with the Medical Monitor of the study
Patient has disease amenable to biopsy and is agreeable to undergo a biopsy; NOTE: under unusual circumstances, submission of ascites material may be acceptable if a biopsy is not possible; this exception will require approval by one of the study principal investigators
Subjects must be willing to undergo an incisional or excisional lymph node biopsy of accessible adenopathy or provide the most recent, available archived tumor biopsy.
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
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
Diagnostic stereotactic biopsy: Patients diagnosed with DIPG may choose to have a stereotactic biopsy prior to starting radiation therapy.
A pre-treatment tumor biopsy demonstrating high TAM content as assessed per the central laboratory
Consent to paired tumor biopsy, for accessible tumors
Current treatment with warfarin; for patients not on an anti-platelet agent such as aspirin, other anticoagulation is acceptable so long as the treating physician feels that it is safe to hold it on the day of the biopsy until after the biopsy has been safely completed
Biopsy of a metastatic lesion is not required for protocol entry but all patients with reasonably accessible lesions (chest wall, breast, skin, subcutaneous, superficial lymph nodes, bones and liver metastases) must agree to biopsy (lung and brain metastasis will not be biopsied):\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 with reasonably accessible lesions as described above, who will not agree with the biopsy, will not be enrolled in the trial\r\n* Patients with NO reasonably accessible lesions as described above can be enrolled in the trial
Agree to have prostate biopsy blocks provided to the study for evaluation
At least 1 lesion amenable for outpatient biopsies; 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
At least 1 lesion amenable for outpatient biopsies; this should be a cutaneous or palpable metastatic site or 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
Patients enrolled in the expansion stages must agree to a tumor biopsy to be obtained during the screening period and during Cycle 2 or at the time of PD, if earlier. If a biopsy is deemed by the investigator to not be in the patient's best interest, prior approval must be obtained from the Medical Monitor to waive this requirement.
Patient must have a site of disease for biopsy, and be a candidate for tumor biopsy according to the institution's guidelines. Patient must be willing to undergo a new tumor biopsy at screening, and again during therapy on this study.
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.
Patients must agree to pretreatment tumor biopsy
Willing to attempt a baseline tumor biopsy procedure
Any patient that has had a biopsy only or less than 25% of their tumor removed
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
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.
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
Patient must have histologically or cytologically confirmed intrahepatic cholangiocarcinoma, extrahepatic cholangiocarcinoma, or gallbladder cancer or may undergo a repeat biopsy for histologic confirmation if pre-existing biopsy is not sufficient for diagnosis
Patients must have a primary invasive cutaneous melanoma of Breslow thickness greater than 1 millimetre as determined by diagnostic biopsy (narrow excision, incision or punch biopsy) and subsequent histopathological analysis.
Patient has disease amenable to biopsy and is agreeable to undergo a biopsy; note: under unusual circumstances, submission of ascites material may be acceptable if a biopsy is not possible; this will require approval by one of the study principal investigators
Must have 3 core biopsies involved with cancer (a minimum of 6 core biopsies must be obtained); prostate biopsy must be within seven months from screening; this includes prostate biopsy from men previously followed by active surveillance; less than 3 core biopsies is allowed if the patient has > 1 cm or T3 disease on magnetic resonance imaging (MRI)
FOR EXPANSION PHASE ONLY: Lack of accessible tumor for biopsy
The patient has biopsy-accessible tumor; for patients who had no prior anticancer therapy and had surgical resection within a year and tumor tissue is immediately available, that tumor will be analyzed and no biopsy will be needed
Patients must agree to undergo two research biopsies of a malignant lesion; 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; the goal will be to have a minimum of 3 patients undergo one or both of these research biopsies; accrual may be limited only to subjects whose tumor is safely accessible for biopsy to ensure the accrual goal for research biopsies described above is met (e.g., if 7 of 10 patients are accrued without any biopsies having been obtained, then all subsequent subjects who are registered must qualify for attempted research biopsy in order to be enrolled)
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
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
Patient should agree to a tumor biopsy prior to protocol enrollment; post therapy biopsy is optional
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
Patients must have histologically proven stage IIIB, IV or recurrent non-small cell lung cancer; patients must be willing to undergo a pre-treatment tumor biopsy, either core needle biopsy or equivalent amount or via excisional specimen (cytology specimen not acceptable for this purpose)
Patients must have disease amenable to biopsy at the time of enrollment as biopsies are required for study participation
All patients with disease technically amenable to biopsy will be asked to undergo a biopsy; patient must agree to allow 2 biopsies of any malignant lesion that can be accessed by endoscopy or with the aid or radiology (i.e. CT guided)
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
Histological or cytological documentation of solid tumors for whom single agent irinotecan is recommended; biopsy of primary tumor alone is adequate if the patient has clear evidence of metastatic disease and/or elevated carcinoembryonic antigen (CEA) and the treating physician does not feel biopsy of metastatic disease is clinically warranted
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
Histological documentation of adenocarcinoma of the prostate, with available biopsy pathology; biopsy material must be available for pathologic review
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
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
Pre-treatment fresh core, excision or punch tumor biopsy
Disease location amenable to biopsy in outpatient clinical setting or operative biopsy within routine accepted schedule and practice of clinical care
Patients must be willing to consent to tumor biopsy for research purposes
Participants are not required to have measurable disease but must have an accessible tumor to biopsy
Patients who have already undergone excisional biopsy for qualifying DCIS
Biopsy confirmed malignancy of the gynecologic tract
Disease amenable to core biopsy; patients with pulmonary metastases as their only site of disease may enroll on this trial and will not undergo biopsy
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
Incomplete definitive surgical orchiectomy, including diagnostic biopsy alone
Biopsy accessible tumor deposits
Positive serum anti-poliovirus titer prior to biopsy (except for retreatment)
Hemoglobin >= 9 prior to biopsy
Duodenal cancer on biopsy.
Consent to biopsy of tumor
Interval >= 4 weeks between open brain biopsy and initiation of protocol-based therapy
Biopsy-proven relapsed or refractory non-Hodgkin lymphoma requiring treatment, who have failed, unable to tolerate, or refused other available active therapies; patients should not have other treatment options considered curative (NOTE: for patients with lymphoma without central nervous system [CNS] involvement, a re-biopsy is necessary unless the patient has had a previous biopsy =< 6 months prior to treatment on this protocol if there has been no intervening treatment; patients with biopsy-proven CNS lymphoma at any time are not required to have a re-biopsy to be eligible for this study); NOTE: relapsed NHL is defined as NHL that relapses after at least one prior therapy and does not have available curative therapy; refractory NHL is defined as NHL that has progressed or not responded to most recent therapy and has had at least one prior therapy and have no available curative therapies
The subject has biopsy accessible tumor and is willing to undergo biopsy prior to planned protocol treatment
Patients must have an intact primary (not recurrent) invasive carcinoma of the breast; biopsy confirmation of the primary tumor should be by needle biopsy (preferred); incisional surgical biopsy is allowed as long as there is residual palpable or imageable tumor in the breast
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
Patient must agree to allow 2 separate biopsies of any malignant lesion; biopsies do not need to be done if:\r\n* Tumor is not considered accessible by either the investigator or the person performing the biopsy (it is determined the risk is too high due to location near vital organs or too great of a risk of an adverse event)\r\n* Patient is on anticoagulation and it would be unsafe to temporarily hold the anticoagulation\r\n* Consent of the principal investigator (PI) not to have a biopsy done
(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
MRI and chest x-ray within 6 weeks prior to pre-registration; a postoperative MRI is required for all patients who underwent open biopsy, or resection, but is not mandatory following stereotactic biopsy
Patient must be at least two weeks post any brain surgery (whether stereotactic biopsy, open biopsy or resection) at the time of randomization
Willing to undergo or must have had a lower GI biopsy within 7 days of informed consent to confirm GI GvHD. Biopsy results are not needed to initiate treatment; however, if biopsy results are not consistent with aGvHD, treatment with GLASSIA will be discontinued.
For Phase 2, has archived or fresh tumor biopsy samples (obtained during screening) sufficient for genotyping.
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.
Tumor specimens must be available for immunological studies either from a previous biopsy or a new biopsy obtained before the initiation of the study
Willingness to provide consent for biopsy samples
Biopsy-confirmed histopathological diagnosis of FL. Biopsy specimen should be obtained ?2 years prior to randomization, unless medically contraindicated
Patients must have disease amenable to biopsy and must be medically fit to undergo a biopsy
Men with metastatic castration-resistant prostate cancer (mCRPC), with accessible metastatic soft-tissue lesions for tumor biopsy
>= 3 positive cores within diagnostic biopsy specimens
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
Subjects must have at least one tumor lesion that is suitable for repeat biopsy, and must agree to two tumor biopsies (pre- and post- treatment).
Disease amenable to biopsy and agree to undergo biopsy for molecular analysis
If an open biopsy is performed, the patient must be at least one week post biopsy; this requirement does not apply to patients who undergo stereotactic biopsies
Has a core or excisional baseline tumor biopsy specimen available or willingness to undergo a pre study treatment tumor biopsy to obtain the specimen.
The subject has a tumor suitable for biopsy and is willing to undergo tumor biopsy, preferably of the primary tumor, within 28 days prior to Cycle 1/Visit Day 1;
At least 25% of cells >= 1+ for FRa staining based on diagnostic (i.e., prior to NAC) tumor biopsy
Ability to comply with the collection of tumor biopsies; tumors accessible for biopsy
Biopsy accessible tumor deposits
At least one tumor amenable to excisional, core or forceps (transbronchial) biopsy; patients must be willing to undergo tumor biopsies before starting therapy and after the third (3rd) CDX-1401 injection; additionally, the first 12 patients enrolled must consent to a third tumor biopsy to be performed after the 3rd MPDL3280A infusion
Patient must have a biopsy-accessible tumor to be radiated
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
Patients must have tumor accessible by interventional radiology or surgical intervention and suitable for biopsy with 5-6 passes of a 16 or 18 gauge needle for core biopsy (defined as at least 1 cm^3 tumor/50 mg accessible for biopsy), and must agree to undergo up to two surgical resections/biopsies to collect tumor for research purposes; the first of these biopsies will occur at the beginning of the study, prior to genetic analysis and treatment; the second biopsy will be performed at the time of disease progression/end of study should funding be available
Accessible tumor for biopsy and willingness to provide pre-dose tumor biopsies on Days 1 and Day 15.
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 × 0.1 cm in size or contain at least 50 tumor cells.
Excisional biopsy
Arm 2 only: At least 1 tumor that is amenable to biopsy, as determined by the investigator, and participant must be willing to undergo a biopsy prior to and at least once following anti-macrophage migration inhibitory factor (anti-MIF) antibody treatment
Patients must allow biopsy at the time of fiducial placement
Adequate diagnostic prostate core biopsy specimen for pharmacodynamics evaluation (tissue block, or at least 15 unstained sections), or willingness to consent to and undergo a pretreatment ultrasound-guided biopsy of the prostate
Willingness to consent to research biopsy
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.
The presence of metastatic disease amenable to computed tomography (CT) or ultrasound guided biopsy; this may include thoracolumbar vertebral bodies, pelvis, femur or humerus, or soft tissue or nodal metastasis amenable to biopsy (excluding lung or pleural lesions)
Biopsy accessible tumor (may be waived under certain circumstances)
Willing to take drug during the 2-12 weeks between biopsy and surgical removal of BCC
HER2 0 or 3+ by IHC on pre-treatment biopsy of metastatic lesion (if performed)
No prior treatment (patients on \watch and wait\ may enter the study if a recent biopsy [obtained within the last 6 months] is available)
Skin biopsy specimen of representative lesion obtained at screening of study and deemed diagnostic of mycosis fungoides by principal investigator
Patients must have biopsy accessible disease and must be willing and able to undergo a biopsy
Phase II: The initial 20 patients must have evaluable baseline tumor samples; evaluable samples are defined as those obtained by core biopsy or surgical resection and amendable to histological analysis; samples obtained by fine needle aspiration biopsy are not considered evaluable; patients who do not have evaluable archival tumor samples must consent to a tumor core biopsy prior to starting study treatment and, patients who consent to the baseline tumor biopsy will be eligible to receive study treatment irrespective of whether the samples obtained are evaluable
The biopsy confirming diagnosis can be up to 12 weeks prior to registration as long as there is no intervening therapy; note: if patient has had lymphoma treatment since previous biopsy, a biopsy should be repeated
Has ?20% of cancer in any biopsy core,
Has ? 7 mm of cancer in any biopsy core,
Has ? 33% positive biopsy cores
Woman histologically diagnosed by an open biopsy procedure
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
Must have 3 core biopsies involved with cancer; prostate biopsy must be within seven months from screening; less than 3 core biopsies is allowed if the patient has > 1 cm or T3 disease on MRI
Must have a site of disease amenable to biopsy, and be a candidate for tumor biopsy according to the treating institution's guidelines. Patient must be willing to undergo a new tumor biopsy at screening
All subjects must have a fresh tumor biopsy
Agree to undergo a pre-treatment and on treatment biopsy and have disease amenable to biopsy required in PK/pharmacodynamic dose expansion cohorts.
Must have a site of disease amenable to biopsy, and be a candidate for tumor biopsy according to the treating institution's guidelines. Patient must be willing to undergo a new tumor biopsy at screening/baseline, and during therapy on the study.
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
If an open biopsy is performed, the patient must be at least one week post biopsy; this requirement does not apply to patients who undergo stereotactic biopsies
Patients with suspected but no biopsy confirmed BE
Recommendation for biopsy will result from an imaging work-up originating with a screening exam (mammogram, tomosynthesis, ultrasound, or MRI) that was within 3 months of biopsy
Imaging sets in which a biopsy was recommended, but biopsy was not performed and 2-year imaging follow-up is not available
Women who have a core biopsy or excisional biopsy containing invasive cancer
Biopsy-proven (consisting of >= 10 tissue cores) adenocarcinoma of the prostate with cancer present in at least one biopsy core, either random or targeted, in the most recent biopsy\r\n* All prior biopsies must meet the following: =< 50% of the total number of random biopsy cores positive for cancer\r\n* Gleason score =< (3+4)
No planned prostate biopsies during the intervention until after the post-intervention biopsy
Histologically confirmed, positive HSIL of CIN2+ or higher (only CIN2+/3 subjects will be selected) cervical biopsy, confirmed by external (independent) pathologist panel within the 12 weeks prior to enrollment. If the standard care biopsy is not available for evaluation by the independent pathologist, a fresh biopsy and endocervical curettage will be required. The extent of colposcopic HSIL disease should not involve more than two quadrants of the cervix. Biopsies should be taken from each affected quadrant
Absence of urothelial carcinoma involving the upper urinary tract (documented by radiological imaging or biopsy) preferably within 12 months from the start of treatment; should the imaging or biopsy be performed outside this window it will be up to the physician's discretion to re-scan/biopsy
The presence of atypical ductal hyperplasia (ADH) on core biopsy
Inability to obtain a biopsy of the tumor as deemed by the study interventional radiologist
Subjects may be enrolled at one of three time points in the clinical course of disease:\r\n* Study 1 (New Diagnosis): \r\n** Pediatric patients with newly diagnosed primary central nervous system tumors undergoing surgical resection/biopsy within 21 days or who, within the prior 21 days, have undergone resection/biopsy with substantial residual (greater than half as assessed by the surgeon) tumor\r\n* Study 2 (Possible Tumor Recurrence): \r\n** Pediatric patients with a history of treated primary central nervous system tumor, in whom standard imaging has raised concern for tumor recurrence; tumor tissue for histological analysis must be available from a biopsy/resection planned within the next 21 days or from a prior resection/biopsy if no current biopsy material is available\r\n* Study 3 (Response to Therapy): \r\n** Pediatric patients with a primary central nervous system tumor who will be starting a new regimen (standard or experimental) of chemotherapy within 21 days, have not received radiation therapy during the past six months, and who will not be receiving radiation therapy during the first two cycles of chemotherapy
Tumor site amenable to MRI guided biopsy as determined by the radiologist
Scheduled to undergo a thyroid biopsy, thyroidectomy, or cervical node biopsy
Patients who have biopsy confirmed multi-centric disease
For patients who undergo optional metastatic tumor biopsy following completion of gallium citrate PET:\r\n* Presence of one or more metastases by standard radiographic scans including cross-sectional imaging of the chest/abdomen/pelvis and whole body bone scan that is safely accessible to tumor biopsy in the judgment of treating clinician and/or interventional radiology\r\n* No history of radiation therapy to the target metastatic lesion selected for tumor biopsy\r\n* No contra-indication to biopsy including uncontrolled bleeding diathesis\r\n* Platelets > 75,000/ul\r\n* Prothrombin time (PT) or international normalized ratio (INR) and a partial thromboplastin time (PTT) =< 1.5 times the institutional upper limit of normal (ULN) within 14 days prior to biopsy
Patients who have biopsy confirmed multi-centric disease
Patients with peripheral lung lesions 1-5 cm in size identified on chest CT with the intention to undergo bronchoscopic evaluation and biopsy; the decision to pursue biopsy will be made by the treating physician and agreed upon by the patient
Patients will be asked to consent to 2 to 3 extra biopsy samples to be used for this research project
SUB-STUDY I: Prostate biopsy histology grade >= Gleason 6, positive biopsy > 2 cores
SUB-STUDY I: At least 7 days after most recent prostate biopsy
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
Biopsy or resection of the primary tumor within 14 days the first injection of [18F]F-AraG
For patients undergoing optional tumor biopsy:\r\n* No history of bleeding diathesis\r\n* Patients on anti-coagulation they must be able to safely stop treatment for purposes of tumor biopsy
Biopsy-proven adenocarcinoma of the prostate; biopsy may be performed outside of University of California San Francisco (UCSF), if detailed results of sextant biopsy are available; a minimum of 20 patients out of a planned enrollment of 50 patients must have high-risk disease as defined by primary Gleason score of 4 or 5 on prior prostate biopsy
Pre-enrollment prostate biopsy must consist of at least 8 cores
Biopsy reviewed by a University of Miami pathologist
Requirement for medications, which interfere with platelet function, such as aspirin, which cannot be stopped within 1 week prior to the biopsy (applicable only to patients undergoing biopsy)
Patients must have high-risk neuroblastoma with at least ONE of the following:\r\n* Recurrent/progressive disease at any time; biopsy is not required, even if there is a partial response to intervening therapy\r\n* Refractory disease (i.e. less than a partial response to frontline therapy, including a minimum of 4 cycles of chemotherapy); no biopsy is required for eligibility for this study
An interval of > 6 weeks between the biopsy and MRSI
Prostate biopsy-naive or a single negative biopsy
Have received recommendation for and are scheduled for an ultrasound guided FNAB, ultrasound guided core biopsy, excisional biopsy, lobectomy or complete thyroidectomy of at least one thyroid nodule.
Abnormal uptake in prostate necessitating biopsy
Less than 2 months since any prior prostate biopsy (to decrease false positive uptake from inflammation)
No evidence on biopsy of extracapsular extension
Prostate biopsy within 6 weeks (unless biopsy is planned from extraprostatic tissue)
PRE-ENROLLMENT BIOPSY PARAMETERS: minimum of 12 biopsy cores
FINAL ENROLLMENT BIOPSY PARAMETERS: 12 standard biopsy cores plus targeted regions based upon MRI
Participants must be women who have histological confirmation of metastatic invasive breast cancer that has metastasized outside the region of the primary tumor and axilla; biopsy must be obtained prior to initiation of chemotherapy; it should be performed within 28 days prior to enrollment (patients with a biopsy of recurrent disease that is HER2-positive and have not received HER2-directed therapy since the biopsy can exceed the 28-day window up to 6 months); patients must have metastatic disease in lung, liver, soft-tissue or bone to qualify for the study (more than one site is permissible)
Planned procedures or therapies in between SOC scans and study scan on s-DCT, e.g., biopsy or excision of lung lesion
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
The first 15 patients with adenocarcinoma will be offered an optional tumor biopsy (typically EGD biopsy) at 8 weeks; starting with adenocarcinoma patient #16, patients must have an accessible tumor and must agree to tumor biopsy at 8 weeks; this will continue to be mandatory until a total of 20 patients have undergone biopsy at 8 weeks
Patients with peripheral lung lesions 1-7 cm in size identified on chest CT with the intention to undergo bronchoscopic evaluation and biopsy; the decision to pursue biopsy will be made by the treating physician and agreed upon by the patient
Received a prostate biopsy procedure within 30 days before admission into the study
Have had stereotactic or ultrasound-guided biopsy with marker placement
Men who have elected to proceed with a diagnostic prostate biopsy
A superficial tumor easily and safely accessible for a research biopsy or are being considered for resection or biopsy of their tumor as part of standard of care and have recent pathology
Patients with lesions safely accessible for protocol driven biopsy
Tumor accessible to biopsy
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)
All male patients (all ages) scheduled for standard prostate needle biopsy (first, repeat or active surveillance biopsy) under local anesthesia will be eligible for the study.
The patient must have one negative cystoscopy 3 months following most recent biopsy
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.
Men with anorectal abnormalities preventing TRUS-guided prostate biopsy
For TAK-580 + nivolumab and TAK-202 (plozalizumab) + nivolumab only: Had disease accessible for repeat nonsignificant risk biopsy (those occurring outside the brain, lung/mediastinum, and pancreas, or obtained with endoscopic procedures extending beyond the esophagus, stomach, or bowel) and willingness to undergo serial tumor biopsies.
For Concomitant Treatment: Prior tumor resection or biopsy up to 8 weeks prior to first MRZ dose
Safely accessible tumor lesions (based on investigator's assessment) for serial pre treatment and post treatment biopsies are required for participants receiving TAK-659 monotherapy run-in treatment for 2 weeks followed by TAK-659 plus nivolumab combination treatment [ approximately 10/30 response-evaluable participants]; adequate, newly obtained, core or excisional biopsy of a metastatic tumor lesion not previously irradiated is required. Mandatory biopsies will be taken before TAK-659 monotherapy, after the 2 weeks of TAK-659 monotherapy, and after 6 weeks of TAK-659 plus nivolumab combination therapy. An optional biopsy may be taken at PD with additional consent from the participants.
Safely accessible tumor lesions (based on investigator's assessment) for serial pretreatment and posttreatment biopsies are required for participants receiving TAK-659 monotherapy run-in treatment for 2 weeks followed by TAK-659 plus nivolumab combination treatment (approximately10/30 response-evaluable participants); adequate, newly obtained, core or excisional biopsy of a metastatic tumor lesion not previously irradiated is required. Mandatory biopsies will be taken before TAK-659 monotherapy, after the 2 weeks of TAK-659 monotherapy, and after 6 weeks of TAK-659 plus nivolumab combination therapy. An optional biopsy may be taken at progression with additional consent from the participants.
Safely accessible tumor lesions (based on investigator's assessment) for serial pretreatment and posttreatment biopsies are required for participants receiving TAK-659 monotherapy run-in treatment for 2 weeks followed by TAK-659 plus nivolumab combination treatment (approximately 10/30 response-evaluable participants); adequate, newly obtained, core or excisional biopsy of a metastatic tumor lesion not previously irradiated is required. Mandatory biopsies will be taken before TAK-659 monotherapy, after the 2 weeks of TAK-659 monotherapy, and TAK-659 after 6 weeks of TAK-659 plus nivolumab combination therapy. An optional biopsy may be taken at progression with additional consent from the participants.
Agreeable and clinically feasible pre-treatment biopsy