araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Study of Nivolumab and Relatlimab in Patients With Microsatellite Stable (MSS) Advanced Colorectal Cancer

Summary: The purpose of this study is to evaluate the safety and clinical activity of nivolumab and relatlimab in patients with metastatic or locally advanced microsatellite stable (MSS) colorectal cancer.


Eligibility: Inclusion Criteria:
  -  Age ≥18 years.
  -  ECOG performance status 0 or 1
  -  Have metastatic or locally advanced microsatellite stable (MSS) colorectal adenocarcinoma.
  -  Must have received at least one chemotherapy regimen.
  -  Patients with the presence of at least one measurable lesion using RECIST 1.1.
  -  Patients must have available archival tissue from the surgical resection of their primary tumor.
  -  Patient's acceptance of tumor biopsies.
  -  Life expectancy of greater than 3 months.
  -  Patients must have adequate organ and marrow function defined by study - specified laboratory tests.
  -  Documented LVEF ≥ 50% - 6 month prior to drug administration.
  -  Must use acceptable form of birth control while on study.
  -  Ability to understand and willingness to sign a written informed consent document.
  Exclusion Criteria:
  -  Known history or evidence of brain metastases. Patients with previously treated brain metastases may participate if they are stable for 4 weeks prior to beginning treatment, have no new or enlarging brain metastases, and are not using steroids for at least 1 week prior to treatment.
  -  Require any antineoplastic therapy.
  -  History of prior treatment with anti-PD-1, anti-PD-L1, anti-PD-L2, anti-CTLA-4, or anti-Lag-3 antibodies.
  -  Had chemotherapy, radiation, or steroids within 14 days prior to study treatment.
  -  Hypersensitivity reaction to any monoclonal antibody.
  -  Has uncontrolled intercurrent acute or chronic medical illness.
  -  Has an active known or suspected autoimmune disease.
  -  Has a diagnosis of immunodeficiency.
  -  Prior tissue or organ allograft or allogeneic bone marrow transplantation.
  -  Requires daily supplemental oxygen
  -  History of interstitial lung disease.
  -  Significant heart disease
  -  History of encephalitis, meningitis, or uncontrolled seizures in the year prior to informed consent.
  -  Infection with HIV or hepatitis B or C at screening.
  -  Has an active infection.
  -  Unable to have blood drawn.
  -  Patient with uncontrolled intercurrent illness including, but not limited to, uncontrolled infection, symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia, or psychiatric illness/social situations that would limit compliance with study requirements.
  -  Woman who are pregnant or breastfeeding.

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: A Study of Subcutaneous Nivolumab Monotherapy With or Without Recombinant Human Hyaluronidase PH20 (rHuPH20)

Summary: The purpose of this study is to investigate the effects of nivolumab when given under the skin with or without rHuPH20.
  This study will include participants with 1 of the following advanced or metastatic tumors approved for treatment with nivolumab monotherapy:
  -  non-small cell lung cancer (NSCLC)
  -  renal cell carcinoma (RCC)
  -  unresectable or metastatic melanoma
  -  hepatocellular carcinoma (HCC)
  -  microsatellite instability-high or mismatch repair deficient colorectal cancer (MSI-H/dMMR CRC)


Eligibility: For more information regarding Bristol-Myers Squibb Clinical Trial participation, please visit www.BMSStudyConnect.com
  Inclusion Criteria:
  -  Histologic or cytologic confirmation of advanced (metastatic and/or unresectable) solid tumors of one of the following tumor types:
  1. Metastatic squamous or non-squamous NSCLC
  2. RCC, advanced or metastatic
  3. Melanoma
  4. HCC
  5. CRC, metastatic (MSI-H or dMMR)
  -  Measurable disease as per RECIST version 1.1 criteria
  -  ECOG performance status of 0 or 1
  Exclusion Criteria:
  -  Active brain metastases or leptomeningeal metastases
  -  Ocular melanoma
  -  Active, known, or suspected autoimmune disease
  Other protocol defined inclusion/exclusion criteria could apply

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Diagnostic DNA Methylation Signature in Diagnosing Thyroid Cancer After Fine-Needle Aspiration in Patients With Thyroid Nodules

Summary: This trial studies how well the diagnostic deoxyribonucleic acid (DNA) methylation signature works in detecting thyroid cancer in patients with thyroid nodules. Using diagnostic testing, such as the diagnostic DNA methylation signature, may be a less invasive way to check for thyroid cancer.

Detailed description: PRIMARY OBJECTIVES:
  I. To validate a novel epigenetic thyroid nodule diagnostic test, diagnostic DNA methylation signature (DDMS) in a retrospective-prospective study with leftover of fine needle aspiration biopsies.
  OUTLINE:
  Previously collected FNA aspiration specimen samples are analyzed via DDMS assay. Participants undergo FNA aspiration for collection of tissue samples for analysis via DDMS assay.
  After completion of study, patients are followed up yearly for 5 years.

Eligibility: Inclusion Criteria:
  -  All patients undergoing FNA for thyroid nodule diagnosis.
  -  Any race and ethnicity are eligible for the study.
  -  Patient should have thyroid nodule(s) with indeterminate diagnosis after FNA (Bethesda category of indeterminate FNA [III-V]).

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Tislelizumab (Anti-PD-1 Antibody) in MSI-H or dMMR Solid Tumors

Summary: In this Phase 2, Single-Arm, Multi-Center, Open-Label Study, patients with previously treated locally advanced unresectable or metastatic solid tumors with mismatched repair deficient (dMMR) or microsatellite instability-high (MSI-H) will be treated with anti-PD-1 Monoclonal Antibody Tislelizumab (BGB-A317). Efficacy and safety will be assessed. A short description of the clinical study, including a brief statement of the clinical study's hypothesis, written in language intended for the lay public.


Eligibility: Inclusion Criteria:
  1. Having histological confirmed diagnosis of malignancy
  2. Having locally advanced unresectable or metastatic solid tumors with MSI-H or dMMR
  3. Having received or refused prior cancer therapy regimen(s) for advanced disease.
  4. At least 1 measurable lesion as defined per RECIST Version (v) 1.1
  5. ECOG Performance Status ≤ 1
  6. Adequate organ function
  Exclusion Criteria:
  1. Prior therapy with an anti-PD-1, anti-PD-L1, anti-PD-L2 or any other antibody or drug specifically targeting T-cell co-stimulation or checkpoint pathways
  2. Active leptomeningeal disease or uncontrolled brain metastasis.
  3. Clinically significant pleural effusion, pericardial effusion or ascites
  4. Active autoimmune diseases or history of autoimmune diseases that may relapse
  5. Any active malignancy
  6. Any condition that required systemic treatment with either corticosteroids (> 10 mg daily of prednisone or equivalent) or other immunosuppressive medication ≤ 14 days before the first dose of study drug
  7. Having a history of interstitial lung disease, non-infectious pneumonitis, pulmonary fibrosis, acute lung diseases, or uncontrolled systemic diseases (including but not limited to diabetes, hypertension, etc.)
  8. Patients with uncontrolled diabetes or uncontrolled electrolyte disorders despite standard medical management
  9. Having severe chronic or active infections
  10. A known history of human immunodeficiency virus infection
  11. Child - Pugh B or greater cirrhosis
  12. Any major surgical procedure ≤ 28 days before the first dose of study drug
  13. Prior allogeneic stem cell transplantation or organ transplantation

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: The Implication of Plasma ctDNA Methylation Haplotypes in Detecting Colorectal Cancer and Adenomas

Summary: This is a prospective, multicenter, clinical study. This study is to evaluate the sensitivity of plasma ctDNA methylation haplotypes in detecting colorectal cancer, adenoma and the specificity in healthy individuals.

Detailed description: Colorectal cancer (CRC) is the third most common cancer worldwide, the second deadliest cancer in the United States. DNA methylation is a commonly used biomarker for non-invasive CRC detection in plasma. The low sensitivity of blood-based tests is due to several limitations of detecting ctDNA in early-stage cancer. We developed and validated a high-throughput methylation-based blood test highly sensitive for colorectal cancer and precancerous lesions. This previously established colorectal tumor-specific plasma ctDNA methylation markers (diagnostic model established by next-generation sequencing of 2181 gene loci methylation) had a high sensitivity in CRC patients and a high specificity in healthy individuals in a large retrospective sample study. This prospective, multicenter, clinical study is to further evaluate the sensitivity of plasma ctDNA methylation haplotypes in detecting colorectal cancer, adenoma and the specificity in healthy individuals.

Eligibility: Inclusion Criteria:
  Healthy Individuals:
  -  Written informed consent must be obtained from healthy individuals to comply with the requirements of the study.
  -  Healthy individuals who received colonoscopy.
  Patients with Colorectal Cancer or Adenomas:
  -  Male or female ≥ 18 years of age on the day of signing informed consent.
  -  Patients need to receive surgical resection or endoscopic resection.
  -  Patients must have histologically confirmed stage I-IV colorectal cancer or adenomas
  -  Patients must have a performance status of ≤1 on the ECOG Performance Scale.
  -  Written informed consent must be obtained from patient or patient's legal representative and ability for patient to comply with the requirements of the study.
  Exclusion Criteria:
  -  Patients received adjuvant treatment prior to the surgical resection.
  -  Patients received blood transfusion two weeks before or during the surgical resection.
  -  Patients with unresected advanced colorectal adenoma.
  -  Patients who are positive for Human Immunodeficiency Virus (HIV), Hepatitis B or Hepatitis C.
  -  Patients who are pregnant.
  -  Patients who are alcoholic or drug abusers.
  -  Patients with a history or current evidence of any condition or abnormality that might confound the results of the study, interfere with the patient's participation for the full duration of the study, or is not in the best interest of the patient to participate, in the opinion of the Investigator.

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: MSI in Circulatory DNA of Endometrial Cancer

Summary: This study aims to analyze the microsatellite instability (MSI) in the circulatory tumor DNA and in the tumor tissue in the patients diagnosed with uterine endometrial cancer. These data will be used for the study of "Cohort Study of Universal Screening for Lynch Syndrome in Chinese Patients of Endometrial Cancer" (NCT03291106, clinicaltrials.gov).


Eligibility: Inclusion Criteria:
  -  Confirmed primary endometrial cancer before any surgical or chemotherapy treatment
  -  Signed an approved informed consents
  -  Feasible for sampling
  Exclusion Criteria:
  -  Not meeting all of the inclusion criteria

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Clinicopathological Importance of Colorectal Medullary Carcinoma: Retrospective Cohort Study

Summary: Medullary carcinoma (MC) is a rare tumor with solid growth pattern without glandular differentiation and constitute less than 1% of colorectal cancer. Lymph node positivity and distant organ metastasis were reported to be lower than other poorly differentiated adenocarcinomas. Therefore, the diagnosis of MC is pathologically important in terms of follow-up and treatment. MC is commonly localized in the right colon, has a large tumor size, and is mostly diagnosed in the T4 stage. As MC most likely have defects in DNA MMR, the correct pathological diagnosis is important for the postoperative treatment and the prognosis of the patients.

Detailed description: 427 patients with colorectal cancer who were underwent surgery between January 2011 and December 2017, were evaluated retrospectively into 2 groups as MC (n:13) and non-MC (n:414) in terms of demographic characteristics, pathological data and oncological outcomes.

Eligibility: Inclusion Criteria:
  -  colorectal cancer diagnosis, medullary carcinoma
  Exclusion Criteria:
  -  none

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Comparison to Psychological, Medical and Emotional Influencing Communication and Achievement Factors to Oncogenetics Tests

Summary: The purpose of the study was to analyze the psychological and emotional determinants of domestic dissemination of information about genetic risk of cancer and to compare the level of diffusion syndromes in breast/ ovarian cancer ( BRCA1 / BRCA2) and colon/endometrial ( HNPCC )

Detailed description: The risk associated with a genetic predisposition is among the various forms of risk, the strongest identifiable risk . It enables to offer people at risk an appropriate medical care (screening, prevention ) the clinical benefit is validated today. The person with whom a predisposing mutation has been identified must communicated its related information on the risk of cancer and the ability to perform genetic analysis. It appears that this dissemination of information is not always optimal, as shown in figures from the National Cancer Institute joined the project; the purpose of the study was to analyze the psychological and emotional determinants of domestic dissemination of information about genetic risk of cancer and to compare the level of diffusion syndromes in breast/ ovarian cancer ( BRCA1 / BRCA2) and colon/endometrial ( HNPCC )

Eligibility: Inclusion Criteria:
  -  Patient having a deleterious genetic mutation on genes BRCA1 and/or BRCA2 and or on genes MMR
  -  The patient being of the family (who carried out a full analysis of BRCA1/BRCA2 and/or those MMR )
  Exclusion Criteria:
  -  Patient not carrying a deleterious genetic mutation on the BRCA1/2 genes and/or those of the MMR system,
  -  Patient under guardianship, curator or unable to give his non-opposition,
  -  Adult patients protected by law.

Relevance to patient case: not relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: INST 1204: PIK3CA Mutations as Biomarkers for Metastasis in Colon Cancer

Summary: This proposal seeks to further understand the contribution of the PIK3CA mutations in colon cancer, by correlating the type of hotspot mutation with the development of metastases in stage II and stage Ill patients.
  In order to do this, DNA will be extracted from either frozen or paraffin embedded colon cancer tissues to sequence PIK3CA, KRAS and BRAF. Clinical outcome data will be gathered to include metastases and survival to correlate with PIK3CA, KRAS and BRAF mutational status. Patients with stage II and stage Ill colon cancers will be identified in the University of New Mexico Human Tissue Repository and the NIH PLCO prevention trial biorepository.
  Existing banked tissues of stage II and Ill colon cancers will be collected. There will be no direct contact with living individuals. Epidemiological factors such as age, race, gender and outcome data of metastases and survival will be collected.

Detailed description: This proposal aims to identify PIK3CA mutations as a biomarker for metastasis.
  In order to do this, DNA will be extracted from either frozen or paraffin embedded colon cancer tissues to sequence PIK3CA, KRAS and BRAF. Clinical outcome data will be gathered to include metastases and survival to correlate with PIK3CA, KRAS and BRAF mutational status. Patients with stage II and stage Ill colon cancers will be identified in the University of New Mexico Human Tissue Repository and the NIH PLCO prevention trial biorepository.
  Existing banked tissues of stage II and Ill colon cancers will be collected. There will be no direct contact with living individuals. Epidemiological factors such as age, race, gender and outcome data of metastases and survival will be collected.
  Specific Aims:
  1. To develop and standardize methods for high throughput DNA extraction and analysis from colon tumors of patients with stage II and stage III disease harboring PIK3CA exon 9 and exon 20 mutations.
  2. To determine the correlation between wild type and PIK3CA, PIK3CA exon 9 and PIK3CA exon 20 mutations and development of metastatic disease and overall survival in stage II and stage III patients with colorectal cancer.

Eligibility: Inclusion Criteria:
  -  Specimen from patients with stage II and stage III colon cancer.
  Exclusion Criteria:
  -  Any other stage or type of disease outside of stage II and stage III colon cancer.

Relevance to patient case: not relevant
Patient case: 57-year-old male with lung adenocarcinoma; genetic feature: KRAS (G12V), high tumor mutational burden

Clinical trial: Erlotinib in Women With Previously Untreated Adenocarcinoma of the Lung

Summary: The purpose of this trial is to figure out what effects (good or bad) the investigational drug agent called Tarceva (erlotinib; OSI-774) has on women with previously untreated adenocarcinoma.

Detailed description: Patients will start taking Tarceva daily by mouth on Day 1 and will continue taking this medication daily at home, until participation in the study ends.
  Every 28 days (one cycle) while the patient is taking Tarceva, they will be examined in the outpatient clinic (blood test and physical examination) and the doctor will determine if they should continue taking Tarceva.
  After every two cycles of treatment (every 8 weeks) standard radiological testing (CT scans, MRIs, and/or x-rays) of the cancer site(s) will be done to assess the response to the Tarceva treatment.
  While the patient is on this study and at the end of the study, the patient will undergo blood and urine tests, medical history evaluation, physical exams including measures of vital signs (blood pressure, heart rate, temperature, and respiration), bone scans, tumor biopsy sample, and various radiological tests to monitor the cancer and the patients health.
  The length of time on the study depends upon how the cancer responds to Tarceva and whether or not the patient experiences unacceptable side effects.

Eligibility: Inclusion Criteria:
  -  Female
  -  Diagnosis of adenocarcinoma of the lung
  -  Patient has had at least one core biopsy of her tumor
  -  Must be willing to undergo epidermal growth factor receptor (EGFR) mutation testing of her tumor
  -  Stage IV or IIIB non-small cell lung cancer
  -  Non-smoker or former smoker. Non-smoker is defined as a person who smoked 100 or less cigarettes in her lifetime while a former smoker is defined as a person who has quit smoking one or more years ago.
  -  Three or more weeks since last radiation therapy
  -  Three or more weeks since last major surgery
  -  Must at least be able to walk and capable of taking care of herself although unable to carry out work activities
  -  Life expectancy of 8 weeks or more
  -  Blood tests that show kidneys, liver and bone marrow to be working adequately
  -  Women of child-bearing potential must agree to use adequate contraception prior to study entry and for the entire time enrolled in study
  Exclusion Criteria:
  -  Prior exposure to Tarceva (OSI-774, erlotinib)
  -  Uncontrolled central nervous system problems
  -  Prior chemotherapy regimen
  -  Difficulty swallowing
  -  A disease or disorder that interferes with ability to digest and absorb food
  -  Incomplete healing of previous oncologic or other major surgery
  -  Significant medical history or unstable medical condition such as heart failure, active infection, uncontrolled high blood pressure
  -  Pregnant or breast feeding
  -  A medical condition that could make it unsafe for patient to participate in this study

Relevance to patient case: not relevant
Patient case: 57-year-old male with lung adenocarcinoma; genetic feature: KRAS (G12V), high tumor mutational burden

Clinical trial: Genetic Epidemiological Study of Lung Cancer in Taiwan and Clinical Applications

Summary: Lung adenocarcinoma in Chinese females is hypothesized to be determined by both genetic and environmental factors. In this grant proposal, we propose to map the loci of susceptibility genes of female lung adenocarcinoma based on multiplex families recruited in Taiwan. We focus on a unique pathological type of a unique population in order to reduce heterogeneity of the genetic background. Compared with western women, female Chinese population has a high prevalence of lung adenocarcinoma. Our reasoning is that if we focus on a specific sub-type, which has a familial basis, we will increase the probability of identifying genes associated with female lung adenocarcinoma. The primary goal of this study is to identify the genetic and environmental determinants of female lung adenocarcinoma, and study the relationship between gene polymorphisms and clinical manifestation profiling of lung cancer.

Detailed description: This research proposal intends to integrate epidemiologists, biostatisticians, clinicians, molecular biologists/geneticists to identify susceptible genes for lung cancer, especially for female lung adenocarcinoma, and to study the relationship between gene polymorphisms and clinical outcomes of lung cancer patients. Our objective is to find gene markers for developing useful screening tools for the high risk group in order to prevent or early detect lung cancer, especially female lung adenocarcinoma.
  The specific aims of this subproject include:
  1. Establish and maintain the research network that will recruit and follow up the subjects and families for the GEFLAC study; keeping control of the progress of the study.
  2. Coordinate all the subprojects such as integrating genotyping data with clinical data and environment data.
  3. Continue to employ the candidate gene approach to examine the contribution of specific genes to the lung cancer.
  4. Generate genotyping data for candidate genes in the exploring stage and prioritize SNPs of candidate genes for large scale studies.
  5. Identify susceptible genes/candidate genes to develop multiplex PCR for screening.

Eligibility: Inclusion Criteria:
  -  lung adenocarcinoma
  Exclusion Criteria:
  -

Relevance to patient case: possibly relevant