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

Clinical trial: Clinical Validation of Stool DNA-based SDC2 Methylation Test for Colorectal Cancer Detection

Summary: Pivotal trials of SDC2 methylation biomarker test in stool DNA to estimate clinical sensitivity and specificity in detection of colorectal cancer.

Detailed description: The purpose of this study is to validate the clinical performance of EarlyTect Colon Cancer test which is measuring Syndecan 2 methylation status in stool DNA to detect CRC. Syndecan 2 (SDC2) is a newly developed methylation biomarker for colorectal cancer diagnosis. Methylation status of SDC2 gene in stool DNA is determined by methylation specific qPCR. Sensitivity and specificity will be determined by comparing Stool DNA test from healthy subjects, CRC patients, and other group including polyps and other diseases.

Eligibility: Inclusion criteria:
  -  sample information is complete, including sample number, gender, family history, stage of cancer, treatment history, and other disease information
  -  the CRC patient who has not any treatment (surgery, chemotherapy, or radiation)
  -  non-CRC patient who has not received any treatment (surgery, chemotherapy, or radiation) within the last 6 months
  -  all of above conditions are satisfied, and any one of below can be applicable; 1) confirm to be CRC with colonoscopy and/or pathological examination, 2) confirm to be inflammatory or ulcerative bowel diseases or benign hyperplastic polyp, 3) confirm to be gastrointestinal or liver cancers who are not CRC, 4) schedule to receive colonoscopy and additional confirmation test for CRC with agreement to provide the test results.
  Exclusion criteria: any one of below can be applicable;
  -  the patient information is not complete and/or does not satisfy inclusion criteria
  -  the sample information is not complete and/or does not satisfy inclusion criteria
  -  the CRC patient who has history of colorectal cancer surgery, chemotherapy, or any other treatment
  -  non-CRC patient who received any chemotherapy within the last 6 months
  -  the patient who has limited ability or are vulnerable to accept clinical trial agreement
  -  the patient who is judged as not suitable for clinical trial including a psychiatric disorder by a physician

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

Clinical trial: Efficacy of Postoperative Adjuvant Chemotherapy for Stage II Colon Cancer With High Risk Factors(EPAC1)

Summary: The purpose of this study is to design a prospective randomized clinical trial to explore whether postoperative adjuvant chemotherapy may provide survival benefit for stage II colon cancer patients with high risk factors.Therefore the investigators can provide high level clinical evidence of indications for patients with colon cancer with stage II colon cancer.

Detailed description: The most controversial of adjuvant chemotherapy for colon cancer is whether stage II colon cancer should receive adjuvant chemotherapy or not. Because of the absolute little benefit of adjuvant chemotherapy after curative resection of stage II colon cancer，NCCN and ESMO guidelines do not recommend routine adjuvant chemotherapy for patients with stage II colon cancer unless combined with high risk factors.
  Currently，most studies about stage II colon cancer with high risk factors were retrospective. Some suggested that patients with stage II colon cancer can benefit from adjuvant chemotherapy, however, more got the negative conclusions.
  The study was designed as a multicenter, prospective, randomized, controlled trial.Patients who agreed to participate in the study would be randomly assigned to a treatment group of adjuvant chemotherapy or observation with 50% chance by a central randomization system determined by the computer program.
  After a follow up of at least 3 years, the disease free survival of the two groups will be compared.

Eligibility: Inclusion Criteria:
  1. aged 18 to 75 years;
  2. pathologically confirmed adenocarcinoma of the colon
  3. after curative resection pathological stage was T3-4N0M0;
  4. with at least one of the following factors:
  1. T4 staging
  2. lymph nodes number less than 12
  3. poor differentiation (except MSI-H)
  4. LVI or PNI
  5. obstruction or perforation
  6. Elevated preoperative serum CEA
  5. ECOG Performance status 0-1
  6. no evidence of distant metastases
  7. no preoperative chemotherapy or chemoradiation therapy
  8. ANC > 1.5 cells/mm3, HGB > 10.0 g/dL, PLT > 100,000/mm3, total bilirubin ≤ 1.5 xULN, AST≤ 3 x ULN, ALT ≤ 3 x ULN.
  9. Patients must read, agree to, and sign a statement of Informed Consent prior to participation in this study.
  Exclusion Criteria:
  1. combined with other cancer
  2. Creatinine level greater than 1.5 times the upper limit of normal.
  3. Patients who have received preoperative chemotherapy or chemoradiotherapy.
  4. Patients with a history of a prior malignancy within the past 5 years.
  5. Women who are pregnant or breast-feeding.
  6. patients may not complete the whole schedule of chemotherapy
  7. Patients with any other concurrent medical or psychiatric condition or disease which would make them inappropriate candidates for entry into this 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: Management of Women With BRCA1/2 Mutation

Summary: The aim of this study is to determine general practitionners' role in management of women with BRCA1/2 mutation.
  This study will be conduct between April 2017 and December 2017 at Montpellier University Hospital on women followed-up in the department of genetics and their general practitionners (GP). Patients and their GP will be called by the investigators and questionnaire will be given to them. Questionnaire includes questions for patients and their GP. The primary endpoint was to determine the rate of GP having sufficient knowledge of the adequate management of patients with BRCA1 / 2 mutation. Adequate knowledge includes : systematic search for a family history of cancer, knowing criteria required to refer women in oncogenetic department, and the ability to respond to patients' questions. Secondary endpoint was to determine women' opinion on their GP : whether or not well managed for their BRCA 1 / 2 mutation.

Detailed description: PURPOSE: The aim of this study is to determine general practitionners' role in management of women with BRCA1/2 mutation.
  METHODS:
  This study will be conduct between April 2017 and December 2017 at Montpellier University Hospital on women followed-up in the department of genetics and their general practitionners (GP). Patients and their GP will be called by the investigators and questionnaire will be given to them. Questionnaire includes questions for patients and their GP. The primary endpoint was to determine the rate of GP having sufficient knowledge of the adequate management of patients with BRCA1 / 2 mutation. Adequate knowledge includes : systematic search for a family history of cancer, knowing criteria required to refer women in oncogenetic department, and the ability to respond to patients' questions. Secondary endpoint was to determine women' opinion on their GP : whether or not well managed for their BRCA 1 / 2 mutation.

Eligibility: Inclusion criteria
  -  Aged over 18
  -  Women
  -  Living in France
  -  Having a medical insurance
  Exclusion criteria
  -  Men
  -  Dementia
  -  Non frenchspeaker
  -  Mental retardation
  -  Being the subject of a guardianship or tutelage measure

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

Clinical trial: High Definition Endoscopy and Virtual Chromoendoscopy Versus Standard Resolution Endoscopy in Detection of Colon Polyps

Summary: Over the last years a number of new endoscopic imaging modalities have been introduced (high-definition and virtual chromoendoscopy). Given the theoretical advantage of these new imaging techniques, the investigators aimed to investigate their use for the detection of polyps during colonoscopy.


Eligibility: Inclusion Criteria:
  -  referred for colonoscopy
  -  signed informed consent
  Exclusion Criteria:
  -  subtotal colectomy
  -  known colorectal tumor or polyp prior to colonoscopy
  -  genetic predisposition to colon cancer namely FAP, HNPCC, Hyperplastic polyposis syndrome, juvenile polyposis, Peutz-Jeghers syndrome
  -  inflammatory bowel disease
  -  primary sclerosering cholangitis

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

Clinical trial: Choice Architecture and Colorectal Cancer Screening Outreach

Summary: This pilot study is a 3-arm randomized control trial assessing the effectiveness of sequential or active choice in CRC (colorectal cancer) screening outreach vs. colonoscopy outreach only, in patients between 50-74 years old, who have received care at the University City or Valley Forge CCA (Community Care Associates) practices, are due for screening, and are asymptomatic for CRC. The three arms are: Arm 1: Direct schedule colonoscopy (Control), Arm 2: Direct schedule colonoscopy followed by mailed FIT(Fecal Immunochemical Test) (Sequential Choice), and Arm 3: Choice of direct schedule colonoscopy or mailed FIT (Active Choice).

Detailed description: This pilot study is a 3-arm randomized control trial assessing the effectiveness of sequential or active choice in CRC screening outreach vs. colonoscopy outreach only. The investigators will randomize participants to one of three study arms:
  Arm 1: Direct schedule colonoscopy (Control) Arm 2: Direct schedule colonoscopy followed by mailed FIT (Sequential Choice) Arm 3: Choice of direct schedule colonoscopy or mailed FIT (Active Choice).

Eligibility: Inclusion Criteria:
  -  Between 50 and 74 years old
  -  Has a primary care provider who is a University City or Valley Forge Family Medicine provider
  -  Has had at least 2 office visits at either practice
  -  Is due for colorectal cancer screening
  -  Is asymptomatic for CRC
  -  Subject's zip code is within the Philadelphia-Wilmington-Camden Metropolitan Statistical Area
  Exclusion Criteria:
  -  Has had prior colonoscopy within 10 years, sigmoidoscopy within 5 years, or FOBT/FIT within twelve months of chart review (we will exclude patients who self-report any of the above procedures)
  -  Has a history of CRC or colonic polyps
  -  Has a history of GI cancer
  -  Has a history of confirmed Inflammatory Bowel Disease (IBD)
  -  has a history of colitis other than Crohns disease or ulcerative colitis)
  -  Has a first degree relative that has been diagnosed with CRC
  -  Has had a colectomy
  -  Has been diagnosed with Familial Adenomatous Polyposis (FAP)
  -  Has been diagnosed with Lynch Syndrome (i.e. HNPCC)
  -  Has iron-deficiency anemia
  -  Has a history of lower GI bleeding
  -  Has metastatic (Stage IV) blood or solid tumor cancer
  -  Has end stage renal disease
  -  Has cirrhosis
  -  Has heart failure
  -  Has dementia
  -  Has any other condition that, in the opinion of the investigator, excludes the patient from participating in this 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: p53 Activation in Platinum-Resistant High Grade Serous Ovarian Cancer, a Study of PLD With APR-246

Summary: The purpose of this study is to make a preliminary assessment of the efficacy of a combined APR-246 and PLD chemotherapy regimen in patients with platinum-resistant recurrent high grade serous ovarian cancer (HGSOC) with mutated TP53. In addition, the study aims to assess the safety profile of the combined APR-246 and PLD chemotherapy regimen, to evaluate potential biomarkers, and to assess the biological activity in tumor and surrogate tissues. The trial will enroll at least 25 evaluable patients.


Eligibility: Inclusion Criteria:
  -  Confirmed High Grade Serous Ovarian Cancer, and positive nuclear immunohistochemical (IHC) staining for p53
  -  Disease Progression between 4 weeks - 6 months after the last platinum-based treatment was administered
  -  At least a single measurable lesion
  -  Adequate organ function prior to registration
  -  Toxicities from previous cancer therapies (excluding alopecia) must have recovered to grade 1 (defined by National Cancer Institute [NCI] Common Terminology Criteria for Adverse Events [CTCAE] version 4.0). Chronic stable grade 2 peripheral neuropathy secondary to neurotoxicity from prior therapies may be considered on a case by case basis
  -  ECOG performance status of 0 to 2
  Exclusion Criteria:
  -  Prior exposure to cumulative doses of doxorubicin >400 mg/m2 or epirubicin >720 mg/m2
  -  Hypersensitivity to PLD or to any of the excipients
  -  Unable to undergo imaging by either CT scan or MRI
  -  Evidence of any other medical conditions (such as psychiatric illness, infectious diseases, neurological conditions, physical examination or laboratory findings) that may interfere with the planned treatment, affect patient compliance or place the patient at high risk from treatment related complications
  -  Concurrent malignancy requiring therapy (excluding non-invasive carcinoma or carcinoma in situ)
  -  Is taking concurrent (or within 4 weeks prior to registration) chemotherapy, immunotherapy, radiotherapy, or any ancillary therapy that is considered to be investigational (i.e., used for non-approved indications(s) and in the context of a research investigation). Supportive care measures are allowed. Palliative limited radiation therapy for pain reduction is allowed

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 Universal Screening for Lynch Syndrome in Chinese Patients of Endometrial Cancer

Summary: In patients diagnosed as endometrial cancer by thorough pathologic examinations, Lynch syndromes are screened by (1)immunohistochemical staining (for MLH1, MSH2, MSH6 and PMS2), (2) tests of microsatellite instability and (3) clinical criteria (Amsterdam I or II criteria and Bethesda criteria). For patients with any suspicious discoveries of Lynch syndromes from aforementioned screening methods, a molecular diagnosis with next-generation sequencing for mismatch repair genes (MLH1, MSH2, MSH6, PMS2, and EPCAM) is given to confirm Lynch syndromes. For patients of Lynch syndromes and endometrial cancer, relatives of blood lineage are tested by Sanger method or qPCR to find out carriers of mutation genes of Lynch syndromes.


Eligibility: Inclusion Criteria:
  -  Survivals of endometrial cancer
  Exclusion Criteria:
  -  Metatatic malignacies to uterine
  -  Leiomyosarcoma of uterus

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

Clinical trial: Effects of (Licochalcone A) and Paclitaxel on Human Oral Squamous Cell Carcinoma Cell Line

Summary: Oral squamous cell carcinoma (OSCC) are considered as a one of the most malignant cancers. It has prognosis due to its distant metastasis and obvious destruction which lead to low survival rate.
  The conventional treatment modalities such as surgery, radiotherapy and chemotherapy are only the suitable strategies until now. Investigators cannot ignore the serious side effects of chemotherapy such as gastrointestinal upset, bone marrow suppression which cannot be overcome. For all these complications, there is a great need and demand to discover a new agents and strategies for treating OSCC.
  Licorice extract, especially Licochalcone A, is one of many natural extracts that have used as a traditional in treatment of inflammation, microbial infections. Regarding antitumor effect, Licochalcone A reveals interesting results in programmed cell death and apoptosis in cancer cells such as prostate, bladder, colon and gastric cancer.

Detailed description: Oral squamous cell carcinoma (OSCC) is considered the most common human body malignant tumor. It has poor prognosis regarding its distant lymph node metastasis and local destruction which lead to low survival rate.
  Paclitaxel is a chemotherapeutic drug of the taxols group that is used in the treatment of lung, ovarian and prostate cancer. It is also used to treat breast, head and neck cancer as well as sarcoma and leukemia. Recent studies and researches explored that Paclitaxel has an important role in mitotic arrest activation and induction, which subsequently lead to cell death.
  The conventional treatment strategies such as surgery, radiotherapy and chemotherapy come with low levels of expectations regarding prognosis and survival rate. On the other hand, serious side effects of chemotherapy such as renal toxicity, gastrointestinal upset and bone marrow suppression remain hazards which cannot be avoided.Thus, there is a great need to discover new agents and strategies for treating OSCC or even enhancing the effect of chemotherapy in order to reduce the dose given.
  Licorice extract, Licochalcone A, is one of many natural extracts of Glycyrrhiza inflata plant. It has been used in treatment of inflammation, infections and cancer.

Eligibility: Inclusion Criteria:
  1. All head and neck squamous cell carcinoma cell lines
  2. Licochalcone extracts
  3. Taxols group of chemotherapy
  Exclusion Criteria:
  1. Animal experimental studies
  2. Any cancer cell line other than squamous cell carcinoma cell lines.
  3. Any chemotherapeutics other than Taxols group.

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 GEOLynch Cohort Study

Summary: The GEOLynch cohort study has been established to investigate the influence of genetic, environmental and other factors on tumour risk in persons with Lynch syndrome.

Detailed description: The GEOLynch cohort study includes persons with Lynch syndrome (LS) only. Persons with LS carry an inherited mutation in one of the DNA mismatch repair genes MLH1, MSH2, MSH6 or PMS2 which increases their risk of several types of cancer, especially colorectal and endometrial cancer. Additionally, mutations in the EPCAM gene that result in epigenetic silencing of the MSH2 gene cause LS. Since 2006, persons with LS are invited to participate in the GEOLynch cohort study via the Netherlands Foundation for the Detection of Hereditary Tumours, the Radboud University Medical Center Nijmegen or the University Medical Centre Groningen. Moreover, persons with LS can participate in the study after contacting the researcher themselves. Participants are asked to complete a food frequency questionnaire and questionnaires about dietary supplement use, physical activity, weight, height and medication use. A buccal swab was asked of every participant recruited between 2006 and 2008. From 2012 on, newly recruited participants are asked to donate a blood sample instead of a buccal swab. Furthermore, participants who had been recruited between 2006 and 2008 were asked to complete the questionnaires again and to donate a blood sample too. Hence, follow-up measurements are available for a subset of participants. DNA has been subtracted from the buccal swabs to genotype SNPs of the IGF gene axis and polymorphisms of MTHFR C377T. Blood samples are biobanked to facilitate future analyses of biomarkers, nutrients, DNA etc. Clinical characteristics regarding performed colonoscopies and tumour diagnoses of all participants is gathered from medical records and a linkage to the nationwide network and registry of histo- and cytopathology in the Netherlands (PALGA Foundation ). Hazard ratios will be calculated to investigate the influence of genetic, environmental and other factor on tumour risk. Repeated measures analyses will be used if follow-up measurements are taken into account.

Eligibility: Inclusion Criteria:
  -  Persons with a known mutation in a gene that causes Lynch syndrome, i.e. with an inherited monoallelic pathogenic germline mutation in either the MLH1, MSH2, MSH6, PMS2 or EPCAM gene.
  -  Aged between 18 and 80 years at inclusion.
  Exclusion Criteria:
  -  Additional carrier of another hereditary colon cancer predisposition syndrome (e.g. FAP)
  -  (Chronic) Inflammatory bowel disease
  -  Non-Dutch speaking
  -  Dementia or another mental condition that makes it impossible to fill out questionnaires
  -  Terminally ill persons

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

Clinical trial: Laparoscopic Surgery for T4 Tumor of the Colon Cancer (LST4C Trial)

Summary: The purpose of this study is to compare the short- and long-term survival of laparoscopic surgery and conventional open surgery for T4 colon cancer

Detailed description: The investigators previous study indicated that laparoscopic surgery is feasible in T4 colon cancers with comparable clinical and oncologic outcomes. Laparoscopy can be considered as an alternative approach for T4 colon cancers with the advantage of faster recovery. However, the clinical value of laparoscopic surgery for T4 colon cancer was only validated in some retrospective study and some prospective study in single institute with small sample of patients. The aim of the present study is to compare the short-and long-term survival outcomes of laparoscopic surgery and conventional open surgery for T4 colon cancer as well as the mortality and the morbidity. The number of patients needed to get a 80% power is 1960. The average number of patients/surgical center is approximately 200 in each of 10 surgical centers. The preoperative, intraoperative and postoperative period will be in complete accordance with the usual care of the center. The baseline demographics and conditions as well as the perioperative items and the postoperative occurrences will be recorded through a prior designed equestionnaire.
  Systematically analyze and compare the disease free survival rate, the mortality, the morbidity, and the proportion of completion of laparoscopic surgery of the two surgical strategies (laparoscopy VS conventional open surgery).

Eligibility: Inclusion Criteria:
  -  Able to provide written informed consent
  -  Histologically confirmed diagnosis of colon carcinoma
  -  CT or MRI verified as T4 colon cancer without involvement of other organs
  -  Without multiple lesion other than carcinoma in situ
  -  Tumor size < 8 cm
  -  No bowel obstruction
  -  Sufficient organ function
  -  No history of gastrointestinal surgery
  -  18 years of age or older
  -  Performance Status (ECOG) 0, 1 or 2 and life expectancy > 12 weeks
  -  Operable patients
  Exclusion Criteria:
  -  • Women who are pregnant (confirmed by serum b-HCG in women of reproductive age) or breast feeding
  -  Unstable or uncompensated respiratory or cardiac disease
  -  Serious active infections
  -  Hypersensitivity to capecitabine/fluorouracil or oxaliplatin
  -  Stomatitis, ulceration in the mouth or gastrointestinal tract
  -  Severe diarrhea
  -  Peripheral sensory neuropathy with functional impairment

Relevance to patient case: not relevant