araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

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

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


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

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: miRNA Machinery in Melanoma, Melanoma Metastases and Benign Melanocytic Naevi

Summary: MicroRNAs (miRNAs) are very small endogenous RNA molecules about 22-25 nucleotides in length, capable of post-transcriptional gene regulation. miRNAs bind to their target messenger RNAs (mRNAs), leading to cleavage or suppression of target mRNA translation based on the degree of complementarity. miRNAs have recently been shown to play pivotal roles in diverse developmental and cellular processes and linked to a variety of skin diseases and cancers. In the present study, the investigators examines the expression profiles of miRNA machinery components such as miRNA maturation and transport factors, microprocessor complex and RISC subunits in cutaneous melanoma, cutaneous melanoma metastases and benign melanocytic nevi.

Detailed description: Patients with cutaneous melanoma, cutaneous melanoma metastases and benign melanocytic nevi were included in the study. Punch biopsies were harvested from the center of the tumors. The miRNA machinery components were detected by quantitative real-time reverse transcriptase polymerase chain reaction.

Eligibility: Inclusion Criteria:
  -  cutaneous melanoma
  -  cutaneous melanoma metastases
  -  benign melanocytic nevi
  Exclusion Criteria:
  -  other forms of malignancy

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Thoratec's Reduce Driveline Trauma Through Stabilization and Exit Site Management Study

Summary: The purpose of this study is to evaluate the feasibility of a Percutaneous Lead Management Kit for HeartMate II driveline stabilization and exit site management.

Detailed description: The Percutaneous Lead Management Kit is a combination of commercially available components that are packaged together in a kit to be used for HeartMate II driveline exit site cleaning, dressing and stabilization. The RESIST study is a prospective, non-randomized study to evaluate the wearability and usability of the Percutaneous Lead Management Kit. Evaluation of the Percutaneous Lead Management Kit for wearability and usability will be performed for 30 days from enrollment. Study patients will also be followed for up to 6 months for any evidence of driveline infection.

Eligibility: Inclusion Criteria:
  -  Signed informed consent form
  -  16 years of age or older
  -  Supported by HeartMate II LVAD continuously for at least 6 months and not currently hospitalized
  -  Will continue on LVAD support for at least another 30 days
  -  No driveline or systemic infection
  -  Willing and able to perform kit dressing changes at least once every 7 days for 30 days
  -  Can fill out study forms
  -  Can use a digital camera
  -  Willing to return to clinic for final study visit in 30 days
  Exclusion Criteria:
  -  High risk for non-compliance
  -  Ongoing mechanical circulatory support other than HeartMate II LVAD
  -  Sensitivity to kit components
  -  Skin condition that may react to kit component adhesives
  -  Already using all components of Percutaneous Lead Management Kit

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

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 melanoma; genetic feature: KIT (K642E)

Clinical trial: cKIT, BRAF/NRAS Mutations in Advanced Melanoma : Clinical Outcome in Response to Tyrosine-kinase Inhibitors - KitMel Project

Summary: Background: Metastatic melanoma has a devastating prognosis and is one of the top causes of cancer death in young patients. Until now, available therapies were few and unreliable, but recent understanding of melanomas' molecular pathways has improve their classification and new clinical strategies have been proposed.
  Initial studies showed that B-Raf/N-Ras mutations (respectively V600E and Q61) are the most frequent alteration being present in 70 to 80% of melanomas, characterizing non Chronic Sun-induced Damage skins (CSD). These include Superficial Spreading Melanomas (SSM) and Nodular Melanomas (NM). Other studies showed that c-Kit mutations are presently the predominant activating mutation (20 - 40 %) in Acro-Lentiginous Melanomas (ALM), Mucous Melanomas (MM) and in melanomas arising on CSD skin. c-Kit mutation pattern is more complex with four exons being affected leading to different mutations, which incidence and biological impact are less documented.
  BRAF/NRAS genetics alterations drive constantly cell growth, being thus attractive targets. Spectacular results have indeed been obtained with the BRAF inhibitor that targets the V600E BRAF-mutated form. Data from GIST disease revealed that the different c-Kit mutations modulate differently c-Kit function and the response to targeted therapies.
  Because c-Kit targeted therapy is a critical clinical issue, the investigators aimed to identify the most frequent mutations present in our population to propose appropriate screening test and adapt the therapy.
  Methods: 250 melanoma samples corresponding to an homogeneous white-Caucasian population (Brittany, France) will be screened. c-Kit exons 11, 13, 17 and 18 will be sequenced (direct sequencing and pyrosequencing when possible). c-Kit copy number will be quantified by q-PCR and level of c-Kit determined by immunohistochemistry (IHC, CD117). Samples will also be analyzed for B-Raf mutations in codon 464, 466, 469 and 600, and for N-Ras mutations in codon 12, 13 and 61 (Pyrosequencing).
  Expected Results:
  Taken together, the investigators anticipate that the present genetic analysis of the tumours from patients with advanced melanoma will first document the type and frequency of cKit mutations, will confirm or not that BRAF, NRAS and cKit mutations are mutually exclusive and document their repartition in the melanomas sub-types. Finally this study will clue researchers in to how well patients will respond to a therapy that targets the growth-promoting proteins BRAF/NRAS and cKIT.


Eligibility: Inclusion Criteria:
  -  melanoma
  -  white caucasian population

Relevance to patient case: possibly relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Cervical Cancer Screening Project Part C

Summary: This proposal has been developed through collaboration between the University of Minnesota and New American Community Services (NACS), and the research design is based on a needs assessment conducted by the community partner. The investigators will test the hypotheses that women who are offered home vaginal bio-specimen collection will have higher rate of cervical cancer screening completion than that of women referred for clinic-based Pap test. All participants will be given identical education materials on cervical cancer screening and HPV, currently in use by the Minnesota Sage Program.

Detailed description: The trial will pilot text a protocol for home vaginal bio-specimen collection for human papillomavirus (HPV) testing for cervical cancer screening. The main objective is to estimate the successful screening completion rate among a sample of Somali women who have not undergone cervical cancer screening for three or more years. Women will be randomized to either home vaginal bio-specimen collection or referral to undergo a clinic-based Pap test.

Eligibility: Inclusion Criteria:
  -  Somali female age 25-70 years
  -  have lived in the U.S. 10 years or less
  -  have not had a Pap test (by self report) in the last 3 years
  Exclusion Criteria:
  -  Women with a self reported past history of any of the following will not be eligible:
  -  total hysterectomy
  -  cervical cancer
  -  active history of cervical dysplasia

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Phase II Safety Study of Vemurafenib Followed by Ipilimumab in Subjects With V600 BRAF Mutated Advanced Melanoma

Summary: The purpose of this study is to assess the safety profile of vemurafenib, 960 mg, administered for 6 weeks, followed by ipilimumab monotherapy in patients with BRAF V600 mutated advanced/metastatic melanoma.


Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com
  Key Inclusion Criteria:
  -  Men and women 18 years of age and older
  -  Histologic diagnosis of malignant melanoma tested positive for the BRAF V600 mutation
  -  Previously untreated unresectable Stage III or Stage IV melanoma
  -  Complete set of brain/neck, chest, abdomen/pelvis axial radiographs taken within 28 days of first dose of study drug
  -  Measurable melanoma by physical or radiographic examination
  -  Brain metastases stable after radiation for at least 1 month and off corticosteroid therapy for ≥30 days prior to enrollment
  -  Eastern Cooperative Oncology Group performance status of 0 or 1
  -  Adequate hematologic parameters and renal and hepatic function
  Key Exclusion Criteria:
  -  Primary ocular melanoma
  -  Active brain metastases with symptoms or requiring corticosteroid treatment
  -  Any other malignancy from which the patient has been disease-free for less than 2 years, with the exception of adequately treated and cured basal or squamous cell skin cancer, superficial bladder cancer, or carcinoma in situ of the cervix
  -  History of or current active autoimmune diseases, including but not limited to inflammatory bowel diseases, rheumatoid arthritis, autoimmune thyroiditis, autoimmune hepatitis, systemic sclerosis, systemic lupus erythematosus, autoimmune vasculitis, autoimmune neuropathies
  -  History of or current immunodeficiency disease, splenectomy, or splenic irradiation
  -  Prior anticancer therapy or investigational products <4 weeks prior to enrollment
  -  Prior therapy with a BRAF or MEK inhibitor and prior investigational anticancer immunotherapies;
  -  Prior therapies with immunosuppressive agents within the past 2 years
  -  Concomitant therapy with any anticancer or potent immunosuppressive agent, surgery, radiotherapy, other investigational anticancer therapies, or chronic use of systemic corticosteroids

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Clinical and Histopathologic Characteristics of BAP1 Mutations

Summary: The goal of this protocol is to determine the prevalence of somatic and germline mutations in BAP1 (BRCA associated protein-1) among patients with mesothelioma , choroidal nevus, primary uveal melanoma (UM), or metastatic UM seen at our institution.


Eligibility: Inclusion Criteria:
  All consents:
  -  > or = to 18 years of age
  -  Ability to provide informed consent
  Consent 1:
  Mesothelioma
  -  Histologically proven diagnosis of Mesothelioma OR Choroidal nevus
  -  Diagnosis of choroidal nevus by direct examination and/or ultrasound/optical coherence tomography and possibly fluorescein angiography OR Primary uveal melanoma
  -  Diagnosis of uveal melanoma by direct examination and/or ultrasound/optical coherence tomography and possibly fluorescein angiography
  Consent 2:
  Mesothelioma
  -  Histologically proven diagnosis of Mesothelioma AND
  -  BAP1 mutation or loss of expression identified in tumor sample
  OR one of the following:
  -  Age<50 at diagnosis
  -  No history of asbestos exposure
  -  Personal history of choroidal nevus, uveal melanoma, melanoma, renal cell carcinoma, or cholangiocarcinoma
  -  Family history of choroidal nevus, uveal melanoma, mesothelioma, renal cell carcinoma, or cholangiocarcinoma
  -  History of malignancy in more than two first-degree relatives OR Choroidal nevus
  -  Diagnosis of choroidal nevus by direct examination and/or ultrasound/optical coherence tomography and possibly fluorescein angiography AND one of the following:
  -  More than one clinical risk factor, which may include: orange pigment, thickness > 1 < 2.5mm
  -  Personal history of uveal melanoma, skin melanoma, mesothelioma renal cell carcinoma, or cholangiocarcinoma
  -  Family history of choroidal nevus, uveal melanoma, mesothelioma renal cell carcinoma, or cholangiocarcinoma OR Primary uveal melanoma
  -  Diagnosis of uveal melanoma by direct examination and/or ultrasound/optical coherence tomography and possibly fluorescein angiography
  AND one of the following:
  -  Personal history of uveal melanoma, skin melanoma, mesothelioma, renal cell carcinoma, or cholangiocarcinoma
  -  Family history of choroidal nevus, uveal melanoma, mesothelioma, renal cell carcinoma, or cholangiocarcinoma
  -  History of malignancy in more than two first-degree relatives OR Metastatic uveal melanoma
  -  Histologically proven diagnosis of metastatic uveal melanoma AND
  -  BAP1 mutation or loss of expression identified in tumor sample
  OR one of the following:
  -  Personal history of uveal melanoma, skin melanoma, mesothelioma renal cell carcinoma, or cholangiocarcinoma
  -  Family history of choroidal nevus, uveal melanoma, mesothelioma renal cell carcinoma, or cholangiocarcinoma
  -  History of malignancy in more than two first-degree relatives
  Consent 3:
  -  Relative of patient with germline BAP1 mutation identified through identified testing
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: A Phase II Study of Imatinib Versus Interferon as Adjuvant Therapy in KIT-mutated Melanoma

Summary: The purpose of this study is to compare the relapse free survival and overall survival of Imatinib (Gleevec) or high dose Interferon (Intron) in treating melanoma which has primary tumor and regional lymphonode (if have) removed in patients whose disease carries a c-kit mutation. It is assumed that Gleevec may be more effective on relapse free survival as the adjuvant treatment compared with Interferon.

Detailed description: If mutation tests show that the patient is eligible and they choose to participate in the study, they will be randomized and receive imatinib/Interferon. Each imatinib pill will be 100mg and the participants will take 4 pills once daily (400mg).Participants randomized to the interferon arm will receive Interferon 1500wiu/m2 d1-5 for 4 weeks followed by 900wiu IH TIW for 11 months. The following study procedures will also be performed at routine intervals throughout the course of treatment including blood tests, medical history updates, physical exams and Chest/Abdomen/Pelvic CT examinations.Participants will be on this study for one year and then be followed up to relapse or distal metastasis.

Eligibility: Inclusion Criteria:
  -  Melanoma patients whose primary tumor and regional lymphonodes (if have)have been resected
  -  Histologically documented AJCC stage IIB to IIIC
  -  C-kit mutation documented from either primary or metastatic lymphnode site
  -  ECOG performance status 0 or 1
  -  Age 18 years or older
  -  Creatinine < 1.5 x ULN
  -  ANC > 1500 ul
  -  Platelets > 100,000 ul
  -  Total bilirubin, AST, and ALT < 2 x ULN
  -  Amylase and lipase < 1.5 x ULN
  -  no prior chemotherapy or investigational drug
  Exclusion Criteria:
  -  Severe and/or uncontrolled medical disease
  -  Pregnant or nursing mothers
  -  Any other significant medical, surgical, or psychiatric condition that may interfere with compliance
  -  Patient is < 5 years free of another primary malignancy except: basal cell skin cancer or a cervical carcinoma in situ
  -  Concurrent treatment with Warfarin
  -  Prior treatment with c-kit inhibitor
  -  Patient with Grade III/IV cardiac problems as defined by NYHA criteria
  -  No H2 blockers or proton pump inhibitors
  -  Known chronic liver disease
  -  Known diagnosis of HIV infection
  -  Major surgery within 2 weeks prior to study entry
  -  Patient has received any other investigational agent within 28 days of first study drug dosing
  -  Chemotherapy within 4 weeks prior to study entry

Relevance to patient case: possibly relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: A Phase 1b Open Label, Dose Escalation Study of PLX3397 in Combination With Vemurafenib in V600-mutated BRAF Melanoma

Summary: The purpose of this research study is to test the safety of an investigational new drug called PLX3397 when used in combination with Vemurafenib (Zelboraf™) at different dose levels. Vemurafenib has been approved by the United States Food and Drug Administration (FDA)/European Medicines Agency (EMA) for the treatment of a specific category of unresectable or metastatic melanoma.


Eligibility: Inclusion Criteria:
  -  Male or female ≥18 years old.
  -  Patients with histologically confirmed unresectable Stage III or Stage IV metastatic melanoma who have not been previously treated with a selective BRAF inhibitor.
  -  Presence of a BRAF V600 mutation in the tumor tissue using the cobas BRAF mutation assay or comparable standard of care methodology.
  -  Measurable disease per RECIST v. 1.1 criteria.
  -  ECOG performance status 0 or 1.
  Exclusion Criteria:
  -  Radiation therapy within 14 days of C1D1.
  -  Investigational drug use within 28 days of C1D1.
  -  Patients with active CNS lesions are excluded (i.e., those with radiographically unstable, symptomatic lesions). However, patients treated with stereotactic therapy or surgery are eligible if they remain without evidence of disease progression in the brain for ≥3 weeks.

Relevance to patient case: not relevant