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

Clinical trial: A Study of GSK2118436 in BRAF Mutant Metastatic Melanoma

Summary: BRF113710 is a Phase II, single-arm, open-label study to assess the efficacy, safety, and tolerability of GSK2118436 administered twice daily as a single agent in subjects with BRAF mutant metastatic melanoma. Subjects will receive 150 mg of GSK2118436 twice daily and continue on treatment until disease progression, death, or unacceptable adverse event.


Eligibility: Inclusion Criteria:
  -  Must be at least 18 years of age
  -  Must have histologically confirmed cutaneous metastatic melanoma (Stage IV) that is BRAF mutation-positive (V600 E/K) as determined via central testing with a BRAF mutation assay.
  -  Is treatment naive or has received prior treatment for metastatic melanoma.
  -  Must have measurable disease according to Response Evaluation Criteria in Solid Tumors (RECIST 1.1).
  -  Women of child-bearing potential must have a negative pregnancy test within 14 days prior to the first dose of study treatment.
  -  Women with reproductive potential must be willing to practice acceptable methods of birth control during the study and for up to 4 weeks after the last dose of study medication.
  -  Men with reproductive potential must be willing to practice acceptable methods of birth control during the study and for up to 16 weeks after the last dose of study medication.
  -  Must have Eastern Cooperative Oncology Group (ECOG) Performance Status of 0-1.
  -  Adequate organ function.
  Exclusion Criteria:
  -  Previous treatment with a BRAF or MEK inhibitor.
  -  Cancer therapy (chemotherapy with delayed toxicity, radiation therapy, immunotherapy, biologic therapy, or major surgery) within the last 3 weeks; chemotherapy regimens without delayed toxicity within the last 2 weeks; or use of any investigational anti-cancer or other drug within 28 days or 5 half-lives, whichever is longer, preceding the first dose of GSK2118436.
  -  A history of known Human Immunodeficiency Virus (HIV), Hepatitis B Virus (HBV), or Hepatitis C Virus (HCV) infection.
  -  History or evidence of brain metastases on MRI or head CT if MRI is not able to be performed.
  -  History of other malignancy. Subjects who have been disease-free for 5 years, or subjects with a history of completely resected non-melanoma skin cancer or successfully treated in situ carcinoma are eligible.
  -  Certain cardiac abnormalities.

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

Clinical trial: A Retrospective Study of C-kit Mutation Status in Asian Patients With Advanced Gastro-intestinal Stromal Tumors (GIST) Treated With Imatinib.

Summary: Imatinib is the current standard treatment for advanced GIST. Previous studies have shown that GIST genotype was associated with treatment outcomes with exon 11 having superior outcome compared with exon 9 or WT.10, 11 In patients with exon 9 kit mutation, the response rate was higher at when imatinib was given at 800mg daily compared with the standard dose of 400mg daily. Although the data linking tyrosine kinase mutation status and imatinib response in metastatic GISTs is intriguing, more information is needed before mutation testing is adopted as part of the routine analysis of high-risk or overtly malignant KIT-expressing GISTs.25 Despite the fact that exon 9 mutations are associated with a lower response rate, overall survival does not appear to be better with high-dose therapy. The investigators propose to conduct a retrospective analysis of mutational analysis on patients with GIST and determine the relationship between patient response and imatinib dose.


Eligibility: Inclusion Criteria:
  1. Histologic diagnosis of advanced stage or metastatic GIST
  2. Asian patient (as defined by the investigator)
  3. First line treatment with imatinib
  4. Availability of tumor samples for kit mutation analysis
  5. Availability of tumor response rate and or time to progression data
  Exclusion Criteria:
  -

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 Comparing GSK2118436 to Dacarbazine (DTIC) in Previously Untreated Subjects With BRAF Mutation Positive Advanced (Stage III) or Metastatic (Stage IV) Melanoma

Summary: BRF113683 is a Phase III, randomized, open-label study comparing the efficacy, safety, and tolerability of GSK2118436 to dacarbazine (DTIC), in subjects with BRAF mutant advanced (Stage III) or metastatic (Stage IV) melanoma. Subjects will be randomized to receive 150 mg of GSK2118436 twice daily or 1000 mg/m2 DTIC every 3 weeks and continue on treatment until disease progression, death, or unacceptable adverse event. Subjects who progress on DTIC will be allowed to crossover to an optional extension arm of the study to receive GSK2118436.


Eligibility: Inclusion Criteria:
  -  Adults at least 18 years of age
  -  Has advanced (unresectable Stage III) or metastatic (Stage IV) melanoma that is BRAF mutation positive (V600E)
  -  Is treatment naive for advanced (unresectable) or metastatic melanoma, with the exception of Interleukin 2 (IL-2) which is allowed.
  -  Has measurable disease according to RECIST 1.1 criteria.
  -  Women of child-bearing potential must have a negative pregnancy test within 14 days prior to the first dose of study treatment.
  -  Women with reproductive potential must be willing to practice acceptable methods of birth control during the study and for up to 4 weeks after the last dose of study medication.
  -  Men with reproductive potential must be willing to practice acceptable methods of birth control during the study and for up to 16 weeks after the last dose of study medication.
  -  Must have adequate organ function.
  -  Must have Eastern Cooperative Oncology Group (ECOG) Performance Status of 0-1.
  Exclusion Criteria:
  -  Currently receiving cancer therapy (chemotherapy, radiation therapy, immunotherapy, biologic therapy or surgery).
  -  Evidence of active central nervous system (CNS) disease.
  -  Previous treatment for metastatic melanoma, including treatment with BRAF or MEK inhibitor.
  -  A history of other malignancy. Subjects who have been disease-free for 5 years or subjects with a history of complete resected non-melanoma skin cancer or successfully treated in situ carcinoma are eligible.
  -  History of Human Immunodeficiency Virus (HIV) infection.
  -  Certain cardiac abnormalities

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 Crenolanib for the Treatment of Patients With Advanced GIST With the D842-related Mutations and Deletions in the PDGFRA Gene

Summary: This Phase II study is designed to evaluate the antitumor efficacy and pharmacokinetics of crenolanib (CP-868,596) in patients with D842-related mutant metastatic GIST.

Detailed description: Crenolanib (CP-868,596) is an orally bioavailable, selective inhibitor of PDGFR receptor tyrosine kinase with IC50s of 0.4 ng/mL and 0.8 ng/mL for PDGFRα and PDGFRβ, respectively.
  In preclinical models of cell lines with the D842V mutation in the PDGFRA gene, crenolanib (CP-868,596) blocked phosphorylation of PDGFRα at nanomolar concentrations, suggesting that it may provide a clinical benefit to patients with D842V mutant GIST.
  In addition, crenolanib was also active in inhibiting phosphorylation of cell lines with two point mutations (double mutants) PDGFRA V561D + D842V and PDGFRA T674I + D842V.

Eligibility: Inclusion Criteria
  -  Male or female, of any racial or ethnic group
  -  Age 18 years or older
  -  Life expectancy of greater than 12 weeks
  -  Patient able and willing to provide informed consent
  -  Normal liver function, defined as AST and ALT ≤2.5x ULN, and Total Bilirubin ≤ 2x ULN.
  -  Total creatinine ≤ 1.5x ULN
  -  ECOG Performance Status 0 - 2 (Appendix II)
  -  Patients must have histologically or cytologically confirmed GIST with a D842-related mutation or deletion on the PDGFRA gene
  -  Patients must have measurable disease, defined as at least one lesion that can be accurately measured in at least one dimension (longest diameter to be recorded) as >20 mm with conventional techniques or as >10 mm with spiral CT scan. See Section 10.1.2 for the evaluation of measurable disease.
  -  Patients must have recovered from any prior therapy and completed the minimum of, either 5 half-lives of prior therapy or 2 weeks must have elapsed since prior treatment
  Exclusion Criteria
  -  Patient unable to provide informed consent
  -  ECOG Performance status > 2
  -  Any concurrent anticancer therapy, immunotherapy, or hormonal therapy.
  -  Any other investigational agents taken within 2 weeks of start of study drug or if study drug will commence within 5 half-lives of prior therapy
  -  Patients with known or active Hepatitis B or C; liver cirrhosis.
  -  Patients with active fungal, viral, and bacterial infections
  -  Positive serum pregnancy test
  -  Pregnant or lactating women
  -  Patients on concomitant medications that induce or inhibit CYP3A4 (Appendix III)
  -  Patients with severe and/or uncontrolled concurrent medical disease that in the opinion of the investigator could cause unacceptable safety risks or compromise compliance with the protocol e.g. impairment of gastrointestinal (GI) function, or GI disease that may significantly alter the absorption of the study drugs

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 Role of Prostaglandins in Radiation-induced Mucositis

Summary: This study will evaluate the role of cyclooxygenase pathways in radiation-induced and chemoradiation-induced mucositis.

Detailed description: Oral mucositis is a significant toxicity of radiation therapy and chemoradiation therapy in head and neck cancer patients. However the mechanisms that induce such mucositis are not completely understood. Previous work evaluating mucositis in bone marrow transplant patients has suggested that prostaglandin levels may be associated with the appearance of mucositis.
  The present study will measure the levels in saliva of the prostaglandins PGE2 and PGI2 before, during, immediately after, and several weeks after radiotherapy for head and neck cancer. These salivary levels will be correlated with clinical observation of mucositis and patient reporting of pain levels.
  Improved understanding of the mechanism of mucositis may lead to the development of more effective targeted agents to prevent this problem.

Eligibility: Inclusion Criteria:
  -  Histologically proven locoregional Stage 4 squamous cell carcinoma of the oral cavity, larynx, oropharynx or hypopharynx
  -  Receiving radiation therapy or chemoradiation therapy to the oropharynx
  -  Older than 18 years old
  -  ECOG performance status of 0-2
  -  Life expectancy greater than 2 months
  -  Signed informed consent
  Exclusion Criteria:
  -  Previous chemotherapy for this malignancy
  -  Previous radiotherapy to the head and neck
  -  Other cancer diagnosis within the last 5 years except for non-melanoma skin cancer or non-metastatic prostate cancer
  -  Patient taking NSAIDs

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

Clinical trial: Masitinib in Non-Resectable or Metastatic Stage 3/4 Melanoma Carrying a Mutation in the Juxta Membrane Domain of c-Kit

Summary: The objective is to assess the efficacy and safety of masitinib at 7.5 mg/kg/day in the treatment of patients with non-resectable or metastatic stage 3 or stage 4 melanoma carrying a mutation in the juxta membrane domain of c-Kit and who have not previously been treated for melanoma.

Detailed description: Masitinib is a selective tyrosine kinase inhibitor with potent activity against the juxta membrane domain of c-Kit. Masitinib is also thought to promote survival via modulation of immunostimulation-mediated anticancer effects and modulation of the tumor microenvironment. The objective of this study was to evaluate the efficacy and safety of masitinib with respect to dacarbazine in the treatment of non-resectable or metastatic stage 3 or stage 4 melanoma carrying a mutation in the juxta membrane domain of c-Kit. Following a protocol amendment, the dacarbarzine treatment group was closed and recruitment restricted to masitinib treatment of chemo-naïve (first-line) patients.

Eligibility: Main inclusion criteria include:
  -  Patient with histologically or cytologically confirmed non-resectable or metastatic stage 3 (non-resectable IIIB or IIIC, AJCC TNM staging system 7th edition) or stage 4 melanoma
  -  Patient with detectable c-Kit JM mutation (mutation in exon 9, 11 or 13) confirmed by DNA or RNA sequencing, which is expected to be mainly found after screening of mucosal or acral melanoma or melanoma on skin with chronic sun-induced damages (defined by a microscopically marked elastosis involving the skin surrounding their primary melanoma).
  -  Patient not previously treated for melanoma (first-line)
  Main exclusion criteria include:
  -  Pregnant, or nursing female patient
  -  Patient with active brain metastases.
  -  Prior treatment with a tyrosine kinase c-Kit inhibitor

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

Clinical trial: Clinical Protocol SeCore, uTYPE and 3500 Dx System

Summary: The purpose of this study is to compare the Invitrogen SeCore(R) sequencing system and uTYPE(R) interpretation software to the predicate device Invitrogen SSP UniTray(R) with UniMatch(R) interpretation software and show 95% concordance with 90% confidence.

Detailed description: Testing will be performed on A, B, C, DRB1, DRB3/4/5, DQB1, and DPB1 loci. Additionally, testing will be performed using the following locus specific Group Specific Sequencing Primers: A, B, Cw, DPB1, DQB1 and DRB.

Eligibility: Inclusion Criteria:
  -  Deidentified leftover blood samples

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

Clinical trial: Qualitative and Quantitative HIV RNA Detection in Saliva Using the Oragene RNA Kit

Summary: The purpose of this study is to determine if the Oragene.RNA kit is able to detect HIV RNA in saliva.

Detailed description: There is an important need for a rapid, non-invasive, sensitive and specific method for detection of HIV RNA, particularly in clinical settings in which patients at risk for HIV exposure are assessed and screened. A rapid and non-invasive method for quantitative testing of HIV RNA would be also valuable to monitor suppression of HIV RNA as a primary surrogate marker of combination antiretroviral therapy efficacy. An Ottawa-based biotech company (DNA Genotek Inc) has developed and sells to research and clinical labs world-wide a kit (Oragene� DNA Self-collection kit) that permits the collection, stabilization at room temperature, and purification of DNA present in saliva. They have recently developed a kit (Oragene��RNA) that is purported to stabilize RNA in saliva, a non-invasive source of a biological fluid.

Eligibility: Inclusion Criteria:
  -  Four groups of 10 patients each will be recruited:
  -  Controls (HIV and HCV seronegative by previous testing)
  -  HIV seropositive with HIV RNA &gt;1000 copies/mL and not on combination antiretroviral therapy. No concurrent HCV infection.
  -  HIV seropositive with HIV RNA &lt;50 copies/mL as a consequence of combination antiretroviral therapy use. No concurrent HCV infection.
  -  HIV seropositive with HIV RNA &gt;1000 copies/mL and not on combination antiretroviral therapy. HCV RNA positive and not on antiviral therapy.
  Exclusion Criteria:
  -  Not fitting one of the 4 groups

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

Clinical trial: Effectiveness of Direct-to-Patient Outreach on Colorectal Cancer Screening Within a Low Income and Diverse Population

Summary: The purpose of this study is to determine if the direct mailing of fecal occult blood testing (FOBT) kits to patients who are due for colorectal cancer screening is an effective way to improve colorectal cancer screening rates within a low income and racially/ethnically diverse population.

Detailed description: Patients ages 50 to 80 who are identified through the electronic health record as not being up to date on colorectal cancer screening are eligible for the study and will be randomly assigned to the intervention or usual care group. Individuals in the intervention group will be mailed a letter informing them that they are due for colorectal cancer screening, educational material regarding colorectal cancer screening, a fecal occult blood testing (FOBT) kit, directions on how to use and return the FOBT kit. The proportion of patients assigned to the intervention versus usual care groups who complete a guideline recommended form of colorectal cancer screening within 4 months of the initiation of outreach will be compared.

Eligibility: Inclusion Criteria:
  Ages 50 to 80 as of 12/31/2009 At least 2 visits to the community health center between 7/1/2008 and 12/31/2009
  Exclusion criteria:
  Documented fecal occult blood testing (FOBT) within 1 year (between 1/1/2009 and 12/31/2009) Documented sigmoidoscopy within 5 years (between 1/1/2005 and 12/31/2009) Documented colonoscopy within 10 years (between 1/1/2000 and 12/31/2009)

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 of Sunitinib In Young Patients With Advanced Gastrointestinal Stromal Tumor

Summary: Children and young adults with gastrointestinal stromal tumors (GIST) will be treated with sunitinib. The safety (including pharmacokinetics) and tolerability of sunitinib will be studied in these patients. In addition, tumor responses and overall survival will be assessed.


Eligibility: Inclusion Criteria:
  -  Histological diagnosis of GIST.
  -  Patients must have demonstrated either disease progression or intolerance to imatinib mesylate, have non-mutant Stem Cell Factor Receptor gene (KIT) GIST, or cannot obtain imatinib in their country
  -  Measurable by Response Evaluation Criterion in Solid Tumors (RECIST) or evaluable disease.
  Exclusion Criteria:
  -  Current treatment with another investigational agent.
  -  Prior sunitinib treatment.
  -  Prior therapy with known risk for cardiovascular complications.

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

Clinical trial: Study on the Evolution of Genes Mutation Related With Gastrointestinal Stromal Tumors

Summary: Mutations of tumor-related genes are dynamic. Gastrointestinal stromal tumor cells often are obviously more invasive in case of recurrence. The great majority of relapses may be associated with secondary mutation in the GIST related genes. Full gene sequences of c-KIT、PDGFRA and DOG1, which is extracted from the specimen cells of repeated surgical resection or biopsy tissue in GIST patients with postoperative recurrence, are analyzed with the screening-sequencing approach, in order to investigate the characteristics and variations associated with the different gene mutations of c-KIT、PDGFRA and DOG1 in GIST patients and be likely to find out the evolutionary pattern, try to learn the facts about the effect of tyrosine kinase inhibitors on the GIST related genes, make a survey of any association of c-KIT、PDGFRA and DOG1 gene mutations and provide the basis for seeking molecular marker of GIST for monitoring course of disease, and offer a theoretical basis and new therapeutic strategies for application of clinical treatment.


Eligibility: Inclusion Criteria:
  -  patients with Gist at the Department of Gastrointestinal and Glands Surgery of the First Affiliated Hospital of Guangxi Medical University in China.
  Exclusion Criteria:
  -  patients with hepatitis and tuberculosis

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

Clinical trial: Pazopanib in Advanced Gastrointestinal Stromal Tumors Refractory to Imatinib and Sunitinib

Summary: Patients with metastatic or locally advanced gastrointestinal stromal tumors (GIST) who develop resistance against the two hitherto approved drugs for this disease, the tyrosin kinase inhibitors (TKIs) imatinib and sunitinib, have a poor prognosis. Sometimes a further response may be achieved by other drugs, mainly other TKIs, which have been explored in different studies but not yet have been approved for clinical use. Pazopanib is a TKI inhibiting the tyrosin kinases KIT, PDGFRA, and VEGF 1-3, all of which have important roles in the pathogenesis of GIST. Theoretically, it may function in GIST, and it deserves investigational trials. The drug is approved for metastatic renal cancer and is relatively well tolerated. In this trial (SSG XXI), the disease control rate (DCR) = (CR+PR+SD) after 12 weeks of treatment will be assessed as the primary endpoint, and at the same time trough levels will be measured. Secondary endpoints include ORR, PFS, toxicity, and disease control rate in relation to trough level week 12 and in relation to the primary mutation of the tumor (if known). The goal is to include 72 patients in the trial, which is open and single arm.


Eligibility: Eligibility Criteria:
  -  Metastatic and/or locally advanced GIST, with diagnosis based on histology with positive c-kit and/or DOG-1, or with a GIST-typical mutation in KIT or PDGFR
  -  Measurable disease on CT (computed tomography) as defined by RECIST criteria; at least one measurable lesion not given radiotherapy
  -  History of progressive disease on CT according to RECIST criteria after both imatinib and sunitinib treatment, and also after nilotinib if this drug has been given
  -  No other TKIs given than imatinib, sunitinib and nilotinib
  -  Age at least 18 years at the time of diagnosis of GIST
  -  WHO performance status 0-2
  -  Resolution of all toxic side effects from earlier TKI treatment and any other potential non-TKI treatment to grade 1 or below
  -  Sufficient organ functions as defined in the protocol
  -  Absence of earlier or present certain other conditions as defined in the protocol
  -  No pregnancy or lactation
  -  Women with childbearing potential must accept the use of adequate contraception throughout the study period
  -  Written informed consent

Relevance to patient case: not relevant