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

Clinical trial: Gastric Acid Suppression and Probiotic Colonization

Summary: Probiotics are over-the-counter dietary products with microorganisms that are generally consumed for health benefit. However, the durability of these microorganisms is unclear, particularly when it passes through the highly acidic environment of the stomach. We will test the colonization of these microorganisms among individuals who consume probiotics with and without acid suppression therapy.

Detailed description: Probiotics are over-the-counter dietary products with microorganisms that are generally consumed for health benefit. However, the durability of these microorganisms is unclear, particularly when it passes through the highly acidic environment of the stomach. We will test the colonization of these microorganisms among individuals who consume probiotics with and without acid suppression therapy.
  All activities will be related to research. Participants will be randomized to receive either over-the-counter acid suppression medication or placebo from weeks -2 through week 4. All participants will receive VSL #3 (over-the-counter probiotic) from weeks 0 through 4. Survey data, serum, and stool samples will be collected at weeks -2, 0, and 4.
  The intervention medication and probiotics have a very low side effect profile and are available over the counter. All data collection methods are non-invasive.
  Elucidation of the effects of acid suppression on probiotic colonization will allow us to better understand the utility of probiotics use by individuals on acid suppression medications.

Eligibility: Inclusion Criteria:
  -  Healthy volunteers ages 18 years and ≤ 75 years.
  -  Able to visit the study Doctor's office 3 times, answer 3 questionnaires, and provide stools and blood samples.
  Exclusion Criteria:
  -  Gastric cancer, Barrett's esophagus cancer, any gastrointestinal condition, or soy or gluten sensitivity
  -  Previous abdominal surgery
  -  Currently pregnant or nursing
  -  Had H. Pylori Infection
  -  Diagnosed with any chronic medical condition other than hypertension or hyperlipidemia
  -  Currently consuming herbs or probiotics

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

Clinical trial: Systemic Screening for Hereditary Colorectal Cancer in China

Summary: The purpose of the this study is to determine the prevalence of germline cancer susceptibility gene mutation among Chinese population, and to find best ways to screen patients with colorectal cancer in China. To accomplish this objective, the investigators will establish a large sample database of hereditary colorectal cancer related information using multigene panel testing based on Next-Generation Sequencing.

Detailed description: Hereditary factors play a very important role in colorectal cancer risk. Identification of the germline cancer gene mutation at the time of colorectal cancer presentation has significant implications for the patients and families, as it directs follow up and clinical options. Professional guidelines recommend patients with colorectal cancer receive a phenotype-driven genetic testing strategies. For example，Lynch syndrome was identified in 2%-4% of patients with CRC using micro-satellite instability (MSI) or DNA mismatch repair (MMR) protein immunohistochemistry (IHC) tumor testing in preselected patients for germline MMR gene testing. However, there is few of clinical characteristics or germline gene mutation data from Chinese population. With the advent of next-generation sequencing (NGS), genetic testing for hereditary CRC has shifted from phenotype-specific single gene assessment to broad panels providing simultaneous assessment of multiple genes implicated in various hereditary cancer syndromes. This study plans to screen and establish a database of 500 consecutive newly diagnosed patients with CRC using multigene panel testing based on Next-Generation Sequencing. The purpose of this study is to:
  1. Determine the prevalence of hereditary colorectal cancer and spectrum of germline cancer gene mutation among Chinese population.
  2. Evaluate the cost-effectiveness and optimize the design of multigene panel testing.
  3. Establish a statewide screening model for hereditary colorectal cancer.

Eligibility: Inclusion Criteria:
  1. Newly diagnosed with colorectal adenocarcinoma (all stages) patients. For individuals who are old than 70 years old should meet the revised Bethesda Guidelines or polyposis syndromes testing criteria.
  2. Agree to provide related information.
  Exclusion Criteria:
  1. Individuals who are under the age of 18.
  2. Individuals who refuse to test.

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 Imaging, Blood, and Tissue Samples to Guide Treatment of Colon Cancer and Related Liver Tumors

Summary: The purpose of this study is to explore novel ways of diagnosing colon cancer and predicting its propensity to spread to other organs such as the liver.


Eligibility: Inclusion Criteria:
  -  Patients must be undergoing one of the following procedures as part of their routine care in order to meet the inclusion criteria:
  -  Operation for presumed stage I-IV colon cancer including colectomy, hepatectomy, or abdominal surgery (e.g. insertion of HAIP)
  -  Colectomy for presumed benign or pre-malignant colon tumors (e.g. large nonneoplastic polyps or adenomas)
  -  Open, laparoscopic, or robotic resections
  -  ≥18 years old
  Exclusion Criteria:
  -  Extrahepatic CRC metastasis
  -  No preoperative portal venous phase CT scan performed up to two months prior to day of surgery Pathology demonstrating a malignant tumor other than colorectal adenocarcinoma.
  -  Stage IV colon cancer with resectable hepatic disease undergoing hepatectomy with active primary colon tumor still in place (despite chemo-radiation therapy) and no plans for colectomy.
  -  Receipt of experimental therapies for colon cancer (e.g. checkpoint inhibitors or novel targeted agents). Of note, approved targeted agents (such as anti-angiogenic agents, EGFR inhibitors etc) are not an exclusion criterion.
  -  History of non-colonic malignancy w/in 5 years (except non-melanomatous skin cancer)
  -  Colon cancer with microsatellite instability (MSI-high) if known preoperatively
  -  Known hereditary colon cancer syndrome such as familial adenomatous polyposis (FAP) or hereditary nonpolyposis colorectal cancer (HNPCC)
  -  Known liver disease (e.g. non-alcoholic steatohepatitis, cirrhosis, viral or other form of hepatitis, etc)
  -  INR >2 or known clotting factor deficiency
  -  Anticipated need for full anticoagulation during hospitalization
  -  Receipt of medications that increase significantly the risk of bleeding after liver biopsy (at the surgeon‟s discretion)
  -  Intraoperative discovery of pathology that precludes the planned surgical resection or liver biopsy, or makes resection futile (such as peritoneal carcinomatosis or other extrahepatic metastatic disease)
  -  Operating surgeon deems research interventions to be more than a minimal risk for the patient

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

Clinical trial: CPI-006 Alone and in Combination With CPI-444 and With Pembrolizumab for Patients With Advanced Cancers

Summary: This is a phase 1/1b open label, multicenter, dose-selection study of CPI-006, a Type 2 humanized IgG1 antibody inhibiting enzymatic activity of CD73 and adenosine production. This trial will study the safety, tolerability, and anti-tumor activity of CPI-006 as a single agent, in combination with CPI-444, a small molecule targeting the adenosine-A2A receptor on immune cells, and in combination with pembrolizumab, an anti-PD1 antibody against various solid tumors and Non-Hodgkin lymphoma.

Detailed description: This is a phase 1/1b open label, multicenter, dose-selection study of CPI-006, a Type 2 humanized IgG1 antibody inhibiting enzymatic activity of CD73 and adenosine production. This trial will study the safety, tolerability, and anti-tumor activity of CPI-006 as a single agent, in combination with CPI-444, a small molecule targeting the adenosine-A2A receptor on immune cells, and in combination with pembrolizumab, an anti-PD1 antibody against various solid tumors and Non-Hodgkin lymphoma. This trial is composed of dose escalation and dose expansion cohorts.

Eligibility: Inclusion Criteria:
  1. Eastern Cooperative Oncology Group (ECOG) Performance Status 0-1.
  2. Documented incurable cancer with one of the following histologies: nonsmall cell lung cancer, renal cell cancer, triple negative breast cancer, colorectal cancer with microsatellite instability(MSI), bladder cancer, cervical cancer, uterine cancer, sarcoma, endometrial cancer, and metastatic castration resistant prostate cancer.
  3. At least 1 measurable lesion per Response Evaluation Criteria in Solid Tumors (RECIST 1.1).
  4. At least 1 but not more than 5 prior systemic therapies for advanced/ recurrent or progressing disease.
  5. Willingness to provide tumor biopsies.
  Exclusion Criteria
  1. History of severe hypersensitivity reaction to monoclonal antibodies.
  2. Subjects who have received prior therapy with regimens containing cytotoxicT-lymphocyte antigen-4 (CTLA-4), programmed cell death ligand 1 (PDL1), or PD1 antagonists are NOT permitted to enroll unless all adverse events (AEs) while receiving prior immunotherapy have resolved to Grade 1 or baseline prior to screening.
  3. History of (non-infectious) pneumonitis that required steroids or subject has current pneumonitis.
  4. The use of any investigational medication or device in the 30 days prior to screening and throughout the study is prohibited.
  5. Symptomatic, untreated, or actively progressing central nervous system (CNS) metastases.

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

Clinical trial: Universal Endometrial Cancer DNA Sequencing for Detection of Lynch Syndrome and Personalized Care

Summary: This clinical trial studies universal screening for deoxyribonucleic acid (DNA) mismatch repair deficiency in patients with endometrial cancer, mutations in the genes responsible for Lynch syndrome (inherited forms of endometrial cancers) and other DNA changes that could help guide treatment strategies. Universal tumor DNA sequencing may help doctors better understand how to personalize care, increase length of life, and increase quality of life in patients with endometrial cancer and their relatives.

Detailed description: PRIMARY OBJECTIVES:
  I. Molecular classification of tumor abnormalities through innovative upfront next-generation DNA sequencing.
  II. Identify endometrial cancer (EC) patients with inherited EC, specifically Lynch syndrome (LS), using both tumor and normal (blood) DNA testing.
  III. Develop a comprehensive approach to genetic risk assessment and management including improved cascade testing in at-risk relatives.
  IV. Provide local access to genetic counseling for patients with harmful germline mutations.
  V. Identify molecular signatures that may be associated with favorable response to specific treatments (including chemotherapeutic agents, non-surgical options, and novel clinical trials [in particular, patients with mismatch repair (MMR)-deficient or POLE-mutant tumors]).
  VI. Determine if recurrence likelihood can be predicted from molecular signature.
  VII. Identify EC patients with select molecular signatures for recruitment to long-term follow-up, cancer prevention, and treatment studies.
  OUTLINE:
  Patients with endometrial cancer undergo clinical testing for inherited cancer mutations using blood DNA and via next-generation sequencing of tumor samples. Patients testing positive for Lynch syndrome or other cancer susceptibilities will undergo genetic counseling and testing and counseling will be offered to their family members.

Eligibility: Inclusion Criteria:
  -  Adult women who had a hysterectomy or diagnostic biopsy proving endometrial adenocarcinoma (any stage) between 10/1/2017 and 4/30/2020, and received care at one of the participating hospitals
  -  Adult relatives of the EC patients found to have LS
  Exclusion Criteria:
  -  Individuals must be able to speak and read English; non-English speaking individuals will be excluded
  -  Individuals must be able to consent for themselves; those who are unable to consent for themselves for any reason will be excluded
  -  Prisoners will be specifically excluded from participation in the study
  -  Women who have uterine sarcomas are excluded
  -  Pregnant women are not eligible for the study

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 Relationship Between Microsatellite Instability and Efficacy of Fluorouracil Based Adjuvant Chemotherapy in Gastric Cancer After Operation

Summary: The relationship between Microsatellite instability and efficacy of fluorouracil based adjuvant chemotherapy in gastric cancer after operation.

Detailed description: To explore the relationship between Microsatellite instability and efficacy of fluorouracil based adjuvant chemotherapy in gastric cancer after operation.

Eligibility: Inclusion Criteria:
  1. Histopathology or cytopathology proven gastric cancer;
  2. Operable advanced gastric cancer patients: primary lesions can be completely excision, no distant metastasis;
  3. Postoperative patients who can tolerate 5-FU based (5-FU，S-1 or Capecitabine) adjuvant chemotherapy;
  4. Life expectancy of at least 6 months;
  5. ECOG（Eastern Cooperative Oncology Group ） score 0-1;
  6. Age: 18~80 years old;
  7. Normal hemodynamic indices before the recruitment (including blood cell count and liver/kidney function).
  -  For example: WBC（White blood cell count ）>4.0×109/L; NEU（Neutrophils）>1.5×109/L; PLT（Platelet）>100×109/L;
  8. Roughly normal cardiopulmonary function: No coronary heart disease, myocardial infarction, pulmonary heart disease, refractory hypertension;
  9. Not concomitant with other uncontrollable benign diseases before the recruitment;
  9. Voluntarily signed the informed consent.
  Exclusion Criteria:
  1. Advanced gastric cancer patients with distant metastasis and inoperable ;
  2. Patients who cannot tolerate 5-FU based adjuvant chemotherapy;
  3. Pregnant or lactating women;
  4. Patients who have no desire to participate in the study.

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

Clinical trial: Detect Microsatellite Instability Status in Blood Sample of Advanced Colorectal Cancer Patients by Next-Generation Sequencing

Summary: The method to analyze the microsatellite instability (MSI) status by next-generation sequencing (NGS) has been established to assess the deficiency of DNA mismatch repair (MMR) system. The aim of our study is to evaluate the feasibility and reliability of this NGS method by testing the circulating tumor DNA (ctDNA) in blood sample of advanced colorectal cancer patients. If the result is positive, the MSI status could be easily learned without the acquisition of tissue samples.


Eligibility: Inclusion Criteria:
  -  a biopsy proven histological diagnosis of colorectal carcinoma
  -  MSI status of tissue sample known by IHC or PCR method
  -  willing to participate and informed consent signed
  Exclusion Criteria:
  -  history of other malignant tumors
  -  patients with inflammatory bowel disease
  -  patients with familial adenomatous polyposis
  -  patients treated by surgery or adjuvant treatment
  -  pregnant or lactating women

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

Clinical trial: Detection of MSI in Circulating Tumor DNA of Colorectal Carcinoma Patients

Summary: This pilot trial studies how well serial liquid biopsies work in detecting microsatellite instability in participants with stage IV colorectal cancer. Serial liquid biopsies may help doctors learn better methods to track cancer in the bloodstream and how to use these to improve cancer treatments.

Detailed description: PRIMARY OBJECTIVES:
  I. To test the hypothesis that there is high level of concordance between the electrophoretic mobility profile of microsatellite biomarkers in circulating cell-free deoxyribonucleic acid (ccfDNA) versus in primary tumor tissues in patients with colorectal carcinomas displaying microsatellite instability.
  II. To test the hypothesis that changes in the electrophoretic mobility profile of microsatellite biomarkers in liquid biopsies from patients with colorectal carcinoma correlate with therapeutic responsiveness measured based on Response Evaluation Criteria in Solid Tumors (RECIST) criteria.
  III. To determine whether microsatellite alleles generated as a result of microsatellite instability detectable in liquid biopsy specimens from patients with colorectal carcinoma represent the entire cancer cell population or only a subset of cancer cells differentially affected by genomic instability.
  OUTLINE:
  Participants undergo collection of blood samples to evaluate microsatellite instability via serial liquid biopsies at baseline, then every 6 weeks and at progression or 9 months.

Eligibility: Inclusion Criteria:
  -  Patients newly diagnosed with stage IV colorectal cancer and with defined microsatellite instability status before initiation of systemic immunotherapy.
  -  Trackable cancer-driver mutation in the primary tumor documented before initiation of chemotherapy.
  -  Zubrod performance status of 0 or 1.
  -  Patients have measurable disease according to RECIST version (v)1.1.
  -  Ability to understand and willing to sign a written informed consent.
  Exclusion Criteria:
  -  Severe anemia (hemoglobin [Hb] < 8 g/dL).

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

Clinical trial: Identifying MSI Status From ctDNA in Chinese Patients With Refractory Advanced Solid Tumors

Summary: This is a molecular epidemiological investigation aiming to identify microsatellite instability status from circulating tumor DNA in Chinese patients with refractory advanced solid tumors.

Detailed description: This study is conducted in Chinese patients with advanced refractory metastatic solid tumors. A total of 8-10 mL of blood will be collected from eligible patients and used for extracting circulating tumor DNA. Blood-MSI status will be tested based on SPANOM technique developed by 3D Medicines Inc. Shanghai, China. Patients are encouraged to provide tissues collected from progressive disease for tissue-MSI testing (not required for inclusion).

Eligibility: Inclusion Criteria:
  1. Male or female, age≥18 years old.
  2. Confirmed malignant solid tumor by histopathology or cytopathology.
  3. Colorectal cancer: progression after second-line therapy. Non-colorectal cancer: progression after first-line therapy.
  4. Time duration from the last time of anti-cancer treatment to blood sample collection for MSI testing ≥ two weeks or five times half-life period of anti-cancer drugs
  5. Signed the informed consent with name and time.
  Exclusion Criteria:
  1. Hematological malignancy
  2. Patients who received immuotherapies.
  3. Patients who received blood transfusion within one month before blood collection.
  4. Pregnancy.

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

Clinical trial: Fluoroscopic &Ultrasonographic Guidance of Superior Hypogastric Plexus Neurolysis in Intractable Pelvic Pain

Summary: fluoroscopic group & includes 30 patients where SHPB will be done Fluoroscopic-guided (the posterior oblique trajectory technique.the double modality group & includes 30 patients where SHPB will be done using our described new technique of performing the modified Mishra technique by injecting 3-5 ml of contrast media (lohexol=omnipaque) after getting the target position.


Eligibility: Inclusion Criteria:
  -  Age > 18 years.
  -  Intractable pelvic cancer pain (VAS > 40 mm)
  -  Pain is refractory to pharmacotherapy (both opioids and adjuvant therapy) or opioids' side effects are not tolerated.
  Exclusion criteria
  -  Local or systemic sepsis.
  -  Uncorrectable coagulopathy.
  -  Neuropsychiatric illness.
  -  History of drug abuse.
  -  Pregnant or lactating patients.
  -  Distorted local anatomy.
  -  Patients who are known to be allergic to the used medications.
  -  Cardiovascular or respiratory instability.

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

Clinical trial: Study of Nivolumab and Relatlimab in Advanced Mismatch Repair Deficient Cancers Resistant to Prior PD-(L)1 Inhibitor

Summary: The purpose of this study is to evaluate the safety and clinical activity of nivolumab and relatlimab in patients with microsatellite instability high (MSI-H) solid tumors refractory to prior PD-(L)1 therapy.


Eligibility: Inclusion Criteria:
  -  Age ≥18 years.
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0 or 1
  -  Have metastatic or locally advanced mismatch repair deficient/MSI-H disease.
  -  Patients must have received prior PD-1/PD-L1 inhibitor therapy
  -  Have disease progression.
  -  Patients with the presence of at least one measurable lesion.
  -  Life expectancy of greater than 3 months.
  -  Patients must have adequate organ and marrow function defined by study - specified laboratory tests.
  -  Documented left ventricular ejection fraction (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.
  -  Require any antineoplastic therapy.
  -  History of prior treatment with anti-LAG3.
  -  Had chemotherapy, radiation, or steroids within 14 days prior to study treatment.
  -  Have received any investigational drugs, a live vaccine, any allergen hyposensitization therapy, growth factors or major surgery within 28 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.
  -  Prior life-threatening toxicity to anti-PD-1, anti-PD-L1, anti-PD-L2,or anti-CTLA4
  -  Woman who are pregnant or breastfeeding.

Relevance to patient case: not relevant