araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: A Trial of Capecitabine (Xeloda), Oxaliplatin and Irinotecan in Combination With Bevacizumab in 1st Line Treatment of Metastatic Colorectal Cancer

Summary: A Phase I-II Trial of Capecitabine (Xeloda), Oxaliplatin and Irinotecan in Combination with Bevacizumab in 1st Line Treatment of Metastatic Colorectal Cancer

Detailed description: A Phase I-II Trial of Capecitabine (Xeloda), Oxaliplatin and Irinotecan in Combination with Bevacizumab in 1st Line Treatment of Metastatic Colorectal Cancer

Eligibility: Inclusion Criteria:
  -  Patients with diagnosed Metastatic Colorectal Cancer
  Exclusion Criteria:
  -  Patients with diagnosis other than Metastatic Colorectal Cancer

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: A Phase II Study of Single Agent MEK162 in Patients With Advanced Melanoma

Summary: The study will assess the safety and efficacy of single-agent MEK162 in adult patients with locally advanced and unresectable or metastatic malignant cutaneous melanoma, harboring BRAFV600E or NRAS mutations.


Eligibility: Inclusion Criteria:
  -  Locally advanced or metastatic cutaneous melanoma AJCC Stage IIIB to IV, not potentially curable with surgery
  -  BRAF or NRAS mutation in tumor tissue
  -  All patients enrolled should provide sufficient fresh or archival tumor sample at baseline to enable confirmation of BRAF or NRAS mutations and the additional analyses described in the protocol
  -  Evidence of measurable tumor disease as per RECIST
  -  WHO performance status of 0-2
  -  Adequate organ function and laboratory parameters
  Exclusion Criteria:
  -  History or evidence of central serous retinopathy (CSR), retinal vein occlusion (RVO) or any eye condition that would be considered a risk factor for CSR or RVO
  -  Patients with unstable CNS metastasis
  -  Prior treatment with a MEK- inhibitor
  -  Impaired cardiovascular function
  -  HIV, active Hepatitis B, and/or active Hepatitis C infection
  -  Pregnant or nursing (lactating) women
  -  Women of child-bearing potential UNLESS they comply with protocol contraceptive requirements
  Other protocol-defined inclusion/exclusion criteria may apply.

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: Implementation of Laparoscopy-assisted Surgery for Colon Cancer

Summary: The purpose of this study is to study the implementation of laparoscopy-assisted surgery for cure of colon cancer in daily surgical practice.

Detailed description: Prospective observational study of laparoscopy-assisted surgery for resectable colon cancer with regard to short term and long term outcomes

Eligibility: Inclusion Criteria:
  -  Age >17 years
  -  diagnosis of colon cancer either endoscopically, radiologically or histologically proven
  -  No evidence of disseminated disease on CT scan
  -  T1-3 according to preoperative CT scan
  -  written informed consent to participate
  Exclusion Criteria:
  -  preoperative diagnosis of locally advanced tumor (T4)
  -  suspicion of pathological lymph nodes outside anticipated resection area
  -  contraindications against laparoscopic surgery, e.g. known bowel adhesions, anesthesiological concerns
  -  lack of informed consent

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: A Study of Avastin (Bevacizumab) in Combination With mFOLFOX6 in Treatment-Naïve Patients With Metastatic Colorectal Cancer With or Without K-RAS Mutations, and Comparison to Cetuximab

Summary: This randomized, open-label study will evaluate the safety and efficacy of Avastin (Bevacizumab) added to standard mFOLFOX6 chemotherapy in treatment-naïve patients with Stage IV metastatic colorectal cancer. According to K-RAS gene mutation status, patients will be assigned or randomized to receive either Avastin 5 mg/kg intravenously (iv) on Day 1 of each 2-week cycle or cetuximab 400 mg/m2 iv on Day 1 followed by 250 mg/m2 iv every week, in addition to mFOLFOX6 every 2 weeks. Anticipated time on study treatment is until disease progression or unacceptable toxicity occurs.


Eligibility: Inclusion Criteria:
  -  Adult patients >/= 18 years of age
  -  Histologically confirmed adenocarcinoma of the colon or rectum
  -  Stage IV metastatic disease with at least one measurable metastatic lesion according to RECIST criteria
  -  Tumour tissue sample available for assessment of K-RAS and BRAF genes
  -  Prior radiotherapy must have been completed 4 weeks before randomization
  -  Adequate bone marrow, kidney and liver function
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0-1
  Exclusion Criteria:
  -  Previous chemotherapy for metastatic disease
  -  Completion of adjuvant treatment for colorectal cancer (Stage I, II and III) in the 12 months preceding randomization
  -  Prior treatment with bevacizumab, cetuximab or other EGFR inhibitors
  -  Clinical or radiographic evidence of brain metastases
  -  Clinically significant cardiovascular disease or disorder
  -  History of neoplastic disease other than colorectal cancer in the 3 years prior to start of study treatment, except for successfully treated non-invasive carcinomas such as cervical cancer in situ, basal cell carcinoma of the skin or superficial bladder tumours
  -  HIV, hepatitis B or C infection

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: Ph I Ipilimumab Vemurafenib Combo in Patients With v-Raf Murine Sarcoma Viral Oncogene Homolog B1 (BRAF)

Summary: Treatment of subjects who have metastatic melanoma that expresses an activated mutant form of the BRAF oncogene (V600E) with a combination of the specific BRAF inhibitor, Vemurafenib, and the Cytotoxic T Lymphocyte Antigen 4 (CTLA-4) inhibitor mAb Ipilimumab will be safe and feasible and will show preliminary evidence of anti-tumor efficacy and survival in comparison to historical results following treatment with either agent alone.


Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com.
  Inclusion Criteria:
  -  Metastatic melanoma with activating V600 BRAF mutation
  -  Measurable Tumor
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status (PS) 0-1
  Exclusion Criteria:
  -  Autoimmune disease
  -  Active Brain Metastasis (must be stable after radiation for at least one month)
  -  Prior therapy with immune stimulating agents

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: BRAF V600E Mutations In Papillary Thyroid Carcinoma

Summary: The purpose of this study is to determine whether BRAF V600E mutation in our patients with papillary thyroid cancer has an association with poor prognosis.

Detailed description: Papillary thyroid carcinoma (PTC) is the most common type of thyroid malignancy and BRAF V600E mutation is the most common genetic alteration identified in PTC, ranging from 25 to 80%, with the average rate about 45%. Various studies demonstrated a relationship between BRAF V600E mutation and aggressive characteristics of the cancer, including the worse patient prognosis. But,there are no studies from Turkey regarding this topic. So the investigators will examine BRAF V600E mutation in our patients with PTC and try to assess the role of this mutation in prognosis and further management of the patients.

Eligibility: Inclusion Criteria:
  -  Patients with papillary thyroid cancer
  Exclusion Criteria:
  -  Patients who do not want to be a part of this study

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: the Effect of the Transversus Abdominis Plane (TAP) Block on the Minimal Laparotomy : a Randomized Controlled Trial

Summary: Transversus abdominis plane block (TAP block) is a new regional block for abdominal wall.It had been reported the effect of post-operative pain control in minor abdominal surgery, such as inguinal hernia repair and appendectomy. On the other hand, because of the accurate of the pre-operative images, the minimal laparotomy for colon cancer was accomplished. Thus, the purpose of this study is to investigate the effect, such as analgesic effect, hemodynamic stability, and post-operative morphine consumption, of TAP block in minimal laparotomy.

Detailed description: outcome measures:
  -  Hemodynamic parameters (mean artery pressure, heart rate): recorded at time points of before induction of general anesthesia (baseline), after tracheal intubation immediately, after surgery started 1, 2, 3, 4, 5, 10, 15, 20, 25, and 30 min; then recorded them every 10 mins.
  -  Post-operative morphine consumption: recorded morphine consumption at the time intervals of post-operative 0~6 h, 6~12 h, 12~24 h, 24~36 h, and 36~48 h ,respectively. The total amount of morphine consumption was also counted.

Eligibility: Inclusion Criteria:
  -  Anesthesiologists physical status I-III, ≧ 18 years of age, and needed double-lumen endotracheal tube (DLT) for thoracic surger
  Exclusion Criteria:
  -  increased risk for regurgitation and pulmonary aspiration, history of gastroesophageal reflux, and pregnancy
  -  a tracheostomy or prolonged ventilation on ICU was planned, patients were also excluded

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: Biomarkers to Distinguish Benign From Malignant Thyroid Neoplasm

Summary: This protocol will evaluate microRNA biomarkers in blood and fine-needle aspirate biopsies (FNAB) of thyroid nodules. MicroRNA profiles will be determined and evaluated for their utility in pre-operative diagnosis, in particular to distinguish benign from malignant throid neoplasms. Post-surgical fresh-frozen thyroid cancer tissue will be assessed for somatic mutations, mRNA, and microRNA expression patterns. FFPE tissue will be used to obtain H&E and unstained slides to specific biomarker results using immunohistochemistry.

Detailed description: This protocol requires the collection of blood (5 ml), fine-needle aspirate biopsies (FNAB), and post-surgical thyroid cancer tissue. The post surgical tissue includes fresh-frozen tissue that is considered waste and in excess of that required for pathologic diagnosis, and archived formalin-fixed, paraffin-embedded tissue (FFPE). The blood will be used as a substrate for assessing known markers, including microRNA expression patterns that may be useful to predict disease and thyroid cancer morphotype. The FNABs will be used to screen the potential of markers for pre-operative diagnosis. The post-surgical fresh-frozen thyroid cancer tissue will be used to isolate DNA and RNA in order to assess somatic mutations (RAS and PAX8/PPAR-gamma rearrangement) and messenger RNA, and microRNA expression patterns. The FFPE tissue will be used to obtain H&E and unstained slides to validate results using immunohistochemistry. The goal of these studies is to define molecular markers that will accurately distinguish benign from malignant disease and the multiple thyroid cancer phenotypes. Current methods of distinguishing benign from malignant disease requires a detailed post-surgical analysis and no known markers have yet been identified to reliably differentiate the multiple thyroid cancer morphotypes.

Eligibility: Inclusion Criteria:
  -  Patient with palpable thyroid nodule suspicious for thyroid neoplasm
  -  Patient selected to undergo fine needle biopsy for cytologic diagnosis
  -  Male (18 years of age or older)
  -  Female (18 years of age or older)

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: A Phase I Study of Oral LGX818 in Adult Patients With Advanced or Metastatic BRAF Mutant Melanoma

Summary: CLGX818X2101 is a first-time in-human, phase I study to establish the maximum tolerated dose (MTD) and/or recommended phase 2 dose (RP2D) of daily administered LGX818 (daily, twice daily and/or every-other-day), a RAF kinase inhibitor. Patients with locally advanced or metastatic melanoma harboring the BRAF V600 mutation (during dose escalation phase and expansion phase) and patients with metastatic colorectal cancer harboring the BRAF V600 mutation (during the expansion phase) will be enrolled. The study consists of a dose escalation part were cohorts of patients will receive escalating oral doses of LGX818, followed by a safety dose expansion part were patients will be treated with oral dose of LGX818 given at the MTD or RP2D.


Eligibility: Inclusion Criteria:
  For the dose escalation phase:
  1. Histologically confirmed diagnosis of locally advanced or metastatic melanoma (stage IIIB to IV per American Joint Committee on Cancer [AJCC]). For the dose expansion phase: (i) Histologically confirmed diagnosis of locally advanced or metastatic melanoma (stage IIIB to IV per American Joint Committee on Cancer [AJCC]), or (ii) confirmed diagnosis and non-resectable advanced metastatic colorectal cancer (mCRC) for which no further effective standard therapy exists.
  2. Written documentation of BRAF V600E mutation, or any other BRAF V600 mutation.
  3. Evidence of measurable disease
  Exclusion Criteria:
  1. Previous therapy with a MEK inhibitor.
  2. Symptomatic or untreated leptomeningeal disease.
  3. Symptomatic or untreated brain metastasis.Patients previously treated for these conditions that are asymptomatic in the absence of corticosteroid therapy are allowed to enroll. Brain metastasis must be stable with verification by imaging.
  4. Known acute or chronic pancreatitis.
  5. Clinically significant cardiac disease
  6. Impairment of gastrointestinal (GI) function or GI disease that may significantly alter the absorption of oral LGX818
  7. Previous or concurrent malignancy. Exceptions to this exclusion criteria include: adequately treated basal cell or squamous cell skin cancer; in situ carcinoma of the cervix, treated curatively and without evidence of recurrence for at least 3 years prior to study entry; or other solid tumor treated curatively, and without evidence of recurrence for at least 3 years prior to study entry.
  8. Pregnant or nursing (lactating) women, where pregnancy is defined as the state of a female after conception and until the termination of gestation, confirmed by a positive hCG laboratory test (> 5 mIU/mL).
  9. History of thromboembolic or cerebrovascular events within the last 6 months
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: First-line FOLFOXIRI Plus Bevacizumab in BRAF Mutant Metastatic Colorectal Cancer

Summary: The purpose of this study is to prospectively verify if FOLFOXIRI plus bevacizumab as first-line treatment could be considered a promising approach to improve the outcome of BRAF mutant metastatic colorectal cancer patients


Eligibility: Inclusion Criteria:
  -  Histologically confirmed colorectal adenocarcinoma;
  -  Availability of formalin-fixed paraffin embedded tumor block from primary and/or metastasis;
  -  BRAF V600E mutant status of primary colorectal cancer and/or related metastasis;
  -  Unresectable and measurable metastatic disease according to RECIST criteria;
  -  Male or female, aged > 18 years and < 75 years;
  -  ECOG PS < 2 if aged < 71 years;
  -  ECOG PS = 0 if aged 71-75 years;
  -  Life expectancy of more than 3 months;
  -  Adequate haematological function: ANC ≥ 1.5 x 10^9/L; platelets ≥ 100 x 10^9/L, Hb ≥ 9 g/dL;
  -  Adequate liver function: serum bilirubin ≤ 1.5 x ULN; alkaline phosphatase and transaminases ≤ 2.5 x ULN (in case of liver metastases ≤ 5 x ULN);
  -  Serum creatinine ≤ 1.5 x ULN;
  -  Previous adjuvant chemotherapy is allowed if more than 12 months have elapsed between the end of adjuvant therapy and first relapse;
  -  At least 6 weeks from prior extended radiotherapy and 4 weeks from surgery;
  -  Written informed consent to experimental treatment and molecular analyses.
  Exclusion Criteria:
  -  Presence or history of CNS metastasis;
  -  Serious, non-healing wound, ulcer, or bone fracture;
  -  Evidence of bleeding diathesis or coagulopathy;
  -  Uncontrolled hypertension;
  -  Clinically significant (i.e. active) cardiovascular disease for example cerebrovascular accidents (CVA) (≤6 months before treatment start), myocardial infarction (≤ 6 months before treatment start), unstable angina, NYHA ≥ grade 2 chronic heart failure (CHF), uncontrolled arrhythmia;
  -  Current or recent (within 10 days prior to study treatment start) ongoing treatment with anticoagulants for therapeutic purposes;
  -  Chronic, daily treatment with high-dose aspirin (>325 mg/day);
  -  Symptomatic peripheral neuropathy ≥ 2 grade NCIC-CTG criteria;
  -  Active uncontrolled infections;
  -  Treatment with any investigational drug within 30 days prior to enrolment;
  -  Other co-existing malignancies or malignancies diagnosed within the last 5 years with the exception of curatively treated basal and squamous cell carcinoma of the skin or in situ cancer of the cervix;
  -  Major surgical procedure, open biopsy, or significant traumatic injury within 28 days prior to study treatment start;
  -  Lack of physical integrity of the upper gastrointestinal tract or malabsorption syndrome;
  -  Fertile women (< 2 years after last menstruation) and men of childbearing potential not willing to use effective means of contraception.

Relevance to patient case: definitely relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: An Observational Study of Adjuvant Treatment With Capecitabine (Xeloda) in Combination With Oxaliplatin in Participants With Stage III Colon Cancer

Summary: This observational study evaluates the efficacy and safety of capecitabine in combination with oxaliplatin in the adjuvant setting in participants with Stage III colon cancer. Data were collected from each participant for up to 36 months or until disease recurrence.


Eligibility: Inclusion Criteria:
  -  Adult participants, >/= 18 years of age
  -  Treatment in line with the currently approved indication in the Summary of Product Characteristics
  Exclusion Criteria:
  -  Contraindications according to the current Summary of Product Characteristics

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: Safety and Efficacy of Using MASTER to Perform Endoscopic Submucosal Dissection in Human

Summary: This trial is to evaluate the safety and efficacy of using MASTER, a robotics enhanced endosurgical system to perform endoscopic submucosal dissection (ESD) of gastric/colon cancer in human.

Detailed description: This trial is to evaluate the safety and efficacy of using MASTER, a novel robotics enhanced endosurgical system to perform endoscopic submucosal dissection (ESD) of gastric/colon cancer in human. The MASTER is a master-and-slave robotic system that is deployed through a standard dual-channel therapeutic endoscope. It introduces robotic control of endoscopic surgical tools and tasks through an ergonomic human-machine interface built around the original endoscopic paradigm. In doing so, it separates control of instrumental motion from that of endoscopic movement such that surgical tasks may be independently executed by a second operator via a human-machine interface. With it, endoscopically deployed instruments can be independently controlled, allowing thus bimanual coordination of effector instruments to facilitate actions such as retraction/exposure, traction/countertraction, approximation and dissection of tissue. Using the MASTER, operational dexterity is increased, thus making it easier for the operator to perform the ESD procedure as compared with using the conventional endoscope. This study will measure the ease of using the MASTER to perform the various surgical tasks involved in the ESD procedure, the time taken to perform the procedure, and record complications, if any, occurred during and after the procedure.

Eligibility: Inclusion Criteria:
  -  patient diagnosed with early gastric or colon cancer, is deemed suitable to undergo endoscopic submucosal dissection and is able/willing to give informed consent.
  Exclusion Criteria:
  -  case is deemed not suitable for endoscopic submucosal dissection
  -  is on warfarin or other blood thinning agents and those with bleeding disorders
  -  has uncorrected coagulopathy or severe thrombocytopenia precluding biopsy
  -  has serious co-morbidities such as heart disease, renal impairment and cancer
  -  has recently underwent surgery or has a personal history of stomach/colon cancer or surgery
  -  is unable/unwilling to give informed consent
  -  is pregnant or breast-feeding women patients who cannot undergo gastroscopies

Relevance to patient case: not relevant
Patient case: 35-year-old male with Colon cancer. Genetic variant: BRAF (V600E). Other conditions: None.

Clinical trial: Genetic Analysis to Evaluate the Racial Difference in the Outcome of Patients With Colon Cancer

Summary: This is a retrospective genetic analysis of stored tumor tissue samples to evaluate the distribution of Recurrence Score® and gene groups of stage II colon cancer in African American (AA) and Caucasian individuals. Other covariant factors in the medical chart will be analyzed as well. Three institutions will contribute patients to this study with a total patient number goal of approximately 200 with approximately 100 being AA and approximately 100 being Caucasian. As enrollment in this study proceeds a Caucasian subject will be matched for every African American enrolled.


Eligibility: Inclusion Criteria:
  -  Subjects must be 18 years of age or older.
  -  Subjects must be AA or Caucasian.
  -  Subjects with pathologic stage II colon cancer; Irrespective of number of nodes examined.
  Exclusion Criteria:
  -  Patients of races other than AA or Caucasian.
  -  No tumor block available from initial diagnosis.
  -  No tumor or very little tumor (<5% tumor present) in block as assessed by examination of the H&E slide by the Genomic Health, Inc (GHI) - designated pathologist.
  -  Tumor types other than adenocarcinoma NOS (not otherwise specified) and mucinous carcinoma as assessed by examination of the H&E slide by the GHI-designated pathologist.
  -  Insufficient RNA (<5 ng/μL or 300 ng) for RT-PCR (radiation therapy - pathologic complete response) analysis.
  -  Failure of assay to meet pre-specified quality control (QC) specifications.

Relevance to patient case: not relevant