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

Clinical trial: Metagenomic Evaluation of the Gut Microbiome in Patients With Lynch Syndrome and Other Hereditary Colonic Polyposis Syndromes

Summary: The purpose of this study is to understand the role bacteria that normally live in the colon may play in colorectal cancer risk, in addition to the hereditary risk to colorectal cancer. The investigators will collect stool specimens as well as additional colon biopsy specimens during the patient's scheduled colonoscopy procedure. The investigators will also collect a questionnaire about diet and lifestyle. The samples will be used to study the impact of diet on naturally-occurring oral and gut bacteria and their influences on human health including risk of cancer.


Eligibility: Inclusion Criteria:
  -  Male or Female age 18 or older
  -  Hereditary colorectal cancer syndrome with one of the following:
  -  Lynch syndrome, as defined by the presence of a deleterious germline mutation in the MLH1, MSH2, MSH6, PMS2 or EPCAM genes
  -  Other hereditary colonic polyposis syndromes, as defined by the presence of a deleterious germline mutation in any one of the following polyposis genes (APC, biallelic MYH, STK11, SMAD4, BMPR1A, or other CRC-risk associated genes at discretion of PI)
  Exclusion Criteria:
  -  Unable to provide informed consent for testing
  -  Unable to complete English language questionnaire
  -  Receiving active chemotherapy
  -  Having completed active chemotherapy less then 12 months prior to day of scheduled lower endoscopy
  -  No infectious or drug induced colitis less then 12 months prior to day of scheduled lower endoscopy
  -  No history of inflammatory colitis (Crohn's disease or ulcerative colitis)

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 Multicenter Study of Active Specific Immunotherapy With OncoVax® in Patients With Stage II Colon Cancer

Summary: OncoVAX® is the first cancer vaccine that both prevents cancer recurrence and
  addresses the diversity of cancer cells. In this pivotal randomized, multicenter Phase
  IIIb study in patients with Stage II colon cancer, OncoVAX is designed to use a patient's
  own cancer cells to mobilize the body's immune system to prevent the return of colon
  cancer following surgery.

Detailed description: OncoVAX is an active specific immunotherapeutic (ASI) stimulating a patient's immune
  response to autologous (patient-specific) tumor cells. It is comprised of sterile, live but
  non-dividing tumor cells obtained following standard-of-care surgical tumor resection for
  Stage II colon cancer. Within 35 days following surgery, patients are immunized with
  OncoVAX to prevent disease recurrence, which is incurable and occurs in up to 35% of
  patients. Patients are given three vaccinations once per week for three weeks, followed
  by a booster vaccination after six months. A previously completed Phase III trial
  published in The Lancet showed that OncoVAX cut the risk of recurrence by 61% in
  patients with Stage II colon cancer. The primary endpoint is Disease-Free Survival:
  defined as the time from curative surgery to the objective test confirming tumor
  recurrence or death due to any cause. The secondary endpoints are Overall Survival
  and Recurrence-Free-Interval. An interim analysis will be performed at a significance
  level of 0.005 once 2/3 of anticipated events have occurred, resulting in a significance
  level of 0.0483 at the end of the study. A total of 550 patients is planned, randomized
  1:1 to receive OncoVAX® plus surgery (n=275) or surgery alone (n=275).

Eligibility: Inclusion Criteria:
  -  Patients must have Stage II (IIA = T3N0M0, IIB = T4aN0M0, IIC = T4bN0M0) disease.
  -  Patients must have undergone curative resection and have no evidence of residual or metastatic disease.
  -  Following curative resection patients must have a CEA within normal limits. If elevated prior to resection, it must return to normal within 21 days post surgery and prior to randomization.
  Exclusion Criteria:
  -  Patients with prior radiation therapy or chemotherapy or a prior malignancy of any type will be excluded. However, subjects with prior, curatively-treated squamous cell or basal cell carcinoma of the skin or carcinoma in situ of the cervix will be eligible for participation in this study.
  -  Patients with more than one malignant primary colon cancer will be excluded.

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 Pilot Study Evaluate the Safety and Efficacy of Sirolimus in Patients With PIK3CA Mutation and/or PIK3CA Amplification Refractory Solid Tumors

Summary: This study is a single-arm, phase II study of sirolimus in patient with PIK3CA mutation and PIK3CA amplication Refractory solid tumors.
  sirolimus 1mg will be administered orally qd daily.
  To investigate the efficacy of sirolimus in patients with PIK3CA mutation and PIK3CA amplication Refractory solid tumors.


Eligibility: Inclusion Criteria:
  1. Provision of fully informed consent prior to any study specific procedures.
  2. Patients must be ≥20 years of age.
  3. PIK3CA amplification and/or PIK3CA mutation Refractory Solid Tumors.
  4. ECOG performance status 0-2.
  5. Have measurable or evaluated disease based on RECIST1.1. as determined by investigator.
  6. Adequate Organ Function Laboratory Values
  -  Absolute neutrophil count ≥ 1.5 x 109/L, Hemoglobin ≥ 9g/dL, Platelets ≥ 100 x 109/L
  -  bilirubin ≤ 1.5 x upper limit of normal AST/ALT ≤ 2.5 x upper limit of normal (5.0 X upper limit of normal , for subjects with liver metastases)
  -  creatinine ≤1.5 x UNL
  7. Patients of child-bearing potential should be using adequate contraceptive measures (two forms of highly reliable methods) should not be breast feeding and must have a negative pregnancy test prior to start of dosing.
  8. Adequate heart function.
  Exclusion Criteria:
  1. Patients with second primary cancer, except: adequately treated non-melanoma skin cancer, curatively treated in-situ cancer of the cervix, or other solid tumours curatively treated with no evidence of disease for ≤5 years.
  2. Has known active central nervous system (CNS) metastases.
  3. Has an active infection requiring systemic therapy.
  4. Pregnancy or breast feeding
  5. Patients with cardiac problem.

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

Clinical trial: Afatinib and Selumetinib in Advanced KRAS Mutant and PIK3CA Wildtype Non-small Cell Lung Cancer

Summary: This is a multi-center open-label proof-of-concept study consisting of two parts: PART A - a phase I dose-finding study (3 + 3 classical design) evaluating the RP2D of afatinib in combination with selumetinib in KRASm NSCLC; and PART B - a randomized phase II study investigating the progression free survival and safety of selumetinib/afatinib combination therapy compared to standard of care chemotherapy in KRASm NSCLC.


Eligibility: Inclusion Criteria:
  -  Histological or cytological proof of advanced NSCLC; for PART B: treated with first line therapy for metastatic disease only.
  -  Written documentation of a known pathogenic KRAS (exon 2, 3 or 4) mutation and PIK3CA wildtype (defined as absence of mutations in exon 9 and 20)
  -  Able and willing to give written informed consent
  -  Able and willing to undergo blood sampling for PK and PD analysis
  -  Life expectancy >=3 months allowing adequate follow up of toxicity evaluation and antitumor activity.
  -  WHO performance status of 0 or 1.
  -  Able and willing to undergo a tumor biopsies prior to start, after two weeks (part A only) and upon progression of disease
  -  Measurable disease according to RECIST 1.1
  -  Adequate organ system function measured by laboratory values
  Exclusion Criteria:
  -  Any treatment with investigational drugs within 30 days prior to receiving the first dose of investigational treatment.
  -  History of another malignancy Exception PART A: Patients who have been disease-free for at least 3 years, or patients with a history of completely resected non-melanoma skin cancer and/or patients with indolent second malignancies are eligible. Exception PART B: Adequately treated carcinoma in situ of the cervix and adequately treated basal cell carcinoma of the skin. 3. Symptomatic or untreated leptomeningeal disease.
  -  Symptomatic brain metastasis.
  -  Patients previously treated with any drug combination known to interfere with EGFR, HER2, HER3, HER4 or MAPK- and PI3K-pathway components, including inhibitors of PTEN, PI3K, AKT, mTOR, BRAF, MEK and ERK.
  -  History of interstitial lung disease or pneumonitis
  -  Radio-, immuno- or chemotherapy within the last 2 weeks prior to receiving the first dose of investigational treatment. Palliative radiation (1x 8Gy) is allowed.
  -  Opthalmological diseases
  -  Patients with left ventricular ejection fraction (LVEF) < 55%
  -  Patients with cardiac comorbidities
  -  Concomitant or recent use (in the past 14 days) of strong inhibitors and inducers of CYP1A2, CYP2C19, CYP3A4, 3A5 and P-glycoprotein (P-gp)

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 the CD40 Agonistic Monoclonal Antibody APX005M

Summary: This study is a phase 1 open-label dose escalation study of the immuno-activating monoclonal antibody APX005M in adults with solid tumors. Study is intended to establish the maximum tolerated dose and the overall safety and tolerability of APX005M in 3 different administration schedules.

Detailed description: APX005M-001 is an open-label study and comprises a dose-escalation portion of approximately 8 dose level cohorts, plus an expansion cohort.
  Eligible subjects with solid tumors will receive intravenous APX005M every 3 week, every 2 week or every 1 week until disease progression, unacceptable toxicity or death, whichever occurs first.
  Study objectives include:
  -  Evaluate safety of APX005M
  -  Determine the maximum tolerated dose of APX005M
  -  Determine the pharmacokinetic parameters of APX005M: the maximal drug concentration (Cmax), area under the curve of serum concentration over time (Area Under the Curve/ AUC), and half-life (t½).
  -  Preliminary assessment of clinical response

Eligibility: Key Inclusion Criteria:
  -  Histologically documented diagnosis of solid tumor
  -  For subjects in the every 2 week and every 1 week dosing cohorts histologically or cytologically documented diagnosis of urothelial carcinoma, melanoma, squamous cell carcinoma of the head and neck, non-small cell lung cancer, or any solid tumor with high microsatellite instability status (MSI-high)
  -  No known effective therapy options are available
  -  Measurable disease by RECIST 1.1
  -  ECOG performance status of 0 or 1
  -  Adequate bone marrow, liver and kidney function
  -  No toxicities related to prior treatment related toxicities with the exception of alopecia and neuropathy
  -  Negative pregnancy test for women of child bearing potential
  Key Exclusion Criteria:
  -  Any history of or current hematologic malignancy
  -  Major surgery or treatment with any other investigational agent within 4 weeks
  -  Uncontrolled diabetes or hypertension
  -  History of arterial thromboembolic event
  -  History of congestive heart failure, symptomatic ischemia, conduction abnormalities uncontrolled by conventional intervention, or myocardial infarction
  -  Active known clinically serious infections

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

Clinical trial: Synergistic Anti-tumor Effect of ChangTai Keli for Colon Cancer Patients

Summary: The aim of this study is to evaluate the synergistic anti-tumor effect of ChangTai Keli based on chemotherapy for colon cancer patients by a randomized, parallel-group, double-blind, multicenter clinical study.

Detailed description: Although many therapies exist and are being developed to relieve symptoms for colon cancer, there are few randomized controlled clinical trials to evaluate comprehensive Traditional Chinese medicine (TCM) interventions in colon cancer. The aim of this study is to evaluate the synergistic anti-tumor effect of ChangTai Keli based on chemotherapy for colon cancer patients. This is a multi-center, randomized, double-blind, placebo-controlled study to evaluate the synergistic anti-tumor effect of TCM on colon cancer patients. Following a run-in period, approximately 360 subjects will be randomly assigned to conventional chemotherapy treatment group, ChangTai Keli and conventional chemotherapy treatment group for 26 weeks. After the 26 weeks treatment period, subjects in two treatments arms will follow-up 36 months.

Eligibility: Inclusion Criteria:
  1. collaboration from hospital oncology patients in hospital. Confirmed by pathology or cytology for colon cancer, Ⅱ A - Ⅳ period of patients with colon cancer line (or late postoperative palliative chemotherapy).
  2. age > 18 years of age, and the 75 - year - old patient or less;
  3. fitness score (ECOG PS) 2 minutes or less, expected lifetime > 6 months;
  4. volunteered for the clinical research, and sign the informed consent.
  Exclusion Criteria:
  1. patients with other primary malignant tumors within 1 year;
  2. intentional, severe liver and kidney disease patients with serious obstacle and function;
  3. pregnancy or lactation women, mental disorders to cooperate to complete the healer;
  4. is in other subjects or attended other drugs test interval < 3 months.
  5. do not meet 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: QoLiCOL - Quality of Life in Colon Cancer

Summary: All patients presenting at participating hospitals during the recruitment period with a newly diagnosed colon cancer, regardless of stage and planned treatment, will be eligible for inclusion. They will answer a questionnaire on health related quality of life, physical symptoms, functional impairments and socioeconomic status at diagnosis and after 12, 36 months. Clinical data including recurrence, survival, surgical treatment, oncologic result (pathology report) and adjuvant treatment will be collected from the Swedish ColoRectal Cancer Registry (SCRCR)

Detailed description: QoLiCOL is an explorative, prospective, longitudinal, non-interventional, international, multicenter study of health-related quality of life, physical symptoms, functional impairments and socioeconomic burden in colon cancer patients. All patients presenting at participating hospitals during the recruitment period with a newly diagnosed rectal cancer, regardless of stage and planned treatment, will be eligible for inclusion. Patients will be followed for 3 years. They will be asked to answer questionnaires at three different time points during follow-up: at diagnosis and after 12 and 36 months. Clinical data, including recurrence, surgical treatment, oncologic result (pathology report) and adjuvant treatment will be collected from the national quality registry for rectal cancer in Denmark and Sweden. As these registries differ in some areas between the countries, additional data will be collected through short CRF:s.

Eligibility: Inclusion Criteria:
  -  Colon cancer newly diagnosed.
  -  Planned treatment presented
  Exclusion Criteria:
  -  No Colon cancer diagnosis,
  -  below 18 years of age,
  -  no informed consent or withdrawn informed consent.

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

Clinical trial: NBI Versus Indigo Carmine During Colonoscopy in Lynch Syndrome

Summary: This study compares two colonoscopy techniques (with Narrow Band Imaging versus with indigo carmine chromoendoscopy) in patients having Lynch Syndrome

Detailed description: Chromoendoscopy using indigo carmine dye is recommended every 1 to 2 years in patients having Lynch Syndrome (LS). However, it is a time-consuming procedure, requiring a prior learning and has an additional cost, the reason why it is not yet systematically practiced in all endoscopy centers. The "Narrow Band Imaging" (NBI) is a recent virtual chromoendoscopy technique using optical filters at the light source of the endoscope to highlight the vascular structures of the mucosa by pressing a button. NBI is currently used to better characterize dysplasia lesions in the esophageal, gastric, and colon mucosa. A new generation (3rd generation) of NBI is currently available on some endoscopes, it can deliver more brightness and contrast, and could allow for better detection of flat lesions. Until today, no study has directly compared colonic chromoendoscopy with Indigo carmine to virtual chromoendoscopy with NBI (3rd generation) in LS patients. The hypothesis that this research aims to verify is that the new generation NBI system might do at least as well as indigo carmine in colonic adenoma detection in LS. This study aims to compare colonoscopy with virtual chromoendoscopy using 3rd generation NBI system to chromoendoscopy with indigo carmine in LS patients, in a back-to-back, prospective non inferiority design, in which all patients will have both techniques in the following order: NBI first followed by Indigo carmine.

Eligibility: Inclusion Criteria:
  -  Lynch Syndrome with an identified mutation in one of the genes MutL Homolog 1 (MLH1), MutL Homolog 2 (MLH2), MutS homolog6 (MSH6), PMS2 or epithelial cellular adhesion molecule (EpCAM)
  -  Age between 18 and 80
  -  Indication of a screening colonoscopy
  Exclusion Criteria:
  -  Any sign of intestinal occlusion contra-indicating bowel preparation
  -  History of total or subtotal colectomy
  -  Any serious medical condition contra-indicating colonoscopy under general anesthesia
  -  Pregnant or breast feeding women
  -  Any coagulation disorder contra-indicating biopsies or endoscopic resections
  -  Any history of hypersensitivity to indigo carmine
  -  Adults subject to a legal protection measure (guardianship or curatorship)

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

Clinical trial: Transanal Decompression Tube Versus Stent for Acute Malignant Left-sided Colonic and Rectal Obstruction

Summary: The purpose of this study is to compare the clinical outcomes of transanal decompression tube as a bridge to surgery with stent as a bridge to surgery for acute malignant left-sided colonic and rectal obstruction.

Detailed description: Approximately 8-47 % of patients with colorectal cancer will present with colonic obstruction. Left-sided colonic and rectal cancer is responsible for nearly 70% of acute colonic obstruction. Emergency colonic surgery for acute obstruction is associated with a higher mortality and morbidity rate than elective surgery. Preoperative decompression results in a less dilated bowel that is more amenable to an elective surgery. Both transanal decompression tube and stent can serve a good preoperative decompression effect and serve a good bridge to surgery. Investigators aim to compare the clinical outcomes of transanal decompression tube as a bridge to surgery with stent as a bridge to surgery for acute malignant left-sided colonic and rectal obstruction.

Eligibility: Inclusion Criteria:
  1. definite diagnosis of left-side colonic or rectal obstruction;
  2. symptomatic colonic obstruction for less than 1 week;
  3. colonic obstruction caused by a histologically proven malignant colonic tumor
  Exclusion Criteria:
  1. suspected benign colonic or rectal obstruction;
  2. right-side colonic obstruction;
  3. patients with signs of peritonitis;
  4. dysfunction of blood coagulation, active bleeding, active infection, and significant cardiac or pulmonary disease;
  5. patients who do not want to undergo surgery.

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

Clinical trial: Circulating Tumor DNA and Follow-up of BRCA1 Mutation Carriers (CirCa 01)

Summary: BRCA1 carriers who are at high risk of developing either a relapse and/or a new cancer growth will be included. These patients will be followed up during 30 months (2,5 years) with mutated TP53 mutation detection or during 42 months (3,5 years) with mutated TP53 mutation detection and circulating tumor cells detection (CTC) performed at each hospital visit (for technical reason only patients included at Institut Curie will be proposed to participate to the CTC substudy).


Eligibility: Inclusion Criteria:
  1. Patient with no evidence of any invasive tumor mass at inclusion (clinical and, if any, radiological exams)
  2. Carriers of known germline BRCA1 deleterious mutation (a personal history of cancer is NOT mandatory).
  3. Age ≥ 30 years for patient with personal previous history of cancer
  4. Age ≥ 40 years for patient without personal previous history of cancer
  5. Patient who a follow-up visit is scheduled in the including center at least once a year
  6. Patient having health care insurance
  7. Signed informed consent by patient
  Exclusion Criteria:
  1. Patient presenting with invasive tumor masses (e.g. stage IV cancer or localized cancer not yet surgically removed)
  2. Carriers of germline BRCA1 variant of unknown significance
  3. Carriers of germline BRCA2 deleterious mutation or variant
  4. Individuals with a low risk of BRCA1-related tumor growth, i.e. women who underwent prophylactic bilateral mastectomy AND adnexectomy.
  5. Any medical or other condition that in the Investigator's opinion rendered the patient unsuitable for this study
  6. Patient deprived from ability to decide on her own.
  7. Patient unable to have a regular follow up for geographical, social or psychological reasons.

Relevance to patient case: not relevant