No other active malignancy that the investigator determines would interfere with the treatment and safety analysis
the analysis of results
Patients with inadequate tissue for analysis
Provide tissue for biomarker analysis from a newly or recently-obtained biopsy (within 90 days of Study Day 1) of a tumor lesion not previously irradiated
Patients must agree, as part of the informed consent, to provide blood for pharmacokinetics analysis
Available tumor tissue for biomarker analysis
HLA A2+ by deoxyribonucleic acid (DNA) sequence analysis (by history with documentation or as part of this study)
Consent to provide an archival tumor tissue sample (if available) and to undergo baseline and on treatment tumor biopsies for pharmacodynamic biomarker analysis
Non-dysplastic or indefinite for dysplasia BE, confirmed by histopathological analysis
Tumor tissue from the resected site of disease must be provided for biomarker analyses; in order to be treated, a patient must have tissue available for PD-L1 expression analysis by immunohistochemistry (ICH) as determined by the New York University Langone Medical Center (NYULMC) Pathology lab; if insufficient tumor tissue content is provided for analysis, acquisition of additional archived tumor tissue (block and/or slides) for the biomarker analysis is required
Insufficient tissue on diagnostic core breast biopsy for analysis
Histologically confirmed adenocarcinoma of the prostate (with previous diagnostic tissue available for tumor marker analysis)
Patients must have analysis of PD-L1 expression in cancer cells quantitated by immunohistochemistry analysis
Provision of suitable tumor tissue for the analysis of Axl kinase expression and PD-L1 expression.
Evaluable tumor tissue (archived or new biopsy) must be available for pre-treatment biomarker analysis and baseline immune monitoring studies
Tissue available for analysis at time of enrollment for biomarker analysis (may be obtained via biopsy prior to initiation of treatment, or submission of available archival tissue: 10-15 slides, or 5 slides with 3 sections per slide
At the time of biopsy, prior to administration of virus, the presence of recurrent tumor must be confirmed by histopathological analysis
At the time of biopsy, prior to administration of virus, the presence of recurrent tumor must be confirmed by histopathological analysis
Available tissue to perform protein and genomic analysis
Has sufficient tumor tissue (slides or blocks) available for central confirmatory testing of IHC and/or cytogenetics/FISH and/or DNA mutation analysis (required for study entry but enrollment based on local results)
If the patient consents to enroll, then blood will be drawn and stored for biomarker analysis
The subject must be willing to undergo the two paired tumor tissue biopsy procedures to obtain samples for biomarker analysis; tissue obtained must not be previously irradiated
Following biopsy, prior to administration of D2C7-IT, the presence of recurrent tumor must be confirmed by histopathological analysis
>= 5 mm by imaging/pathology of core to ensure enough pre- and post-treatment tissue for analysis
Availability of tumor tissue for mesothelin expression testing and for further biomarker analysis
Genotyping data available or in process (data must be available at time of initial registration if randomization probabilities differ across biomarker subgroups as determined by the Dana-Farber Cancer Institute [DFCI] Coordinating Center) to assign biomarker subgroups through whole exome sequencing, whole genome copy number analysis, or a combination
Sufficient pathologic material must be available for central analysis and review
Sufficient tumor tissue for planned analysis
Provides an archival or newly obtained tumor tissue sample and blood samples for biomarker analysis.
analysis of results
Tumor biopsy material must be provided for all patients for the purpose of biomarker analysis
MPM tumor sample for determination of ASS1 status. ASS1-deficiency is not required for study entry at study start, but tumor sample for ASS1 status is required. This study will employ an adaptive biomarker-driven design with an interim analysis to be conducted at the end of the phase 2 portion. The interim analysis will evaluate the treatment effect of ADI PEG 20 in combination with pemetrexed and cisplatin on overall survival (OS) in the overall population (biphasic and sarcomatoid histology patients) and pre-defined subpopulation of biomarker-positive patients (ASS1-deficient subpopulation). Thus ASS1 deficiency may be required for the phase 3 portion of the study, pending the interim analysis. ASS1-deficiency, demonstrated on tissue specimen (cytospin samples are not acceptable), will be defined in the laboratory manual. If archived tissue is not sufficient or not available, then tissue must be obtained by biopsy.
Tumor tissue must be provided for biomarker analysis
Patients must have Clinical Laboratory Improvement Act (CLIA) confirmed somatic KRAS G12R mutation as determined by sequence analysis of matched normal deoxyribonucleic acid (DNA) from any specimen obtained from the individual; patients must provide tumor sample for KRAS analysis or be willing to undergo mandatory screening biopsy
Have provided tissue from an archival or newly obtained tissue sample of a tumor lesion, sufficient for analysis of programmed cell death 1 ligand 1 (PD-L1) and other biomarkers; patients who have had PD-L1 analysis previously performed at Merck can substitute earlier analysis results and are not required to submit additional tissue for PD-L1 testing; expression of PD-L1 is NOT required for study entry
Adequate tumor content as determined by institutional pathologist for nucleic acid extraction and DNA sequence analysis
Patients with confirmed p53 mutation by molecular analysis and/or evidence of p53 overexpression by immunohistochemistry (>= 10% of cells within tumor staining positive) will be eligible; this will be assessed semi-quantitatively by a Clinical Laboratory Improvement Act (CLIA) approved pathology core pathologist, using CLIA approved mutational analysis or immuno-histochemistry techniques on formalin-fixed paraffin-embedded tissue; in the case of equivocal immunohistochemistry (IHC) results, p53 involvement may be confirmed by detection of p53 molecular analysis on tumor deoxyribonucleic acid (DNA); patients on whom molecular analysis of p53 mutations is already available, will not require IHC analysis; molecular analysis may be performed as an additional research procedure at the end of the study (distinct from eligibility determination) if the principal investigator (PI) deems it of scientific value and research funding is available to cover the cost; patients must have PD-L1 positive ovarian cancer in order to be eligible for this clinical trial (defined as >= 1% PD-L1 expression within the tumor section, assessed by immunohistochemical staining)
Confirmed p53 involvement: patients with p53 over-expression by immunohistochemistry (>= 10% of cells within the tumor staining positive) or those with a p53 mutation as determined by mutational analysis of tumor tissue will be eligible; patients with prior exposure to p53-based vaccines will be eligible
A cell block or core biopsy must be submitted for central review and analysis of SMAD4 status as soon as possible following step 1 registration
Must have tumor tissue available for biomarker analysis. Biopsy should be excisional, incisional, punch, or core needle
Participant must consent to provide archived tissue or cytology sample of NSCLC lesion for analysis.
Patients must agree to have blood specimens submitted for pharmacokinetic analysis
Patients must agree to blood samples during screening and at the end of treatment for cytogenetic analysis.
Able to provide biopsy tissue for biomarker analysis
analysis of results
Available archived tumor tissue for central analysis
Can provide tissue for PD-L1 and mesothelin biomarker analysis
Primary tumor is available for shipment to central laboratory for analysis of FR? expression by IHC.
Have sufficient tumor tissue available for central analysis.
Subjects must have archival tumor tissues or agree to a tumor biopsy for analysis of predictive biomarkers such as PD-L1. (Fresh tumor biopsies are strongly recommended at baseline for biomarker analysis in subjects with readily accessible tumor lesions and who consent to the biopsies.)
Have tumor tissue available for biomarker analysis.
Must consent to collection of blood samples for PK analysis.
At least one site of disease must be accessible to provide repeat biopsies for tumor tissue for sequence and immunological analysis.
Availability of tumor tissue for biomarker analysis
PART A: Patient has agreed to two newly obtained tumor biopsies and as required re-biopsies (that can be biopsied on investigator’s assessment) and to providing the acquired tissue for biomarker analysis; analysis of one of the fresh biopsy samples for PD-1hiCD8+CTLA4hi in the CD8+CD45+ gate based on flow cytometry will be done; a second fresh biopsy sample is required for further biomarker analysis and confirmation at a later date of low PD-L1 expression using an immunohistochemistry (IHC) assay for PD-L1 expression; a valid flow cytometry result is not required for study participation, but repeated biopsy for reanalysis is strongly recommended for patient with insufficient TILs in the first tissue sample
Patients unwilling to consent to analysis of their tumor tissue.
Tumor tissues (archived or new biopsy) must be provided for biomarker analysis
Willing to provide tumor tissue for PD-L1 biomarker analysis (new or archived specimens with agreement of Sponsor). As of 20 March 2016, participants must be PD-L1 positive to be enrolled.
Mandatory provision of an unstained, archived tumour tissue sample in a quantity sufficient to allow for central analysis of EGFR mutation status.
Available tissue for biomarker analysis
Tumor tissue available for PD-L1 biomarker analysis
Tumor not able to be reliably evaluated by volumetric analysis
No deletion of 17p13 on cytogenetic analysis by FISH
Must consent to collection of whole blood samples for genomic analysis
analysis of results
Archived tumor tissue must be available for all subjects for biomarker analysis and confirmation of the diagnosis before or during treatment; samples must be provided within 4 weeks of enrollment
Enrolled in Human Research Protection Office (HRPO) # 201011766 (“Tissue Acquisition for Analysis of Genetic Progression Factors in Hematologic Malignancies”)
Subjects must be able to provide adequate bone marrow (BM) aspirate and biopsy specimens for histopathological analysis and standard cytogenetic analysis during the screening procedure
Patient must be enrolled in Human Research Protections Office (HRPO) # 201011766 (\Tissue Acquisition for Analysis of Genetic Progression Factors in Hematologic Diseases\)
Patient must have archival prostate tumor block available for analysis of correlatives
At the time of biopsy, prior to administration of virus, the presence of recurrent tumor must be confirmed by histopathological analysis
Blood and urine samples must be provided from all subjects for biomarker analysis before and during treatment with pazopanib
Adequate tumor tissue available for KRAS mutational analysis or known KRAS wild-type status
The participant must have tumor tissue from breast (preferred) or lymph node for exploratory biomarker analysis available prior to randomization.
Ki67 index by central analysis of ?20% on untreated breast tissue
Tumor tissue available and adequate for analysis at screening
Has an archived, diagnostic tumor tissue available for analysis.
Patients must be willing to provide a screening and post-dose biopsy for biomarker analysis (extension phase only)
In the extension phase, patients must be willing to provide a screening and post-dose biopsy for biomarker analysis
Patients must provide a pretreatment saliva sample for genomic analysis
Patient has diagnostic biopsy available for the analysis of PIK3CA mutation and Ki67 level.
Patients with confirmed p53 mutation by molecular analysis and/or evidence of p53 overexpression by immunohistochemistry (>= 10% of cells within the tumor staining positive) will be eligible; this will be assessed semi-quantitatively by a Clinical Laboratory Improvement Amendments (CLIA) approved pathology core pathologist, using CLIA approved mutational analysis or immunohistochemistry techniques on formalin-fixed paraffin-embedded tissue; in the case of equivocal immunohistochemistry (IHC) results, p53 involvement may be confirmed by detection of p53 molecular analysis on tumor deoxyribonucleic acid (DNA); patients on whom molecular analysis of p53 mutations is already available, will not require IHC analysis; molecular analysis may be performed as an additional research procedure at the end of the study (distinct from eligibility determination) if the principal investigator (PI) deems it of scientific value and research funding is available to cover the cost
Sufficient archival tumor specimen is available for HER3 immunohistochemistry (IHC) analysis, or subject is willing to undergo a fresh tumor biopsy for HER3 IHC analysis.
Primary prostate cancer tissue available for analysis is not required for inclusion onto this study but is strongly encouraged
Valid results from central molecular analysis confirming PIK3CA/AKT1/PTEN-altered status in tumor tissue by next-generation sequencing (NGS)
For participants in Part B, C, D, E, and F, a tumor tissue sample is mandatory, when safe and feasible, for biomarker analysis
The participant has archived tumor tissue available for analysis (can be either primary tumor or metastases).
Specimens for cytogenetic analysis are required, and must be obtained prior to therapy initiation; for patient with refractory disease, the diagnostic specimen may be used
Consent to allowing his/her archival tumor tissues to be requested and analyzed; however, the non-availability or inadequate amount samples for analysis will not exclude the patient
Have normal urine analysis within 24 hours pre-surgery
Results of CXCR4 immunohistochemistry or slides from biopsy of primary tumor or metastatic lesions available for study analysis
Archived tissue from the CRC primary tumor in sufficient amounts to allow advanced quantitative real time-polymerase chain reaction (qRT-PCR) analysis; specimen from metastatic sites are not required but highly preferred
Signing consent for study imaging procedure and analysis of prostate biopsy
Patients must agree to have clinical and radiographic endpoints and the results of histopathologic tissue analysis and other laboratory information entered into a research database, as evidenced by signing the informed consent form
The patients will be asked to consent to provide access to data obtained from molecular analysis that has been done on archived tumor tissue that will be correlated with 89Zr-DFO-trastuzumab imaging results
Archived tumor blocks must be provided for all subjects for correlative analysis before or during treatment with pazopanib
Patients must document their willingness to be followed for a period of time; for the purposes of imaging data analysis this will ideally be for at least 12 months after completing the investigational or recently approved therapy, however this may not always be possible; by signing informed consent, the patients are documenting their agreement to have clinical and radiographic endpoints and the results of histopathologic tissue analysis and other laboratory information entered into a research database
Tissue analysis demonstrating pathology other than glioblastoma
Patients must document their willingness to be followed for up to 24 months following enrollment in this imaging trial; by signing informed consent, the patients will document their agreement to have clinical and radiographic endpoints and the results of histopathologic tissue analysis and other laboratory information entered into a research database
Tissue specimen is inadequate for sampling and analysis
Cohort A: Screening visit peripheral blood must be available for retrospective analysis of spliceosome mutations of interest.
the analysis of results