araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: Optimization of VIM Targeting in Essential Tremor Surgery

Summary: Deep brain stimulation (DBS) for essential tremor is based on the intermedius ventralis nucleus of the thalamus (VIM) stimulation. This structure is however very difficult to target, as it remains invisible on imaging. The current procedure based on awake surgery with clinical and electrophysiological testings has several limitations that lead us to develop a probabilistic model to locate precisely the target. This study aims to show that asleep DBS surgery based on this new targeting method leads to at least the same clinical results than the classical procedure.

Detailed description: The intermedius ventralis nucleus of the thalamus (VIM), which represents the target for deep brain stimulation (DBS) in essential tremor, still remains invisible on 1,5 tesla MRI (the only magnetic field available for stereotactic surgery). The target coordinates currently used are based on stereotactic atlases or mean coordinates from retrospective series. They are so imprecise that intra-operative clinical testing and micro-electrode recordings are mandatory to locate the exact position of the VIM. This procedure is long lasting, requires that the patient is awake, and increases the risk of intracerebral haemorrhage and nosocomial infections. Furthermore, some patients are not improved despite a DBS lead implanted in the electrophysiologically and clinically defined target. To overcome these limitations, investigators developed a probabilistic model based on data extracted from imaging of patients with particularly good outcomes after DBS surgery. This machine-learning model allows calculating to coordinates of the VIM according to the position of radio-anatomical landmarks with a mean precision of 1,65mm.
  The aim of this study is to validate this new targeting method on a prospective cohort of patients. DBS surgery will be performed under general anaesthesia, without intra-operative clinical and electrophysiological testing, with a surgical robot and under CT-scan guidance (O-Arm ©).
  Neurostimulation device programming will be performed as usual. Patients' tremor and quality of life will be evaluated pre and post-operatively at 3 months, according to the Fahn-Tolosa-Marin (FTM) scale and with an accelerometry recording (for tremor) and with the mPDQ-39 scale for quality of life. Surgical complications and side effects related to neurostimulation will be gathered all along the follow-up.

Eligibility: Inclusion Criteria:
  -  Severe essential tremor despite the optimal medical management
  -  Age between 18 and 75 years
  -  Normal MRI scan
  -  Mattis Dementia Rating Scale (MDRS) score ≥ 130
  -  Affiliation to the social security
  -  Signed informed consent
  Exclusion Criteria:
  -  Depression (Beck Depression Inventory scale > 20)
  -  Contra-indication to surgery or general anesthesia
  -  Cerebral atrophy on MRI scan
  -  Pregnant or breastfeeding women

Relevance to patient case: not relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: Phase 3 Study of Sitravatinib Plus Nivolumab vs Docetaxel in Patients With Advanced Non-Squamous NSCLC

Summary: This study will compare the efficacy of the investigational agent sitravatinib in combination with nivolumab versus docetaxel in patients with advanced non-squamous NSCLC who have previously experienced disease progression on or after platinum-based chemotherapy in combination with checkpoint inhibitor therapy.

Detailed description: Sitravatinib is a spectrum-selective receptor tyrosine kinase (RTK) inhibitor that inhibits several closely related RTKs, including the TAM family (TYRO3, AXL and MERTK), VEGFR2, KIT and MET. Nivolumab is a human IgG monoclonal antibody that binds to the PD-1 receptor and selectively blocks the interaction with its ligands PD-L1 and PD-L2, thereby releasing PD-1 pathway mediated inhibition of the immune response, including anti-tumor immune response. RTKs have been implicated in mediating an immunosuppressive tumor microenvironment, which has emerged as a potential resistance mechanism to checkpoint inhibitor therapy. Inhibition of these RTKs by sitravatinib may augment anti-tumor immune response and improve outcomes by overcoming resistance to checkpoint inhibitor therapy.

Eligibility: Inclusion Criteria:
  -  Diagnosis of Non-Squamous Non-Small Cell Lung Cancer
  -  Receipt of prior first-line treatment with platinum-based chemotherapy in combination with PD-1/PD-L1 checkpoint inhibitor therapy
  -  Adequate bone marrow and organ function
  -  Candidate to receive docetaxel as second line therapy
  Exclusion Criteria:
  -  Uncontrolled brain metastases
  -  Tumors that have tested positive for EGFR, ROS1, ALK mutations, or ALK fusions
  -  Unacceptable toxicity with prior checkpoint inhibitor therapy
  -  Receipt of systemic anti-cancer therapy post checkpoint inhibitor therapy, other than maintenance chemotherapy in the first-line setting
  -  Impaired heart function

Relevance to patient case: not relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: A Study of HLX10 in Combination With Carboplatin Plus (+) Pemetrexed With or Without HLX04 Compared With Carboplatin+Pemetrexed in 1L Metastatic Non-Squamous Non-Small Cell Lung Cancer (NSCLC)

Summary: This study involves a two-part design. Part 1 is designed to evaluate the safety and tolerability of the 4 drug (HLX10+HLX04+carboplatin+pemetrexed). Part 2 is a randomized, open-label study, which will evaluate the safety and efficacy of HLX10 in combination with carboplatin+pemetrexed with or without HLX04(biosimilar of avastin) compared with treatment with carboplatin+pemetrexed in 1st line Stage IV non-squamous NSCLC. Participants will be randomized in a 1:1:1 ratio to Arm A (HLX10+HLX04+Carboplatin+Pemetrexed), Arm B (HLX10+Carboplatin+Pemetrexed), or Arm C (Carboplatin+Pemetrexed).


Eligibility: Inclusion Criteria:
  1. Histologically or cytologically confirmed, Stage IV non-squamous NSCLC
  2. Participants with no EGFR, ALK and ROS1 mutation.
  3. Participants with no prior treatment for Stage IV non-squamous NSCLC
  4. Measurable disease as defined by RECIST v1.1
  5. Eastern Cooperative Oncology Group performance status 0 or 1
  6. Adequate hematologic and end organ function
  Exclusion Criteria:
  1. Malignancies other than NSCLC within 5 years prior to randomization, with the exception of those with a negligible risk of metastasis or death treated with expected curative outcome
  2. Active central nervous system metastases
  3. Prior treatment with cluster of differentiation immune checkpoint blockade therapies or Bevacizumab
  4. Has received a surgical operation within 4 weeks from the initial drug administration
  5. Active or suspected autoimmune diseases. Subjects in a stable state with no need for systemic immunosuppressant therapy are allowed to enroll.
  6. Currently having or have had interstitial pneumonia, pneumoconiosis, radiation pneumonitis, drug-related pneumonitis and severe impaired pulmonary function that may interfere with the detection and management of suspected drug-related pulmonary toxicity
  7. Any active infection requiring systemic anti-infective therapy within 14 days prior to study drug administration
  8. Uncontrollable active infection(s)
  9. History of immunodeficiency, including HIV antibody positive
  10. active hepatitis B; or hepatitis C virus infections
  11. Has bleeding tendency
  12. History of severe cardiovascular diseases
  13. Known gastrointestinal diseases as follows, Gastrointestinal perforation, abdominal fistula or abdominal abscess within 6 months before signing the informed consent; History of poorly controlled or recurrent inflammatory bowel disease; Active peptic ulcers, or > moderate esophageal varices
  14. Pregnant or breastfeeding female

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

Clinical trial: Gene Testing in Patients With Colon Cancer

Summary: RATIONALE: Analyzing the structure of genes found in a person's cancer cells may help doctors improve methods of treating patients with colon cancer.
  PURPOSE: Clinical trial to study the genes of patients treated with chemotherapy for colon cancer.

Detailed description: OBJECTIVES:
  -  Determine the relationship between disease free survival, overall survival, and tumor replication error status for patients who have received adjuvant chemotherapy for colon cancer on CALGB protocol 8896.
  -  Determine the prognostic and predictive values for response to this therapy in these patients.

Eligibility: DISEASE CHARACTERISTICS:
  -  Patients who received chemotherapy for colon cancer as part of CALGB protocol 8896
  -  Underwent an initial resection for adenocarcinoma of the colon and were determined to have a high risk of tumor recurrence based upon nodal disease or local extension of tumor with obstruction or perforation due to tumor
  -  Surgical specimen blocks available, including tumor tissue and normal tissue

Relevance to patient case: definitely relevant
Patient case: 68-year-old male with colon cancer; genetic feature: MLH1 methylation suppression (microsatellite instability)

Clinical trial: Genetic Markers in Patients With Colorectal Cancer

Summary: RATIONALE: Determination of genetic markers for colorectal cancer may improve the identification of patients who are at highest risk for relapse.
  PURPOSE: This clinical trial is studying the importance of genetic markers for detecting relapse in patients with colorectal cancer.

Detailed description: OBJECTIVES:
  -  Determine the clinical and pathologic significance of unstable DNA elements in colorectal cancer (tumor microsatellite instability).
  -  Determine the clinical and pathologic significance of loss of heterozygosity for chromosomes 5, 8, 17, and 18 (as the primary targets) and of chromosomes 1, 14, and 22 (as the secondary targets) in colorectal cancer.
  OUTLINE: DNA is examined for unstable elements (microsatellite instability and loss of heterozygosity) by analyzing at least 10 separate (CA)n-repeats localized to 5 separate chromosomes (5q, 8p, 15, 17p, and 18q). Loss of heterozygosity is analyzed for at least four chromosomal arms (5q, 8p, 17p, and 18q) and later other chromosomes (e.g., 1, 14, and 22). Immunohistochemistry is used to test for the presence or absence of the genes involved in DNA mismatch repair (hMLH1 and hMSH2).
  Patients do not receive the results of the genetic testing and the results do not influence the type or duration of treatment.
  PROJECTED ACCRUAL: This study will accrue up to 708 specimens.

Eligibility: DISEASE CHARACTERISTICS:
  -  Must have had a resectable adenocarcinoma of the colon or rectum and must have participated in one of the following NCCTG randomized clinical trials:
  -  784852: No Treatment Control Versus Levamisole Versus Levamisole Plus Fluorouracil (5-FU)
  -  794604: No Treatment Control Versus 5-FU by Portal Vein Infusion
  -  794751: Postoperative Radiation Versus Postoperative Radiation Plus Sequential Chemotherapy with Methyl CCNU and 5-FU
  -  844652: An Intergroup Study - An Evaluation of Levamisole Plus 5-FU as Surgical Adjuvant Treatment for Resectable Adenocarcinoma of the Colon
  -  864751: Phase III Protocol for Surgical Adjuvant Therapy of Rectal Carcinoma: A Controller Evaluation of (A) Protracted-Infusion 5-FU as a Radiation Enhancer and (B) 5-FU Plus Methyl-CCNU Chemotherapy
  -  874651: M/N - A Controller Evaluation of Recombinant Interferon-gamma (IFL GM) and 5-FU and Folinic Acid With or Without Levamisole as Adjuvant Treatment for Resectable Adenocarcinoma of the Colon
  -  894651: A Controller Phase III Evaluation of 5-FU Combined With Levamisole and Leucovorin as Adjuvant Treatment for Resectable Colon Cancer
  -  Tissue blocks from the primary colorectal cancer must have been received by the NCCTG operations office

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 Evaluating rhIL-11 in Left-Sided Ulcerative Colitis

Summary: To explore the safety of orally delivered rhIL-11 in patients with mild to moderate left-sided ulcerative colitis.
  To explore the effects of orally administered rhIL-11 on pharmacogenomics in blood samples and in colonic biopsy tissue samples.


Eligibility: Inclusion Criteria:
  -  Documented, signed informed consent to participate in this study
  -  Age greater than or equal to 18 years
  -  Documented diagnosis of ulcerative colitis by standard clinical criteria, including endoscopy (either flexible sigmoidoscopy or colonoscopy, sufficient to define the proximal limit of disease) with biopsy
  Exclusion Criteria:
  -  Crohn's disease
  -  Ulcerative proctitis
  -  Ulcerative colitis extending beyond the splenic flexure

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

Clinical trial: Genetic Study of Familial Factors in Patients With Colon Cancer

Summary: RATIONALE: Genetic studies may help in understanding the genetic processes involved in the development of some types of cancer.
  PURPOSE: Clinical trial to study the cancer-related genes in patients who have colon cancer or adenomatous polyps.

Detailed description: OBJECTIVES:
  -  Identify human colon neoplasia susceptibility genes in patients with colon cancer or adenomatous polyps.
  -  Correlate the inheritance of novel susceptibility alleles for adenomatous polyposis of the colon with colon neoplasia in these patients.
  -  Correlate colon neoplasia susceptibility with the presence of COX-2, sPLA2, and DNMT genes in these patients.
  -  Identify a novel gene that governs increased susceptibility to colon adenoma and cancer in the genome of these patients.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of colon cancer or polyps at age 70 or under
  -  Has a living full sibling with diagnosis of colon cancer or polyps at age 70 or under
  -  No history of familial adenomatous polyposis syndrome
  -  No hereditary nonpolyposis colon cancer, according to Amsterdam criteria
  -  No known I1370K adenomatous polyposis of the colon susceptibility variant
  -  Enrolled on 1 of the following clinical trials:
  -  CLB-9581
  -  CLB-89803
  -  CLB-80001 NOTE: Patients do not need to be receiving protocol therapy. Patients who are outside the treatment protocol's follow-up range are eligible. Patients who discontinued therapy for any reason, including toxic effects, are eligible.
  PATIENT CHARACTERISTICS:
  Age
  -  70 and under at diagnosis
  Other
  -  No significant psychiatric illness that would preclude giving informed consent
  -  No inflammatory bowel disease (in patient or sibling)

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

Clinical trial: Implementation of a New Strategy to Identify HNPCC Patients

Summary: The purpose of this study is to compare two different strategies to implement a new method to identify patients with HNPCC, which appeared cost-effective and feasible. The effectiveness, costs and feasibility of both of the implementation strategies will be assessed.

Detailed description: The Radboud University Nijmegen Medical Centre developed a new method to identify patients with HNPCC. This method appeared cost-effective and feasible. Using this new method 70% of the HNPCC patients will be identified as compared to less than 30% when the current method is used. However, this new method does not implement itself; large gaps exists between best evidence and daily practice. This study will compare an intensive strategy, consisting of distribution of educational materials, education, feedback and reminders, with a minimal strategy, only consisting of distribution of a critical care pathway. The aim is to find the most cost-effective strategy to implement the new method to identify patients with HNPCC in the Netherlands.

Eligibility: Inclusion Criteria:
  -  Colorectal cancer before the age of 50 years
  -  Second colorectal cancer at any age
  -  Colorectal cancer and other HNPCC associated extracolonic cancer irrespective of age at diagnosis
  -  Adenoma with high grade dysplasia diagnosed before the age of 40 years

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

Clinical trial: Screening for Colorectal Neoplasm in First Degree Relatives of the Affected

Summary: To determine the prevalence of colorectal neoplasms in first degree relatives of those affected with sporadic colorectal cancer using colonoscopy as a screening tool. The prevalence will be compared to that of a defined matched cohort.

Detailed description: Colorectal cancer is a second commonest tumor in Hong Kong and the second commonest cause of cancer related death. About 1 in 23 males will develop colorectal cancer in his life time. The disease tends to cluster in families. This may be a combination of factors including shared genes, shared environment or chance. Known familial syndromes occur in only about 5% of cases. The majority is not well understood and labelled sporadic colorectal cancer. The screening strategy in families of subjects with colorectal cancer has not been defined. Colonoscopy is among the most sensitive and specific screening tool for colorectal neoplasm. The current study determines the prevalence of adenomas among first degree relatives of patients diagnosed with colorectal cancer. To quantify risk in this cohort, a case control analysis is used. The prevalence of the cohort is compared to that of a control population. The control group consists of relatives of patients with normal colonoscopic findings during the same study period.

Eligibility: Inclusion Criteria:
  -  First degree relatives (age >40 and <70) of individuals affected with sporadic colorectal cancer (those not associated with inflammatory bowel disease, familial adenomatous polyposis or HNPCC syndrome).
  Exclusion Criteria:
  -  A family history compatible with that of Hereditary Non-polyposis Colon Cancer (HNPCC) based on the Amsterdam criteria [Table 5].
  -  Known Familial Adenomatous Polyposis (FAP) syndrome
  -  Patients and relatives with known inflammatory bowel disease
  -  Relatives that have received colonoscopy examinations in the past 5 years [details of colonoscopic examinations will be sought and information on colonic neoplasms recorded]. Those who have had barium enema examinations are eligible for trial inclusion as barium examinations often have low sensitivity and specificity for adenomas (around 70% respectively)
  -  Severe cardio-pulmonary or other medical co-morbidities that preclude safe colonoscopic examination

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

Clinical trial: Temozolomide & RT Followed by Dose Dense vs Temozolomide & Retinoic Acid in Pts w/Glioblastoma

Summary: Patients have a newly diagnosed brain tumor called a malignant glioma and participate in the study to see if it is possible to increase the benefit of temozolomide when given after radiation. A recent study showed that patients with newly diagnosed glioblastoma lived longer when treated with both temozolomide and radiotherapy followed by 6 months of temozolomide than patients treated with radiotherapy alone. Patients will receive standard low dose temozolomide during radiation. After radiation, they will be randomized to receive either more intense temozolomide or continuous low dose temozolomide.

Detailed description: This is a randomized phase II study that will test two different adjuvant temozolomide regimens in patients with newly diagnosed glioblastoma multiforme. The goal of this study is to identify a regimen that would be appropriate to bring to a phase III trial and compare to the standard dosing regimen of temozolomide recently reported by Stupp et al. in the New England Journal of Medicine. Secondary goals of this study include: prospective analysis of the prognostic impact of MGMT status and generation of preliminary data regarding this treatment strategy for other types of malignant glioma.
  The decision regarding which treatment patients receive is made randomly. Neither them or their doctor can select which treatment the patient will receive. There is reason to believe that both of these doses may benefit treating your brain tumor. After 6 months of chemotherapy, and assuming the brain tumor has not shown any sign of growth, they will begin receiving cis-retinoic acid. Cis retinoic acid has been shown in one study to possibly prevent or delay tumor recurrence.

Eligibility: Inclusion Criteria:
  -  Pathologic evidence of a malignant glioma.
  -  Tissue block or unstained slides must be available for MGMT analysis.
  -  Age 18-70
  -  KPS > 50
  -  Granulocyte count >1.5 X 109/L
  -  Platelet count >99 X 109/L
  -  SGOT < 2.5X upper limit of normal (ULN).
  -  Serum creatinine < 2X ULN.
  -  Bilirubin < 2X ULN.
  -  All patients must sign written informed consent.
  Exclusion Criteria:
  -  Any prior chemotherapy, radiotherapy and biologic therapy for glioma.
  -  Any prior experimental therapy for glioma.
  -  Other concurrent active malignancy (with the exception of cervical carcinoma in situ or basal cell ca of the skin).
  -  Serious medical or psychiatric illness that would in the opinion of the investigator would interfere with the prescribed treatment.
  -  Pregnant or breast feeding women.
  -  Refusal to use effective contraception.

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

Clinical trial: Clinical and Molecular Characterization of Familial Microsatellite Stable Colorectal Cancer

Summary: Two major genetic pathways leading to colorectal carcinoma can well be distinguished; the 'suppressor pathway', which is characterized by inactivation of tumor-suppressor genes and the 'mutator pathway', which is characterized by microsatellite instability. The purpose of this study is to explore a third putative pathway; microsatellite and chromosome stable colorectal cancer where an alternative cancer-causative mechanism might play a role.

Detailed description: Patients with familial colorectal cancer will be characterized with respect to family history, medical history and demographic characteristics. The histopathology of the tumors will be reviewed. Tumor specimens will be analysed on molecular defects.

Eligibility: Inclusion Criteria:
  - Colorectal cancer before the age of 51 years
  Microsatellite stable tumor
  Exclusion Criteria:
  -

Relevance to patient case: not relevant