araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Fotemustine and Dacarbazine Versus Dacarbazine +/- Alpha Interferon in Advanced Malignant Melanoma

Summary: This study evaluated two chemotherapy regimens with and without the addition of interferon in patients with advanced or recurrent melanoma.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed diagnosis of malignant melanoma in advanced stage or recurrent after surgery, and not amenable to further surgery or local therapy.
  -  Presence of measurable disease
  -  Age > or = 18 years and < or = 75 years
  -  Performance status (ECOG) 0 - 2 (Appendix 2)
  -  Life expectancy ³ 3 months
  -  Adequate bone marrow function (ANC ³ 2,000/mmc; PTL ³ 100,000/mmc; Hb ³ 10 gr/dl), normal liver and renal function (bilirubin < 1.25 x N, creatinine < 1.25 x N, SGOT, SGPT < 3 times upper normal limit of testing laboratory.
  -  Written, informed consent prior to study specific procedures, with the understanding that the patient has the right to withdraw from the study at any time, without prejudice.
  -  Prior surgery > 3 weeks from initiating .
  -  If palliative radiation is needed, in case of non target lesions, it must be given prior to initiating chemotherapy. If palliative radiation is required during the study the patient should be permanently discontinued from further treatment.
  -  Adequate contraceptive measures during study participation for sexually active patients of child bearing potential must implement.
  Exclusion Criteria:
  -  Previous or concurrent malignancies at other sites with the exception of surgically cured carcinoma in-site of the cervix and basal or squamous cell carcinoma of the skin.
  -  Prior chemo-immunotherapy ( previous adjuvant immunotherapy is allowed)
  -  Known HIV disease.
  -  Concurrent treatment with other experimental drugs.
  -  Concurrent chemotherapy, immunotherapy, hormonal therapy (excluding contraceptives and replacement steroids), radiation therapy
  -  Pregnant or lactating females Previous or concurrent malignancies at other sites with the exception of surgically cured carcinoma in-site of the cervix and basal or squamous cell carcinoma of the skin.
  Prior chemo-immunotherapy ( previous adjuvant immunotherapy is allowed) Known HIV disease. Concurrent treatment with other experimental drugs. Concurrent chemotherapy, immunotherapy, hormonal therapy (excluding contraceptives and replacement steroids), radiation therapy

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

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: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

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: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Comparative Microarray Analysis in Primary Cutaneous Malignant Melanoma

Summary: Perturbations in microRNA (miRNA) expression profiles has been reported for cutaneous malignant melanoma (CMM). This study will be an exploratory analysis by miRNA expression profiling using microarrays.

Detailed description: Perturbations in microRNA (miRNA) expression profiles has been reported for cutaneous malignant melanoma (CMM). With regards to a rapidly growing number of newly discovered miRNA sequences, the availability of up-to-date miRNA expression profiles for primary cutaneous malignant melanoma (PCMM), cutaneous malignant melanoma metastases (CMMM) and benign melanocytic naevi (BMN) is limited. Patients with PCMM, CMMM and BMN are included in the study to perform an exploratory analysis by miRNA expression profiling using microarrays. Expression levels of miRNA candidates will be validated by TaqMan real-time quantitative polymerase chain reaction (RT-PCR).

Eligibility: Inclusion Criteria:
  -  Primary Cutaneous Malignant Melanoma
  -  Cutaneous Malignant Melanoma Metastases
  -  Benign Melanocytic Naevi
  Exclusion Criteria:
  - Other Skin Cancer than Primary Cutaneous Malignant Melanoma

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

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: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

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: definitely relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

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: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

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: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Study of Nivolumab Given Sequentially With Ipilimumab in Subjects With Advanced or Metastatic Melanoma (CheckMate 064)

Summary: The purpose of this study is to evaluate the safety and efficacy of a sequential combination therapy of Nivolumab and Ipilimumab

Detailed description: In order to evaluate the potential synergistic activity of nivolumab and ipilimumab and also because there may be differences in biology between tumors which are stable or responding to therapy and those that are clinically progressing, this study, CA209064, looked at two sequential combination regimens in which the second agent is administered immediately after a pre-specified duration of therapy with the first agent and not delayed until the time of progression after the first agent. This sequential study design looked at pharmacodynamic changes during treatment with one agent which may predict clinical activity to subsequent treatment with the alternate agent. This was done because it has not been scientifically proven whether or not the order in which nivolumab and ipilimumab are given is clinically important.

Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com
  Inclusion Criteria:
  -  Histologically confirmed unresectable Stage III or IV melanoma
  -  Treatment-naive or experienced disease recurrence or progression during or after one prior systemic regimen for advanced disease
  -  Measurable disease by Computed Tomography/Magnetic resonance imaging (CT/MRI) per Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 criteria
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0 or 1
  -  Known BRAF V600 mutation status or consent to BRAF V600 mutation testing
  -  Sufficient tumor tissue accessible for baseline and post-treatment biopsies.
  Exclusion Criteria:
  -  Active central nervous system (CNS) metastases
  -  Carcinomatous meningitis
  -  Active, known or suspected autoimmune disease
  -  Condition requiring systemic treatment with either corticosteroids (>10 mg daily prednisone equivalent) or other immunosuppressive medications within 14 days of randomization
  -  Prior therapy with anti-Programmed Death-1 (PD1), anti-Programmed Death-Ligand 1 (PD-L1), anti-PD-L2, anti-CD137, or anti-CTLA-4 (cytotoxic T lymphocyte antigen 4) antibody
  -  Prior treatment with other immunotherapies
  -  Prior therapy with BRAF inhibitor within 6 weeks of enrollment

Relevance to patient case: not relevant
Patient case: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

Clinical trial: Evaluation of Anti-mullerian Hormone(AMH) Levels as a Predictive Factor of Response to Weight Loss Treatment in Obese Infertile Women With Poly Cystic Ovary(PCOS)

Summary: This study is a prospective before & after clinical trial to compare the basal and 3 months after diet anti-mullerian hormone levels between responders and non-responders to weight loss diet in obese infertile women with PCOS population

Detailed description: The study population comprised of all obese infertile PCOS patients aged 20-40 years which underwent 3 months weight loss diet in royan institute, Tehran Iran.
  The study is conducted over 12 wk energy restriction. All subjects have the same dietary protocol. At baseline, week 12 the levels of AMH,Follicular Stimulating Hormone (FSH), Lutienizing Hormone(LH),Prolactin (PRL), androgens, sex hormone-binding globulin (SHBG), glucose, and insulin were measured and Free Androgen Index (FAI) and Insulin Resistance (IR) indices is calculated. The laboratory tests are determined by radioimmunoassay in the Laboratory of Endocrinology of Royan institute. AMH is measured in duplicate using an ultrasensitive ELISA kit (AMH-ELIZA Kit; Beckman Coulter, Marseilles, France) according to manufacturer instructions. All measurements are performed using a single kit and at the same time in the Laboratory of clinical Immunology of Royan institute.
  Data collection will be performed by using questionnaire to be filled as per the available records and laboratory results. Data analysis will be done through descriptive and perceptive statistical methods.

Eligibility: Inclusion Criteria:
  - 1- diagnosis of PCOS, according to the Rotterdam Consensus Workshop Group, by 2 of the following 3 criteria: menstrual irregularity (cycle length<26 d or >31 d or variation between consecutive cycles of >3 d); clinical (hirsutism assessed by a Ferriman-Gallwey score > 8) or biochemical [free androgen index (FAI) > 5.4 or testosterone_1.4 nmol/L] hyperandrogenism; or positive ultrasound presentation of polycystic ovaries by transvaginal scan.
  2- Age between 18 -40
  Exclusion Criteria:
  - 1. Body mass index (BMI; in kg/m2) < 30, 2. Type 2 diabetes mellitus and related endocrinopathic disorders [identified by assessment of thyroid-stimulating hormone (TSH), prolactin, and 17_hydroxyprogesterone].
  3. Regular exercise activities during the study. 4. Cases of alcoholism and smoking. 5. The use of endocrine hormonal treatment or insulin-sensitizing agents is not permitted during either phase of the study, and the use of oral contraceptives is not permitted during of the study. Subjects are required to cease taking oral contraceptives 4 wk and hormonal treatment or insulin-sensitizing agents 2 wk before commencement of the short-term study phase.

Relevance to patient case: not relevant