araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 66-year-old female with melanoma; genetic feature: 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: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Studying Tumor Tissue Samples From Patients With Melanoma Who Have Undergone Sentinel Lymph Node Biopsy

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. It may also help the study of cancer in the future.
  PURPOSE: This laboratory study is looking at tumor tissue samples from patients with melanoma who have undergone sentinel lymph node biopsy.

Detailed description: OBJECTIVES:
  -  Develop a predictive model for sentinel lymph node biopsy positivity in patients with melanoma who have undergone sentinel lymph node biopsy.
  -  Develop a survival model for relapse based on sentinel lymph node biopsy positivity.
  -  Assess the genetic determinants in primary melanomas that predict a metastatic phenotype and thereby improve understanding of the biology of the metastases in melanoma.
  OUTLINE: This is a retrospective, case-controlled, multicenter study. Patients are stratified according to Breslow thickness of the tumor (0.75-1.50 mm vs 1.51- 4 mm vs > 4 mm) and gender.
  Archived tumor tissue is analyzed by immunohistochemistry (IHC) for AP2, vascular endothelial growth factor, MMP 2, MCM4, and others, if feasible. Sentinel node biopsies are analyzed by IHC for CD31, LYVE-1, and D2-40 expression. RNA and DNA are also extracted for genetic expression studies and mutation analysis (e.g., BRAF, NRAS, PTEN, CDKN2A).
  Patient data related to relapse and recurrence is collected, if available.
  Peer reviewed and funded or endorsed by Cancer Research UK
  PROJECTED ACCRUAL: A total of 1,000 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Confirmed diagnosis of cutaneous melanoma
  -  Breslow thickness > 0.75 mm
  -  Has undergone sentinel lymph node biopsy
  -  No primary melanoma that has not originated in the skin
  -  No multiple primary melanomas
  -  Currently under clinical followup OR discharged from follow up within the past 3 months
  PATIENT CHARACTERISTICS:
  -  No other malignancy except for nonmelanoma skin cancer or cervical carcinoma in situ
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: A Phase 2 Study to Evaluate Efficacy and Safety of Masitinib in Combination With Methotrexate, in Treatment of Patients With Active Rheumatoid Arthritis

Summary: A 12-week with possible extension, phase II study to compare efficacy and safety of masitinib at 3 and 6 mg/kg/day in combination with methotrexate, in treatment of patients with active rheumatoid arthritis refractory to standard treatments.


Eligibility: Inclusion Criteria:
  1. Disease duration of at least 6 months Meet American College of Rheumatology (ACR) criteria for RA.
  2. ACR functional class I-III
  3. Have active RA
  4. Failed (defined as active RA with stable dose during 3 months) i. methotrexate or ii. any DMARD including anti TNF alpha if patients previously failed methotrexate or iii. methotrexate in combination with any DMARD including anti TNF alpha
  Exclusion Criteria:
  1. Patient had a major surgery within 2 weeks prior to study entry.
  2. Life expectancy < 6 months.

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: 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
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: A Study of AMNN107 in the Treatment of Metastatic and/or Inoperable Melanoma Harboring a c-Kit Mutation

Summary: The purpose of this study is to determine whether nilotinib is efficacious in the treatment of metastatic and/or inoperable melanoma harboring a c-Kit mutation.

Detailed description: This trial began as a multi-center, randomized, Phase III, controlled trial for nilotinib vs (DTIC) dacarbazine to assess the efficacy and safety of nilotinib (400 mg bid) in patients with c-Kit mutated metastatic and/or inoperable melanoma. The study was open to patients with mucosal or acral melanoma.
  Due to substantial difficulties identifying and recruiting eligible patients, the trial design was altered from a randomized, two-arm, Phase III study to a single-arm, Simon two-stage Phase II study with protocol Amendment 2 (27-Jul-2011). While the original protocol required the recruitment of 120 patients, this amendment required the study to recruit only 41 patients (patients randomized to nilotinib prior to Amendment 2 were to be counted in this total, but those randomized to dacarbazine ( DTIC ) DTIC were not). Patients randomized to DTIC were allowed to cross-over to nilotinib, either immediately or at the time of progression.

Eligibility: Inclusion Criteria:
  1. Histologically confirmed mucosal or acral 2. Presence of a c-Kit mutation of exon 9, 11 or 13, or mutations Y822D and mutations D820Y, Y823D of exon 17, as confirmed by the central laboratory 3. Stage III unresectable or stage IV disease 4. The presence of one or more measurable lesions as detected by radiological or photographic methods and assessed according to RECIST 1.0. Lesions must have a size of at least 10mm at longest diameter (using a slice thickness of 5 mm)or double the slice thickness to be considered a target lesion. Target lesions should not be selected in previously irradiated fields unless there is clear evidence of progression 5. WHO performance status 0 - 2
  Exclusion Criteria:
  1. C-Kit mutation of exons 17(except mutations D820Y, Y822D or Y823D) or any other exon not allowed by the inclusion criteria
  2. Patients with c-Kit amplifications only and no mutation
  3. Patients with any history of brain metastases
  4. Patients who have had any prior treatment with TKIs
  5. Patients receiving medications or herbal extracts which interfere with nilotinib metabolism which are not discontinued by the time of the baseline visit
  6. Acute or chronic liver or renal disease considered unrelated to melanoma
  Other protocol-defined inclusion/exclusion criteria may have applied.

Relevance to patient case: possibly relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Study of BMS-650032 With Peginterferon Alfa-2a Plus Ribavirin

Summary: The purpose of this study is to identify one or more doses of BMS-650032 that, when used in combination with pegylated-interferon alpha and ribavirin are safe and demonstrate sufficient activity against hepatitis C virus (Genotypes 1 and 4).


Eligibility: Inclusion Criteria:
  -  Subjects chronically infected with HCV genotype 1 (Phase 2a and Phase 2b)
  -  Subjects chronically infected with HCV genotype 4 (Phase 2b only)
  -  HCV RNA viral load of ≥ 10*5* IU/mL at screening
  -  BMI of 18 - 35 kg/m² at screening
  Exclusion Criteria:
  -  Cirrhosis (Phase 2a only)
  -  Decompensated cirrhosis (Phase 2b)
  -  Co-infection with HBV or HIV
  -  Hepatocellular carcinoma
  -  Prior treatment with anti-HCV drugs

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Facilitating Physical Activity Behavior and Health Outcomes in Breast Cancer Patients Receiving Chemotherapy

Summary: Breast cancer and its treatments can take a toll on the physical and psychosocial well-being of cancer survivors. Few interventions can help breast cancer patients improve their physical strength, stamina, and overall well-being. Developing ways to facilitate PA behavior during chemotherapy for breast cancer are necessary. This trial explores ways that breast cancer patients receiving chemotherapy can learn about and engage in PA during chemotherapy. This trial will also give Southern Alberta breast cancer survivors an opportunity to participate in evidence-based programs designed to facilitate their health, breast cancer recovery, and disease-free survival.
  The investigators primary hypothesis is that women receiving the PA intervention resource kit will report a more positive change in self-reported PA at the end of chemotherapy treatments when compared to the group receiving standard materials.

Detailed description: Primary Objective:
  To compare the effects of an evidence-based intervention consisting of targeted breast-cancer specific PA print materials (i.e., Exercise for health), a step pedometer, a step-walking guidebook (i.e., Step into survivorship), and a physical activity and step journal (INT) to a comparison group receiving a generic, two-page public health PA resource (Standard Material: SM).

Eligibility: Inclusion Criteria:
  -  are diagnosed with stage I -IIIA breast cancer
  -  are scheduled to receive neoadjuvant or adjuvant chemotherapy
  -  did not receive transabdominal rectus abdominus muscle (TRAM) reconstructive surgery
  -  are >18 years of age
  -  receive approval from their treating oncologist to participate
  -  do not have uncontrolled hypertension, cardiac illness, or psychiatric conditions (i.e., indicated in patient medical charts).

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Genome Wide SNP Array-based Approach to Detect Micro-cytogenetic Lesions and KIT Mutation to Improve Treatment Outcomes in Patients With Core-binding Factor Positive Acute Myeloid Leukemia

Summary: Core binding factor (CBF) positive acute myeloid leukemia (AML) consist of 15% of patients in overall AML, expected to harbor a favorable prognosis. However, around a half of cases relapses. Accordingly, more sophisticated classification in CBF positive AMLs is essential to achieve further improvement in the treatment outcome. The current study is designed to evaluate CBF positive AML patients with genome-wide SNP array and KIT mutation study in CBF positive AML patients diagnosed at the Samsung Medical Center and Hwasun Chonnam National University Hospital, Korea between 1994 and 2008.
  1. Construction of the CBF positive AML patient cohort: clinical database establishment (including treatment outcomes and prognosis) and extraction/storage of tumor cell DNAs from marrow samples, then processing of Affymetrix SNP array 6.0.
  2. Construction of prognostic predictive model using pharmacogenomics with the results of genotypes and copy number variations (CNVs).
  3. Detection of hidden microscopic cytogenetic lesions with SNP array technique, and correlation with clinical outcomes in CBF positive AML.
  4. Detection of KIT, FLT3/ITD, and NPM1 gene mutation and its correlation with clinical outcomes in CBF positive AML.
  The current study attempts to analyze genetic data of core binding factor (CBF) positive acute myeloid leukemia (AML) using genome wide SNP array technique with tumor DNAs collected at the time of diagnosis.
  1. To detect microcytogenetic lesions and will analyze its prognostic significance
  2. To analyze genome-wide genotypes and copy number variations (CNVs) using pharmacogenetic approach and will construct a prognostic predictive model
  3. To detect KIT, FLT3/ITD and NPM1 mutation and evaluate its prognostic significance. The present study will establish individualized therapy for CBF positive AML, will provide a basis for molecular marker guided clinical trial in CBF positive AML.


Eligibility: Inclusion Criteria:
  -  patients with core binding factor positive acute myeloid leukemia
  -  18 years or older
  -  patients were treated with standard chemotherapy
  -  patients with available medical record and stored bone marrow specimen at time of diagnosis
  Exclusion Criteria:
  -  no definive criteria

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Study of Nilotinib in Metastatic Melanoma With KIT Aberrations

Summary: Major response was observed to imatinib mesylate in KIT-mutated metastatic rectal melanoma (Hodi FS et al, J Clin Oncol 26:2046-2051, 2008). In the ASCO annual meeting in 2009ar, KIT mutations were reported to be present in 23% of acral and 15.2% of mucosal melanomas (Heinrich MC et al, J Clin Oncol 26:2008 abstr 9016). Nilotinib is a novel tyrosine kinase inhibitor (TKI) targeting KIT, PDGFR, and Bcr-Abl and inhibiting the proliferating of both imatinib-sensitive and imatinib-resistant cells in vitro. Phase I study of nilotinib alone and in combination with imatinib in patients with imatinib-resistant gastrointestinal stromal tumors (GIST) demonstrated significant activity (72% stable disease for nilotinib alone and 56% for nilotinib/imatinib combination) (Blay JY et al, J Clin Oncol 26:2008, abstr 10553).
  Thus, we propose to conduct a phase II study of nilotinib in metastatic melanoma with KIT mutations.


Eligibility: Inclusion Criteria:
  1. Histologically or cytologically proven melanoma with stage IV or unresectable stage III disease
  2. Documented KIT aberration
  3. Adequate organ function as defined by the following criteria:
  -  Serum aspartate transaminase (AST); serum glutamic oxaloacetic transaminase (SGOT)) and serum alanine transaminase (ALT); serum glutamic pyruvic transaminase (SGPT)) ≤ 2.5 x local laboratory upper limit of normal (ULN), or AST and ALT less than or equal to 5 x ULN if liver function abnormalities are due to underlying malignancy
  -  Total serum bilirubin ≤ 1.5 x ULN
  -  Absolute neutrophil count (ANC) ≥ 1500/µL
  -  Platelets ≥ 100,000/µL
  -  Hemoglobin ≥ 9.0 g/dL (may be transfused or erythropoietin treated)
  -  Serum calcium ≤ 12.0 mg/dL
  -  Serum creatinine ≤ 1.5 x ULN
  4. Patients with CNS metastasis must have stable neurologic function without evidence of CNS progression within 8 weeks
  5. May have previous adjuvant therapy with interferon, vaccines or therapy with IL-2, chemotherapy
  6. At least one measurable lesion by RECIST criteria
  7. ECOG PS 0-2
  Exclusion Criteria:
  1. Major surgery or radiation therapy within 4 weeks of starting the study treatment.
  2. History of or known carcinomatous meningitis, or evidence of symptomatic leptomeningeal disease on screening CT or MRI scan.
  3. Ongoing cardiac dysrhythmias of NCI CTCAE grade ≥ 2.
  4. QTc > 470 msec on baseline EKG.
  5. Pregnancy or breastfeeding.

Relevance to patient case: definitely relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Biomarkers in Young Patients With Acute Myeloid Leukemia

Summary: RATIONALE: Studying samples of tissue from patients with cancer in the laboratory may help doctors learn more about biomarkers related to cancer.
  PURPOSE: This research study is studying biomarkers in tissue samples from young patients with acute myeloid leukemia.

Detailed description: OBJECTIVES:
  -  Determine the frequency of ligand-independent phosphorylation of Stat3 in a small cohort of samples from pediatric patients with acute myeloid leukemia including, but not limited to, samples known to express mutated c-kit.
  -  Measure the level of Stat3 phosphorylation in these samples after stimulation of three key cytokine receptors expressed on hematopoietic cells IL-6R, G-CSFR, and c-kit.
  OUTLINE: Cryopreserved samples are analyzed for levels of various components of the Stat3 pathway via western blotting.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of acute myeloid leukemia
  -  One of the following karyotypes:
  -  t(8;21) and WT c-kit
  -  t(8;21) and mutant c-kit
  -  Normal karyotype
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Early Diagnosis of Malignant Transformation of Pigmentary Skin Lesions

Summary: Malignant Melanoma is a deadly skin cancer that can be cured if diagnosed early. To date atypical pigmented skin lesions are diagnosed by appearance alone and many moles and lesions are excised unnecessarily and on the other hand malignant lesions are missed and diagnosed too late. In this study a protein conjugated to a florescent dye is spread on a suspicious pigmented lesion, the hypothesis is that this protein binds to malignant cells only and thus with a special camera that picks up the dye we can find pigmented lesions with early malignant transformation.


Eligibility: Inclusion Criteria:
  -  pigmented lesion indicated for surgical excision
  -  over 18 years of age
  Exclusion Criteria:
  -  pregnancy

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Surgical Outcomes of Vaginal Prolapse Repair With Elevate

Summary: The purpose of this study is to evaluate outcomes in patients having vaginal prolapse repair with the Elevate prolapse repair kit and compare these outcomes to patients who had a repair with Prolift. .

Detailed description: The investigators hypothesize that the less invasive Elevate mesh results in a shorter operative time, lower blood loss, complications, postoperative pain and earlier discharge from the hospital.

Eligibility: Inclusion Criteria:
  -  Women who have had a vaginal repair with Elevate prolapse repair kit
  Exclusion Criteria:

Relevance to patient case: not relevant