araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Genotype-directed Neoadjuvant Chemoradiation for Rectal Carcinoma

Summary: Determine if genotype-directed neoadjuvant chemoradiation, using information from the thymidylate synthase promoter polymorphism, result in a greater degree of tumor downstaging in high risk patients compared to historical controls.


Eligibility: Inclusion Criteria:
  -  Biopsy proven adenocarcinoma of the rectum
  -  Lesion evaluated by surgeon and found to be resectable
  -  Stage T3 or T4 disease on radiography or ultrasound
  -  Karnofsky Performance Status at >60
  -  Laboratory criteria:
  -  Absolute neutrophil count >= 1.5 K
  -  Platelets >= 100 K
  -  Total Bilirubin <= 2.0;
  -  SGOT and Alkaline Phosphatase <= 2 x upper limit of normal
  -  Creatinine < 2.0
  -  Informed consent signed
  -  Patients with distant metastatic disease will be eligible if they satisfy all other conditions.
  Exclusion Criteria:
  -  Pregnant women, children < 18 years, or patients unable to give informed consent
  -  Patients with a past history of pelvic radiotherapy.
  -  Patients with prior malignancy in the past 5 years except: skin cancer or in-situ cervical cancer. However, patients with synchronous adenocarcinomas are eligible provided either (a) the synchronous adenocarcinoma was in a removed pedunculated polyp and did not invade the stalk or (b) the synchronous adenocarcinoma was in a removed polyp that lay within the surgical field (extent of resection would not be changed) or (c) the synchronous adenocarcinoma is smaller than the index rectal cancer and lies completely within the radiation field (clinically favorable second lesion and the extend of radiation and surgery would not be changed).
  -  Patients with known allergy to 5-fluorouracil or irinotecan

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Safety Study of Oral MGCD265 Administered Without Interruption to Subjects With Advanced Malignancies

Summary: In this study, MGCD265, a new anticancer drug under investigation, is given daily to patients with advanced malignancies to study its safety profile.

Detailed description: MGCD265 belongs to a new class of drugs with anticancer potential, known as tyrosine kinase inhibitors. MGCD265 was shown to slow down the growth of human cancer cells in mice. Clinical studies are being pursued to evaluate the safety of MGCD265 in cancer patients.
  In this study, MGCD265 is orally administered on a daily basis to patients with advanced malignancies.

Eligibility: Inclusion Criteria:
  -  Advanced metastatic or unresectable malignancy that is refractory to standard therapy and/or existing therapies are not likely to achieve clinical benefit, and/or the patient declines to receive standard treatment such as chemotherapy.
  -  Evaluable disease;
  -  Last dose of prior chemotherapy, radiation therapy, or investigational agents occurred at least 4 weeks before the start of therapy;
  -  Recovery from the adverse effects ≤ grade 1;
  -  Acceptable ECOG status 0, 1, or 2;
  -  Life expectancy greater than 3 months following study entry;
  -  Adequate laboratory values;
  -  For patients enrolling in the four expansion cohorts:
  -  NSCLC patients must meet criteria for MET and/or Axl expression or,
  -  HNSCC patients must meet criteria for MET and/or Axl expression or,
  -  NSCLC patients must meet criteria for amplification of the MET gene locus, defined MET mutations, or rearrangements involving the AXL or MET gene locus or;
  -  Patients with tumor types such as HNSCC, papillary renal carcinoma, gastric adenocarcinoma, and other solid tumors must meet criteria for amplification of the MET gene locus, defined MET mutations, or rearrangements involving the AXL or MET gene locus
  Exclusion Criteria:
  -  Uncontrolled concurrent illness;
  -  History of cardiovascular illness;
  -  QTc > 470 msec (including subjects on medication);
  -  Left ventricular ejection fraction (LVEF) < 50%;
  -  Immunocompromised subjects;
  -  History of bone marrow transplant;
  -  Lung tumor lesions with increased likelihood of bleeding;
  -  Symptomatic or uncontrolled brain metastases;
  -  Unable to swallow oral medications or with pre-existing gastrointestinal disorders.

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: High-Dose Imatinib for Relapsed/Refractory c-Kit Positive Acute Myelogenous Leukemia (AML)

Summary: This is a multicenter open-label phase II trial of high dose imatinib mesylate in patients with AML in first or second relapse, or with refractory disease. Daily dosing of imatinib 600 mg/day is planned for one month or until progression of disease. Dose increase to 800 mg/ day imatinib is permitted for 2 additional months in the event of response failure. Response is assessed after 1, 2 and 3 months of treatment by bone marrow aspirate.

Detailed description: Daily dosing of imatinib 600 mg/day is planned for one month or until progression of disease. Dose increase to 800 mg/ day imatinib is permitted for 2 additional months in the event of response failure. Novartis provided supplies of imatinib for all patients included in the study.

Eligibility: Inclusion Criteria:
  -  age > 18 years,
  -  AML in first or second relapse,
  -  refractory AML
  -  performance status of 0-2 on the Eastern Cooperative Oncology Group scale,
  -  adequate hepatic and renal functions (AST or ALT <= 5 times the upper limit of normal
  -  creatinine < 2 times the upper limit of normal)
  -  20% blasts in bone marrow,
  -  70% of bone marrow blast population c-kit positive as assessed by immunophenotyping
  -  Bcr-Abl negative chromosomal analysis (assessed by fluorescence in situ hybridization; FISH), and no chromosome 5-12 translocation
  Exclusion Criteria:
  -  Previous treatment by Imatinib
  -  Secondary AML

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Characterisation of Gene Variants in the Angiogenic Pathway

Summary: Anti-angiogenic targeted therapies are used in a wide range of solid tumors including NSCLC, breast cancer, GISTs, CRC, renal cell carcinoma and hepatocellular carcinoma. Somatic mutations in genes related to tumorigenesis have been associated with treatment response whereas germline gene variants have been associated with tumor risk, prognosis and treatment related toxicity.Study objectives are:
  1. To characterise the prevalence and clinicopathological associations of germline and somatic variation in genes involved in the angiogenic pathway in healthy donors and unselected cancer patients
  2. To examine the association between angiogenic gene variants and outcome in patients receiving anti-angiogenic therapy

Detailed description: Angiogenesis plays a key role in the process of tumour growth and metastases. Anti-angiogenic targeted therapies are currently used in a wide range of solid tumors including lung, breast, colorectal, kidney and liver cancer. Somatic variants in genes related to tumorigenesis have been associated with treatment response, whereas germline gene variants have been associated with tumor risk, prognosis and treatment related toxicity. In this study we propose to (1) To characterise the prevalence and clinicopathological associations of germline and somatic variation in genes involved in the angiogenic pathway in healthy donors and unselected cancer patients (2) to examine the association between angiogenic gene variants and outcome in patients receiving anti-angiogenic therapy. Genes related to angiogenesis to be characterised include those encoding platelet derived growth factor receptors, vascular endothelial growth factors, vascular endothelial growth factor receptors, K-Ras, B-Raf, and c-kit. Results from this study may (1) identify patients who are more likely to respond to anti-angiogenic targeted therapy, thus maximising drug efficacy and (2) to identify further targets for potential anti-angiogenic drug therapies.

Eligibility: Inclusion Criteria:
  -  Anti-angiogenic targeted therapies are used in a wide range of solid tumors including NSCLC, breast cancer, GISTs, CRC, renal cell carcinoma and hepatocellular carcinoma

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: A Study In Patients With Advanced Solid Tumor

Summary: This study designed to evaluate the pharmacokinetics and safety of AG-013736 at single doses and multiple doses


Eligibility: Inclusion Criteria:
  -  Patients histologically or cytologically diagnosed with advanced solid tumors
  -  Patients for whom standard therapies have not been effective, or for whom there are no suitable therapies
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status (PS) of 0, 1 or 2
  -  Patients with no uncontrolled hypertension
  Exclusion Criteria:
  -  Patients who have central lung lesions involving major blood vessels
  -  Patients who require anticoagulant therapy.
  -  Patients with active epilepsy seizure or symptoms, with brain metastases requiring treatment, with spinal cord compression and with carcinomatous meningitis.

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Evaluation of the Avaulta Procedure for the Correction of Pelvic Organ Prolapse - Results at 1 Year

Summary: This study is a 1 year review of all patients who had surgery to correct pelvic organ prolapse (i.e. cystocele, rectocele, enterocele) using the Avaulta synthetic mesh kit.

Detailed description: This is a retrospective cohort analysis of all patients who experienced vaginal prolapse and were operated on with the Avaulta synthetic vaginal mesh "kit" from January 2006 to April 2007. The Avaulta synthetic mesh is composed of polypropylene which is a monofilament. The objective of this trial is to compare patients objectively and subjectively at least one year after placement of the Avaulta synthetic vaginal mesh in terms of prolapse symptoms.
  This data will be compared to pre-operative data already collected for these patients as a part of their routine surgical work-up. Mesh-related complications will be quantified, including erosions, new-onset pain, and infections. Success and anatomic recurrence rates will be recorded as well

Eligibility: Inclusion Criteria:
  -  All patiAll patients who underwent surgery with the Avaulta synthetic mesh kit from 1/06 - 4/08.
  Exclusion Criteria:
  -  Unable to give informed consent to participate

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Dacomitinib (PF-00299804) As A Single Oral Agent In Selected Patients With Adenocarcinoma Of The Lung

Summary: This study will explore the safety and efficacy of the oral PanHER inhibitor PF-00299804 in patients with adenocarcinoma of the lung who are either non-smokers (<100 cigarette, cigar or pipe lifetime) or former light smokers ( less than 10 pack-years and stopped at least 15 years) or have known EGFR activating mutation; or patients with HER 2 amplification or mutation.


Eligibility: Inclusion Criteria:
  -  Advanced adenocarcinoma of lung, measurable disease
  -  Non-smoker, or former light (less than 10 pack years and stopped at least 15 years); OR
  -  patients with known EGFR activating mutation regardless of smoking status
  -  ECOG(Eastern Cooperative Oncology Group) 0-1.
  Cohort B (select sites only): patients with HER2 amplified or HER2 mutation-positive NSCLC; may have had prior therapy
  Exclusion Criteria:
  -  Active brain metastases
  -  Prior systemic therapy for advanced disease in Cohort A only. Cohort B can have had any number of prior lines of systemic therapy.
  -  known EGFR wild type NSCLC

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Genetic Risk Factors and Acquired Oncogenic Mutations of Melanoma

Summary: Though it is generally accepted that exposure to sunlight is a major causative factor for skin cancer, the risk for developing melanoma is not directly linked to sun exposure such as in non-melanoma skin cancer. Therefore, a dual pathway has been proposed, distinguishing melanoma that develops on skin that is chronically exposed to sunlight from those that occur on skin that is normally protected. The risk for each type of melanoma is believed to be determined in part by genetic factors. To define these markers reproducibly, the investigators plan to establish a large cohort with comprehensive information regarding sun sensitivity (skin type), history of experienced sun exposure, skin pigmentation phenotypes, total number of nevi, and other types of skin tumors in a central European population. The investigators will obtain blood from all participants for DNA as well as serum analyses. Based on the finding that genetic variants of the melanocortin-1 receptor (MC1R) gene, associated with red hair and fair skin, have been shown to be associated with increased risk for melanoma, particularly those harboring BRAF mutations, the investigators will now focus on the study of recently discovered genetic variants associated with pigmentation. Furthermore, the investigators will study the relation of these variants with oncogenic mutations of melanoma in BRAF, RAS and c-Kit. The study of other genetic variants will follow, once a sufficiently large cohort has been established to reveal an independent genetic risk factor in a multivariate analysis including potential covariates as mentioned above. The identification of genetic risk factors for melanoma will not only help identify individuals with increased risk but also improve our understanding of the molecular background of the development of melanoma.


Eligibility: Inclusion Criteria:
  -  patients with or without melanoma
  Exclusion Criteria:
  -  HIV and Hepatitis C positive individuals.

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: GeneSearch™ Breast Lymph Node (BLN) Assay China Registration Study

Summary: The primary objective of this trial is to compare GeneSearch™ Breast Lymph Node (BLN) Test Kit to permanent pathological section, so as to evaluate the clinical sensitivity and specificity of GeneSearch™ Breast Lymph Node (BLN) Test Kit in detecting axillary sentinel lymph node metastases in breast cancer patients.
  The secondary objective of this trial is to evaluate the positive predictive value and negative predictive value of GeneSearch™ Breast Lymph Node (BLN) Test Kit when used in the detection of axillary sentinel lymph node metastases in breast cancer patients.
  Prospective and multi-center clinical trial


Eligibility: Inclusion Criteria:
  -  Diagnosed previously as breast cancer
  -  patient scheduled for sentinel lymph node dissection
  -  18 years or older
  -  female or male, and
  -  able and willing to give consent to participate in the study
  Exclusion Criteria:
  -  Patients taking part in other research studies that would interfere with their full participation in this study, or
  -  Prior sentinel or partial axillary lymphadenectomy on the same body side

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Trial of Imatinib (Gleevec®) in Selected Patients With Metastatic Melanoma

Summary: This study is a single-armed, open-label, single-center phase II trial of signal transduction inhibitor number 571 (STI-571) systemic therapy in selective patients with metastatic melanoma, and aims to study the efficacy and safety. The primary endpoint is progression-free survival (PFS) and the second endpoints are overall response rate (ORR), overall survival (OS), 1-year OS and safety.

Detailed description: Only patients who meet the inclusion and exclusion criteria will be enrolled. The estimated recruitment duration is 1 year. Imatinib will be given in the dose of 400 mg orally each day unless disease progression or intolerance. The follow-up is 12 months.
  Forty-eight subjects will be recruited for this study. This sample size is justified by the number of patients required to establish an improvement in PFS with statistical significance compared to historical control.
  The standardized RECIST (Response Evaluation Criteria in Solid Tumors) method of unidimensional tumor assessment will be employed to evaluate tumor lesion size per 2 months in the determination of response rate and progression free survival. Repeated radiographic assessment at 4 week intervals is consistent with general oncological practice associated with computerized tomography (CT) or magnetic resonance imaging (MRI) scan testing. All efficacy endpoints will be evaluated by the investigator.
  Safety will be characterized in terms of the incidence, timing, severity, and relatedness of adverse events and laboratory abnormalities. Severity will be graded according to the NCI CTCAE Version 3.0.

Eligibility: Inclusion Criteria:
  1. Histologically confirmed melanoma with metastases and has no received any systemic treatment within 1 month
  2. Evidence of mutations and/or copy number increases of KIT with laboratory examination documented from either primary or metastatic tumor site
  3. ECOG performance status 0, 1, or 2
  4. Estimated life expectancy of 6 months or greater
  5. Age 18 years or older, male of female
  6. At least one measurable site of disease
  7. Adequate organ function
  8. Willingness and ability to comply with scheduled visits, treatment plans, laboratory tests, and other study procedures
  Exclusion Criteria:
  1. Melanoma from primary sites other than acral or mucosal melanoma
  2. Received systemic anti-cancer therapy within 1 month before enrollment for metastatic disease
  3. Diagnosis of any second malignancy within the last 5 years, except for adequately treated basal cell carcinoma, squamous cell skin cancer, or in situ cervical cancer
  4. Severe and/or uncontrolled concomitant medical diseases
  5. pregnant or childbreeding women
  6. Known hypersensitivity to imatinib
  7. Current treatment on another clinical trial

Relevance to patient case: possibly relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Genotype and Phenotype Registry: Enrollment of Normal Control Subjects for Current and Future Research

Summary: Registry program for volunteers who are willing to serve as control subjects in future research studies.

Detailed description: The registry is a collection of volunteers willing to participate as control subjects in research studies. Control subjects are people who do not have a specific disease; therefore they can serve a critical role as a comparison with people who have the disease or other characteristic being studied. Once registered, participants will be notified about studies they may be able to participate in as a control.
  Participation requires:
  1. signing a consent form
  2. answering a short health survey
  3. providing a DNA sample via a mouthwash kit
  The registry allows scientists to select study participants based on whether or not they have a specific genetic change that may be relevant to a disease under investigation. Having the ability to access controls when needed is an extremely valuable resource that will speed up scientific discoveries.

Eligibility: Inclusion Criteria:
  -  Generally healthy
  -  over age 18
  Exclusion Criteria:
  -  under age 18

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Comparison of AZD6244 in Combination With Dacarbazine Versus (vs) Dacarbazine Alone in BRAF Mutation Positive Melanoma Patients

Summary: To assess the efficacy in terms of overall survival of AZD6244 in combination with dacarbazine, compared with dacarbazine alone, in first line patients with BRAF mutation positive advanced cutaneous or unknown primary melanoma


Eligibility: Inclusion Criteria:
  -  Histological or cytological confirmation of advanced (inoperable stage III and stage IV) cutaneous or unknown primary melanoma
  -  Tumor sample confirmed as BRAF mutation positive
  Exclusion Criteria:
  -  Diagnosis of uveal or mucosal melanoma
  -  Any prior Investigational therapy comprising inhibitors of Ras, Raf or MEK
  -  Having received an investigational drug within 30 days of starting treatment, or have not recovered from side effects of an investigational drug

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Study of Tumor Samples in Patients Undergoing Radiation Therapy or Surgery For Primary Melanoma of the Eye

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This clinical trial is studying tumor samples in patients undergoing surgery or radiation therapy for primary melanoma of the eye.

Detailed description: OBJECTIVES:
  Primary
  -  To establish the feasibility of using fine needle aspiration (FNA) and FISH to determine tumor genotype in patients with primary uveal melanoma.
  Secondary
  -  To characterize ophthalmic complication rate of FNA for FISH analysis in patients undergoing plaque radiotherapy.
  -  To estimate disease-free survival in patients with and without tumor monosomy 3 and/or 8q amplification.
  -  To explore the relationship between tumor monosomy 3 and 8q amplification and plasma levels of tumor immune escape and invasion biomarkers (e.g., circulating granulysin, beta2-microglobulin, autotoxin, lysophosphatidic acid, matrix metalloproteinase-7, tissue inhibitor of matrix metalloproteinase, and soluble E- cadherin).
  -  To explore the psychological impact of prognostication in uveal melanoma.
  OUTLINE: Patients undergo plaque radiotherapy, enucleation, or tumor resection based upon standard of care guidelines.
  Trans-scleral fine needle aspiration (FNA) is performed at the time of plaque radiotherapy and ex vivo FNA is performed on enucleation and tumor resection specimens. Tissue samples are analyzed by fluorescence in situ hybridization (FISH). Blood samples are also collected for further analysis.
  After completion of study therapy, patients are followed up periodically.

Eligibility: Inclusion Criteria
  -  Patients must have a clinical diagnosis of melanoma of the iris, ciliary body and/or choroids
  -  Patients must have had a hepatic ultrasound and/or other suitable imaging studies to eliminate metastatic disease
  -  Patients must not have received any local or systemic therapy for uveal melanoma
  -  All patients must be informed of the investigational nature of this study and must provide written informed consent in accordance with institutional and federal guidelines. A copy of the informed consent document signed by the patient must be given to the patient
  -  Patients must have the following pretreatment laboratory findings:
  -  Bilirubin (total) </= 1.5 ml/dl
  -  AST </= 2 x normal
  -  ALT </= 2 x normal
  -  Alkaline phosphatase </= 2 x normal
  Exclusion Criteria
  -  Patients with metastasis
  -  Patients under the age of 18

Relevance to patient case: not relevant