araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: The Correlation of PD-L1 Expression in Non-small Lung Cancer Tissue and Peripheral Blood T Cell and Serum.

Summary: The detection of tissue PD-L1 immunohistochemistry in Non-small cell lung cancer (NSCLC) has an important role in guiding for the treatment of immune detection point. At the same time,tissue detection is time-consuming and laborious, liquid biopsy can reflect the information of tumor tissue,PD-L1 expression in serum and peripheral blood T cell are expected to be simple, rapid, non-invasive means of detection. The project is planned to explore the correlation of PD-L1 expression in non-small lung cancer tissue and peripheral blood T cell and serum..The investigators have designed to detected the expression levels of PD-L1 protein in cancer tissue and detected the expression levels of PD-L1 in peripheral blood T cell and serum.By using variance analysis of repeated measures design information. Thus exploring the correlation of PD-L1 expression in non-small lung cancer tissue and peripheral blood T cell and serum,guiding clinical practice of immunotherapy.


Eligibility: Inclusion Criteria:
  1. Pathological histology and/or cytology confirmed non-small lung cancer;
  2. Voluntarily enrolled to participate in,better compliance, cooperate with experimental observations, and sign informed consent.
  Exclusion Criteria:
  1. Vital organs (e.g., heart, liver, kidney) have serious dysfunction;
  2. Patients with a history of autoimmune disease;
  3. Patients with participating in other clinical trials at the same time;
  4. Other cases that researchers believe that patients should not participate in the present trial.

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: Prognostic Value of PD-L1 in NSCLC

Summary: This is an observational retrospective study. The primary objective is to investigate the expression and potential prognostic role of Programmed Death Ligand 1 (PD-L1) in tumor samples from 350 patients with early stage treatment-naive non-small-cell lung cancer (NSCLC).
  Tissue samples were embedded in a tissue microarray. PD-L1 will be studied by immunohistochemistry using the SP263 antibody. Stained samples will be evaluated independently by two operators. A tumor will be defined as positive when = or >50% of tumor cells express the ligand.
  The investigators will investigate the relationship between PD-L1 protein expression and overall survival and other clinical characteristics with appropriate statistical methods.


Eligibility: Inclusion Criteria:
  -  Early stage treatment-naive NSCLC
  Exclusion Criteria:
  -  Received any pre-surgical treatment
  -  no OS data available

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: Risk Stratification Among Individuals Who Have Many Moles on Their Skin

Summary: The investigators are doing this study to improve our ability to identify which people with many moles on their skin are most likely to develop skin melanoma. The investigators hope to identify features of moles that are associated with melanoma risk. The investigators hope to use this information to customize and tailor melanoma screening to the individual patient based on a better estimate of their individual risk.


Eligibility: Inclusion Criteria:
  -  Patients ≥ 18 years of age
  -  High-risk nevus phenotype (≥ 50 nevi and ≥ 1 atypical nevus)
  -  First presented to MSKCC for cutaneous melanoma-related care within the past 12 months
  -  Cases: recent diagnosis (≤ 12 months) of unequivocal invasive cutaneous melanomas (AJCC Stages I-IV) confirmed by MSKCC pathology
  -  Cases: completion of surgical treatment of primary melanoma
  -  Ability to sign informed consent
  Exclusion Criteria:
  -  Known germline high-penetrance melanoma predisposition mutation (that is, CDKN2A and CDK4)
  -  Cases: history of invasive cutaneous melanoma (AJCC Stages I-IV) not confirmed by MSKCC pathology, history of acrolentiginous type of cutaneous melanoma
  -  Cases: history of systemic adjuvant therapy or treatment of metastatic melanoma, including: MEK inhibitors (trametinib, cobimetinib, etc.), BRAF inhibitors (vemurafenib, dabrafenib, etc.), and immunotherapy (pembrolizumab, nivolumab, atezolizumab, ipilimumab, etc.). Controls: history of Stage 0-IV melanoma confirmed by MSKCC pathology
  -  History of limb amputation or other condition (e.g., tattoos, burns) per investigator discretion that would modify nevus phenotype
  -  Physical inability to undergo total body photography or reflectance confocal microscopy imaging (that is, remain relatively still for durations of 3-5 minutes)
  -  Known hypersensitivity to adhesive rings used for reflectance confocal microscopy
  -  Inability to give informed consent
  -  Have skin afflicted with anther skin condition (for example, psoriasis) that would affect ability to characterize nevus phenotype (per investigator discretion)
  -  Familial cutaneous melanoma history (families with at least one invasive melanoma and two or more other diagnoses of invasive melanoma or pancreatic cancer among first- or second-degree relatives on the same side of the family). We will confirm melanoma family history via medical record documentation, whenever possible, as recommended by previous studies that disproved about half of the reported family histories of melanoma among first-degree relatives in case-control studies.

Relevance to patient case: not relevant
Patient case: 73-year-old male with melanoma; genetic feature: tumor cells negative for PD-L1 expression

Clinical trial: A Study to Assess Programmed Death Ligand-1 (PD-L1) Expression in Cytological Versus Histological Lung Cancer Specimens

Summary: The primary purpose of this non-interventional, multinational study is to assess the feasibility of assessing PD-L1 protein expression on cytological samples as a surrogate for histological samples obtained from participants with any stage of non-small cell lung cancer (NSCLC) or small cell lung cancer (SCLC).


Eligibility: Inclusion Criteria:
  -  Samples must have been collected in a manner that is compliant with local ethics committee guidance
  -  Samples must originate from participants diagnosed with NSCLC or SCLC
  -  Participants must have a pair of at least one cytological and one histological specimen that: Both originate from inside the thorax or from the same ex-thoracic site; Are confirmed to have been collected within a window no more than 6 weeks apart from each other; and are in compliance with the protocol defined sample requirements for histological and cytological specimens
  Exclusion Criteria:
  -  Immune checkpoint inhibitor therapy from 4 weeks prior to collection of the first tumor sample until collection of the second matched sample

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: A Randomized Phase III Trial of Hyperthermic Isolated Limb Perfusion With Melphalan, Tumor Necrosis Factor, and Interferon-Gamma in Patients With Locally Advanced Extremity Melanoma

Summary: Randomized study. Initially, 3 patients will be entered on Arm I as a pilot feasibility study and to standardize the technical aspects of the study. Subsequently, all patients are randomized to Arms I and II.
  Arm I: Regional Hyperthermia plus Regional Single-Agent Chemotherapy. Hyperthermic intravenous limb perfusion, HILP; plus Melphalan, L-PAM, NSC-8806.
  Arm II: Regional Hyperthermia plus Regional Single-Agent Chemotherapy and Biological Response Modifier Therapy. HILP as in Arm I; plus L-PAM; and Tumor Necrosis Factor (Knoll), TNF, NSC-635257; Interferon gamma (Genentech), IFN-G, NSC-600662.

Detailed description: Patients with locally advanced melanoma confined to an extremity (Stage IIIA or Stage IIIAB) will be treated in a randomized Phase III study with hyperthermic isolated limb perfusion. One arm of the study will be a standard 60 minute perfusion with melphalan as a single agent. The second arm of the study will combine melphalan, tumor necrosis factor, and interferon-gamma in the isolated limb perfusion reproducing a regimen shown to have 100% response rates in a Phase II European trial. Patients will be followed for local response rates, duration of response, treatment toxicity, and disease-free survival.

Eligibility: DISEASE CHARACTERISTICS:
  Biopsy-proven Stage IIIA or IIIAB melanoma (M.D. Anderson staging system) of an extremity, as follows:
  Advanced local disease indicated by 2 or more satellite or in-transit metastases.
  Lower limb regional metastases must be distal to the apex of the femoral triangle except inguinal lymph node metastases.
  Upper limb regional metastases must be distal to the deltoid insertion except axillary lymph node metastases.
  No evidence of systemic disease outside the involved extremity.
  Recurrent disease subsequent to prior successful limb perfusion allowed.
  Bidimensional directly measurable dermal or subcutaneous lesion required.
  PRIOR/CONCURRENT THERAPY:
  No prior isolated limb perfusion.
  Biologic Therapy: At least 1 month since Biologic Therapy.
  At least 3 months since regional therapy of the extremity.
  Chemotherapy: At least 1 month since chemotherap.y
  At least 3 months since regional therapy of the extremity.
  Endocrine Therapy: Not specified.
  Radiotherapy: At least 1 month since radiotherapy.
  Surgery: Not specified.
  PATIENT CHARACTERISTICS:
  Age: 18 and over.
  Performance status: ECOG 0 or 1.
  Hematopoietic: Platelets greater than 150,000.
  Hepatic: Bilirubin less than 1.5 mg/dl; Coagulation profile normal.
  Renal: Creatinine less than 2.0 mg/dl.
  Cardiovascular: No evidence of peripheral vascular disease, e.g.:
  No history of claudication.
  OTHER:
  HIV negative.
  No pregnant or nursing women.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: A Phase I Study of gp100 Human Melanoma Peptide Vaccine With Incomplete Freund's Adjuvant

Summary: This is a phase I study of melanoma tumor antigen peptide vaccines. The nine amino acid peptides representing HLA-A2 restricted T cell epitope of the melanoma antigen, gp100 will be administered to patients emulsified in Incomplete Freund's Adjuvant, (IFA). The study is designed to evaluate the toxicity, immunologic effects and potential therapeutic role of repeated doses of gp100 peptide vaccines administered subcutaneously.
  Immune reactivity to the gp100 epitope peptides will be monitored in all patients by analysis of melanoma-specific T cell precursor frequency prior to and after immunization.

Detailed description: This is a phase I study of melanoma tumor antigen peptide vaccines. The nine amino acid peptides representing HLA-A2 restricted T cell epitope of the melanoma antigen, gp100 will be administered to patients emulsified in Incomplete Freund's Adjuvant, (IFA). The study is designed to evaluate the toxicity, immunologic effects and potential therapeutic role of repeated doses of gp100 peptide vaccines administered subcutaneously.
  Immune reactivity to the gp100 epitope peptides will be monitored in all patients by analysis of melanoma-specific T cell precursor frequency prior to and after immunization.

Eligibility: DISEASE CHARACTERISTICS:
  Metastatic melanoma that is HLA-A2 positive.
  No primary melanoma of ocular or mucosal origin.
  Measurable or resected metastatic disease required.
  PRIOR/CONCURRENT THERAPY:
  BIOLOGIC THERAPY: No prior (greater than 30 days) or concurrent Biologic Therapy.
  CHEMOTHERAPY: No prior (greater than 30 days) or concurrent chemotherapy.
  ENDOCRINE THERAPY: No prior (greater than 30 days) or concurrent hormone therapy.
  No requirement for steroids.
  RADIOTHERAPY: No prior (greater than 30 days) or concurrent radiotherapy.
  SURGERY: Not specified.
  PATIENT CHARACTERISTICS:
  Age: 18 and over.
  Performance Status: ECOG 0 or 1.
  Life Expectancy: More than 3 months.
  HEMATOPOIETIC: No coagulation disorder.
  HEPATIC:
  Bilirubin no greater than 2.0 mg/dL.
  No Hepatitis BsAg antibody.
  RENAL: Creatinine no greater than 2.0 mg/dL.
  CARDIOVASCULAR: No major cardiovascular illness.
  PULMONARY: No major respiratory illness.
  OTHER:
  No previous allergic reaction to incomplete Freund's adjuvant.
  HIV negative.
  No active systemic infection.
  Not pregnant or lactating.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Follow-up Protocol for Patients With Cancer/AIDS/Skin Disease

Summary: This protocol is to provide follow-up medical/surgical visits for DCS patients who are long term survivors and may not currently be a participant entered on an active research protocol. No investigational treatments or standard treatments will be administered on this protocol.

Detailed description: Background:
  -  Patients enrolled on CCR clinical protocols may require long term follow-up to assess outcome (e.g., survival) or the effects of prior therapy.
  -  Keeping the primary treatment protocols open after accrual is complete in order to follow patients for long term outcome is an administrative burden on investigators and the IRB.
  Objectives:
  -To provide follow-up for patients who are long term survivors previously enrolled Center for Cancer Research (CCR) trial but who may not currently be enrolled on a research protocol.
  Eligibility:
  -Patients who were previously enrolled on a CCR protocol and who are not eligible for an active NCI intramural primary research protocol.
  Design:
  -  The medical procedures/tests will be based on the patient's diagnosis, treatment and supporting clinical information. This is a follow-up study in which only standard tests and procedures are to be performed.
  -  Clinical information that is relevant to the patients prior protocols will be collected for research purposes.
  -  Procedures that entail more than minimal risk to the patient should not be performed for research purposes on this protocol.

Eligibility: -  ELIGIBILITY CRITERIA:
  Patients of any age who were previously enrolled on a CCR protocol.
  Not eligible for or unwilling to participate in an active NCI intramural primary research protocol.
  CCR investigator decides it is in the best interests of the patient and the CC for the patient to be seen in follow-up visits at the NIH.
  Patient or guardian is able to provide informed consent.

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Immunization of HLA-A201 Patients With Metastatic Melanoma Using a Combination of Immunodominant Peptides From Three Melanoma Antigens, MART-1, GP100 and Tyrosinase

Summary: This is a study of a melanoma tumor antigen peptide vaccine. Peptides representing HLA-A201 restricted T cell epitopes of the melanoma antigens, MART-1, gp100 and tyrosinase will be administered emulsified in Incomplete Freund's Adjuvant, (IFA) to HLA-A201 patients with melanoma. The study is designed to evaluate the potential therapeutic role, immunologic effects and toxicity of repeated doses of this peptide vaccine administered subcutaneously.
  Immune reactivity to the peptide epitope will be monitored in all patients by analysis of melanoma-specific T cell precursors prior to and after immunization.

Detailed description: This is a study of a melanoma tumor antigen peptide vaccine. Peptides representing HLA-A201 restricted T cell epitopes of the melanoma antigens, MART-1, gp100 and tyrosinase will be administered emulsified in Incomplete Freund's Adjuvant, (IFA) to HLA-A201 patients with melanoma. The study is designed to evaluate the potential therapeutic role, immunologic effects and toxicity of repeated doses of this peptide vaccine administered subcutaneously.
  Immune reactivity to the peptide epitope will be monitored in all patients by analysis of melanoma-specific T cell precursors prior to and after immunization.

Eligibility: Any patient 16 years of age or older with measurable metastatic melanoma who has failed standard treatment and has an expected survival of greater than three months.
  Must be HLA-A0201.
  Serum creatinine of 2.0 mg/dl or less.
  Bilirubin 1.6 mg/dl or less.
  WBC 3000/mm(3) or greater.
  Platelet count 90,000 mm(3) or greater.
  Serum AST/ALT less then two times normal.
  ECOG performance status of 0 or 1.
  Patients of both genders must be willing to practice effective birth control during the trial.
  Must not be undergoing or have undergone in the past 3 weeks any other form of therapy except surgery for their cancer.
  Must not have active systemic infections, coagulation disorders, or other major medical illnesses of the cardiovascular or respiratory systems or any known immunodeficiency disease.
  Must not require steroid therapy.
  Must not be pregnant.
  Must not be positive for hepatitis B(s)AG or HIV antibody.
  Must not have had a known allergic reaction to Incomplete Freund's Adjuvant (IFA).

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Immunization of Patients With Metastatic Melanoma Using the GP100 Peptide Preceded by an Endoplasmic Reticulum Insertion Signal Sequence

Summary: Patients with metastatic melanoma who are HLA-A201+ will be immunized with a modified peptide from the gp100 molecule that contains a signal sequence designed to improve peptide presentation by antigen presenting cells. This peptide called gp100:ES209-217 (210M) will be administered either alone or in combination with high or low dose IL-2. Patients will be evaluated for clinical response, as well as undergo studies of the immunologic response to the peptide immunization.

Detailed description: Patients with metastatic melanoma who are HLA-A201+ will be immunized with a modified peptide from the gp100 molecule that contains a signal sequence designed to improve peptide presentation by antigen presenting cells. This peptide called gp100:ES209-217 (210M) will be administered either alone or in combination with high or low dose IL-2. Patients will be evaluated for clinical response, as well as undergo studies of the immunologic response to the peptide immunization.

Eligibility: Any patient age greater than or equal to 18 with measurable metastatic melanoma who has failed standard treatment and has an expected survival of greater than three months will be considered.
  Serum creatinine of 2.0 mg/dl or less.
  Bilirubin 1.6 mg/dl or less.
  WBC 3000/mm(3) or greater.
  Platelet count 90,000 mm(3) or greater.
  Serum AST/ALT less then two times normal.
  ECOG performance status of 0 or 1 or 2.
  Patients of both genders must be willing to practice effective birth control during this trial.
  No patients who are undergoing or have undergone in the past 3 weeks any other form of therapy except surgery for their cancer.
  No patients who have active systemic infections, coagulation disorders, autoimmune disease or other major medical illnesses of the cardiovascular or respiratory systems or any known immunodeficiency disease. Patients with cardiovascular disease will be eligible to receive peptide in IFA alone.
  No patients who require steroid therapy.
  No patients who are pregnant (because of possible side effects on the fetus).
  No patients who are known to be positive for hepatitis BsAG or HIV antibody (because of possible immune effects of these conditions).
  No patients who have any form of primary or secondary immunodeficiency. (The experimental treatment being evaluated in this protocol depends on an intact immune system. Patients who have decreased immune competence may be less responsive to the experimental treatment and more susceptible to its toxicities).

Relevance to patient case: not relevant
Patient case: 86-year-old female with melanoma; genetic feature: high tumor mutational burden

Clinical trial: Microarray Analysis for Human Genetic Disease

Summary: This study will look at genetic changes which occur in the development of male and female breast cancer and other cancer. It will use a new technology called DNA microarray hybridization that looks at a wide array of genes to identify disease-associated patterns in the human genome (complete set of human genes). Numerous studies have linked particular genes to a given disease, but there is very little information on patterns of gene expression (production of proteins from genetic coding) in the entire human genome.
  Pinpointing genetic abnormalities in disease may help classify different forms of cancer and perhaps lead to new avenues of treatment or prevention. A primary goal of this study will be to create a database of gene expression for human cancers and other disorders that will provide the basis for finding genetic abnormalities in disease.
  Tumors specimens used in this study will be taken from tissues biopsied from patients with breast, colon cancer, sarcomas or melanoma as part of their routine care. Patients in the study will be among those receiving care at the: Department of Oncology, University Hospital, University of Lund, Sweden (breast cancer); Department of Medicine, University of Michigan, Ann Arbor, Michigan (breast cancer); Surgery Branch, National Cancer Institute, Bethesda, Maryland (melanoma), Johns Hopkins Univ. (colon cancer), Memorial Sloan Kettering (sarcoma).
  Patients in the study will have a family history taken and will complete a questionnaire. Some patients will be asked to have a blood test. Breast cancer patients will have a mammogram if one has not been done within the last year.

Detailed description: The purpose of our study is to make use of a novel technology that the Cancer Genetics Branch of the NHGRI has been a leader in developing. This technology for genome-wide expression analysis, DNA microarray hybridization, is the focus of our protocol. We will access tissue banks collected by our collaborators that contain excess tissues obtained during routine clinical care. Specimens will be processed for large-scale gene expression analysis and DNA copy number determination using DNA microarrays. The development and analysis of this gene expression and gene copy number database are the primary purpose of this study. Currently available and new bioinformatics tools will be applied to the data for the characterization of disease subsets (e.g., early vs. advanced stage cancer) as well as to mine the data for specific genes which are linked to given disease states.

Eligibility: -  Clinical inclusion/exclusion criteria will be dependent upon the collaborating Institutions' requirements.

Relevance to patient case: not relevant