araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Differences in Evoked Intracellular Interferon Signaling Pathways Using Single Cell Phosphoprotein Profiling

Summary: Purpose:
  The purpose of this exploratory study is to evaluate phosphoprotein profiling to determine differences in the intracellular actions of interferon or interferon stimulated genes among people with different treatment outcomes to interferon based therapy for hepatitis C (HCV). Participants: Patients with genotype 1 HCV who have had interferon based therapy at the University of North Carolina (UNC). Procedures: Thirty patients with varied responses to treatment will be given a single subcutaneous injection of interferon alpha 2b. Prior to the injection and at 30 minutes, 1,2,4,6,12 and 20 hours after injection, blood will be drawn for analysis of phosphoprotein profiling and changes in serum cytokines.


Eligibility: Inclusion Criteria:
  To be eligible for this study, subjects must meet the following inclusion criteria:
  -  Willing and able to provide informed consent
  -  Males or females age 18 - 65 years
  -  For women of childbearing potential, negative blood pregnancy test documented within the 24-hour period prior to IFN-α administration
  -  History of genotype 1 HCV infection previously treated with peginterferon and ribavirin and with a virological response that can be determined from retrospective review of medical records
  -  A washout period of >12 weeks between the last dose of prescribed peginterferon and ribavirin and the screening visit
  Exclusion Criteria
  Subjects with any of the following will not be eligible for participation:
  -  Neutrophil count <1500 cells/mm3, Hgb <12 g/dL in women or 13 g/dL in men, or platelet count <75,000 cells/mm3 at screening
  -  Serum creatinine level >1.5 times the upper limit of normal at screening
  -  Poorly controlled psychiatric illness, as determined by the study physician, which can be exacerbated by interferon therapy
  -  Infection requiring antibiotics, symptomatic viral infection, inflammatory process requiring therapy, or allergic reactions in the week immediately preceding the inpatient study visit
  -  Use of medications that affect the immune system (e.g. glucocorticoids, chronic NSAIDs daily) in the week immediately preceding the inpatient study visit
  -  History of immunologically mediated disease (e.g., inflammatory bowel disease, idiopathic thrombocytopenic purpura, lupus erythematosus, autoimmune hemolytic anemia, psoriasis, rheumatoid arthritis)
  -  Women with ongoing pregnancy or breast-feeding
  -  History or other evidence of bleeding from esophageal varices or other conditions consistent with decompensated liver disease
  -  History of a seizure disorder or current anticonvulsant use
  -  History of major organ transplantation with an existing functional graft
  -  History of thyroid disease poorly controlled on prescribed medications
  -  History or other evidence of severe illness or any other conditions which would make the patient, in the opinion of the investigator, unsuitable for the study

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Interferon Alfa Sensitivity in HIV/HCV Persons Before and After HIV Meds

Summary: The chief purpose of this research is to evaluate interferon alpha sensitivity and cell type specific levels of interferon receptor and interferon stimulated genes and proteins in HIV/ HCV (hepatitis C virus) coinfected persons before and after administration of HIV medications (antiretroviral therapy).

Detailed description: We plan to perform liver biopsy by microlaparoscopy on previously untreated HIV/HCV coinfected persons, then give them a dose of peginterferon alfa 2b. HCV and HIV kinetics will be studied. Afterward, HIV will be treated using antiretroviral therapy and the procedure will be repeated.

Eligibility: Inclusion Criteria:
  -  Adult Human
  -  Able to provide written informed consent
  -  HIV antibody positive
  -  HIV viral load positive
  -  HIV treatment naive
  -  Hepatitis C antibody positive
  -  Hepatitis C viral load positive
  -  Hepatitis C treatment naive
  -  Approved to take HIV medications for minimum 9 months
  -  Willing to use contraception, Life expectancy greater than 2 years
  Exclusion Criteria:
  -  Significant opportunistic infections within 12 month
  -  Hepatitis B positive
  -  Evidence of liver cirrhosis
  -  Decompensated liver disease
  -  Chronic alcohol abuse
  -  Allergy to raltegravir, tenofovir, and/or emtricitabine
  -  Active or suspected malignancy
  -  Sarcoidosis
  -  Active TB
  -  Coronary artery disease
  -  Uncontrolled seizures
  -  Untreated thyroid disease
  -  Untreated diabetes
  -  Weight greater than 125 kg
  -  Severe depression or severe psychiatric disorder
  -  Ongoing alcohol or illicit drug use
  -  Pregnant, nursing, pr planning to become pregnant
  -  Allergy to interferon

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Study of Circulating Tumoral DNA in Metastatic Choroidal Melanoma

Summary: Circulating tumor DNA detection and quantification in patients with metastatic choroidal melanoma.

Detailed description: Technique development: In first step, the different available techniques will be evaluated for specificity and sensibility using serial dilutions of cell lines with or without GNAQ mutation.
  Validation: The tumor DNA detection rate will be estimated from metastatic uveal patient's blood. The investigators will study 40 patients to obtain at least 15 patients bearing a GNAQ mutation in the primitive tumor or in metastasis. With those 15 patients, the investigators will determinate the most sensitive technique and the best cost/efficiency ratio.

Eligibility: Inclusion Criteria:
  -  Age > or = 18 years.
  -  Patient with a metastatic choroidal melanoma.
  -  Patient with tumor or metastasis available for GNAQ (Guanine nucleotide blinding protein) status characterization.
  -  Patient able to stand a blood collection.
  -  Signed written informed consent approved by competent authority and ethic committee.
  Exclusion Criteria:
  -  Patient without social protection/insurance.
  -  Current pregnancy and lactation.
  -  All social, medical, psychological, situations making the study impossible.
  -  Person deprived of liberty.

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Characterisation of T Lymphocytes, NK Cells and Macrophages in Melanoma Patients

Summary: Melanoma tumor tissue ( in particular regressive areas) present a lymphocytic infiltrate with an anti-tumoral specificity. The aim of the study is to analyse at different stages of the disease, tumor samples and to characterise the cellular infiltrate in situ ( in particular T lymphocytes, NK cells and macrophages), the role of inhibitor receptors on in situ immunosuppression, and potential modulation by medical treatments such as dacarbazine.

Detailed description: The study is divided in 4 parts:
  Part 1: study of cellular infiltrate (lymphocytes) performed on large primary melanoma and cutaneous metastasis ( fresh samples) Part 2: NK cells study on metastatic regional lymph nodes ( fresh samples) and blood samples Part 3: a retrospective study of macrophages in sentinel lymph nodes and in corresponding primary melanomas Part 4: study of the cellular modulation by the chemotherapy (DTIC or cisplatin or inhibitor of B-raf) which(who) will be made on two cutaneous metastases by patient (one taken before the treatment(processing) and one taken during the evaluation after 2 or 3 cycles of treatment(processing))

Eligibility: Inclusion Criteria:
  -  Patients with confirmed melanoma-patients informed of the aims of the study , the modalities
  -  Patients who signed the consent form ou a non opposition form signed by the patient or by a relative
  According to study part:
  Part 1: patients with a melanoma larger than 10mm or with cutaneous metastasis Part 2: stage IV melanoma patients who shall undergo a regional lymph node dissection Part 3: retrospective study of patients who underwent a sentinel node procedure Part 4: Patients achieves of inoperable melanomas the stage(stadium) III or IV that must receive in treatment (processing) a chemotherapy (by the dacarbazine or by the cisplatin or by the inhibitor of B-raf) and carrier of at least two cutaneous metastases
  Exclusion Criteria:
  -  Refusal to take part in the study (patient or relative)
  -  Contraindications known to the xylocaine (groups 1,2, and 4)
  -  No affiliated to the social security system (groups 1, 2, and 4)

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Study to Assess the Safety, Tolerability, and Pharmacokinetics of AMP-224 in Patients With Advanced Cancer

Summary: This is a Phase 1, open-label, multi-center, first time in human study of AMP-224 in adult patients with cancer that is not responding to standard therapy. This study will be conducted in two stages consisting of a Dose-Escalation stage and an Expansion Stage.


Eligibility: Inclusion Criteria:
  -  Must be able to provide informed consent
  -  In Dose-Escalation: Must have solid tumor malignancy or cutaneous T-cell lymphoma that has relapsed and is refractory to standard therapy, or for which no standard therapy exists
  -  In Expansion Phase: Must have melanoma or ovarian cancer that is histologically or cytologically confirmed
  -  Ovarian cancer patients must have recurrent of persistent non-mucinous disease, and must not have received more than 2 prior chemotherapeutic regimens
  -  Melanoma patients must have recurrent or persistent non-ocular AJCC Stage IIIC or IV disease that is surgically incurable and unresectable
  -  Melanoma patients with documented BRAF mutation that is known to be responsive to BRAF inhibitors must have failed or be intolerant to such inhibitors
  -  Must have measurable disease
  -  Must be able to provide access to archival (Dose-Escalation Phase) and/or fresh tumor tissue (Dose-Escalation and Expansion Phases) at Screening prior to study entry
  -  Must by at least 18 years old
  -  Must have adequate organ function
  Exclusion Criteria:
  -  Prior cancer therapies must have completed at least 14 days or 5 half-lives (whichever is longer) prior to first dose of AMP-224
  -  Prior treatment with an anti-PD1 antibody therapy
  -  Known antibody response against prior antibody therapy or fusion protein therapeutics
  -  Major surgery within 4 weeks prior to first dose of AMP-224
  -  Prior allogeneic or autologous bone marrow or organ transplantation
  -  Known and/or a history or evidence of autoimmune disease except vitiligo, resolved childhood asthma and stable hypothyroidism
  -  Received an immunomodulatory drug within 2 weeks of first dose of AMP-224
  -  Active infections requiring antibiotics, physician monitoring, or recurrent fevers >100.4 degrees fahrenheit associated with a clinical diagnosis of active infection
  -  Patients with cirrhosis
  -  Clinically significant cardiac or electrocardiogram abnormalities
  -  History or evidence of HIV
  -  Active viral disease (except when the viral infection is associated with the malignancy)
  -  Regular use of illicit drugs or a recent history of substance abuse
  -  Pregnant or breastfeeding women

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

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: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Does the Aid of MelaFind Affect Clinical Management Decisions

Summary: The objective of this study is to determine and compare the performance of dermatologists (in Germany) on the excision decision against the performance of MelaFind, a non-invasive and objective multi-spectral computer vision system designed as a tool to aid dermatologists in the detection of early melanoma. The hypothesis is that MelaFind's sensitivity is superior to the average excisions sensitivity of dermatologists.
  Another objective is to determine and compare the performance of dermatologists (in Germany) with and without the aid of MelaFind. The hypothesis is that the average excision sensitivity of dermatologists with the aid of MelaFind is superior to the average excision sensitivity of dermatologists without the aid of MelaFind.
  A similar study was previously conducted with dermatologists in the US (NCT01011153). An exploratory objective is to compare the excision decisions of dermatologists from the previous study (in the US) to dermatologists in in this study (in Germany).

Detailed description: Early detection of melanoma is critical for favorable prognosis, since patients with earlier stage melanomas have a much higher probability of survival than with later stages. The traditional method of early detection has been with serial total body skin exams where the health care provider examines all skin surfaces, including mucosa, for suspicious pigmented lesions. The diagnostic performance of dermatologists for melanoma depends on the level of dermatological training. More important than being able to make a diagnosis of melanoma on clinical impression is the ability to make an appropriate decision to excise the lesion. To aid dermatologists in the detection of early melanoma, MelaFind was developed, a non-invasive and objective multi-spectral computer vision system technology. It was designed to generate output - MelaFind Positive or MelaFind Negative- for consideration in the lesion management decisions.
  This survey study will determine and compare the average excision sensitivity to melanoma and specificity of dermatologists (in Germany) without MelaFind output to the average excision sensitivity to melanoma and specificity of dermatologists (in Germany) with MelaFind output. Another purpose is to determine and compare the sensitivity to melanoma and specificity of MelaFind to the average excision sensitivity to melanoma and specificity of dermatologists without MelaFind output.

Eligibility: Inclusion Criteria:
  -Only board certified dermatologists
  Exclusion Criteria:
  -May not have previously participated in MELA Protocols 20061, 20081 or 20063

Relevance to patient case: not relevant
Patient case: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

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: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

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: 60-year-old male with melanoma; genetic feature: NTRK1 rearrangement

Clinical trial: Vemurafenib (R05185426) in Poor Performance Status Patients With Unresectable Locally Advanced or Metastatic Melanoma Harboring a V600E/K Mutation

Summary: The purpose of this study is to find out what effects, good and/or bad, vemurafenib has on the patient and the melanoma. Specifically, the investigators want to know how well vemurafenib shrinks melanoma. The investigators also want to find out how well vemurafenib can improve how well the patient functions.


Eligibility: Inclusion Criteria:
  -  Age >18 years old.
  -  Histologic proof of melanoma reviewed and confirmed by MSKCC.
  -  A confirmed EBRAFV600E or KBRAFV600K mutation.
  -  Stage IV melanoma, or advanced stage III not curable by surgery. Patients with active CNS metastases will be allowed on the study.
  -  Measurable disease by RECIST v1.1.
  -  ECOG performance status 3 or 4. The basis for the grading of performance is strict; there must be clear justification of the performance status grade (e.g. patient is confined to bed > 50% of time, or cannot carry out ADLs, or is otherwise disabled by burden of disease such as requiring supplemental O2).
  -  Patients must be able to swallow pills
  -  Adequate hematologic, hepatic and renal function as defined by the following:
  -  Absolute Neutrophil Count ≥ 1.0 x 109/L
  -  Hemoglobin ≥8.0g/dL, occasional transfusions are acceptable as vemurafenib does not have significant hematologic toxicities.
  -  Total bilirubin ≤2.0x the upper limit of normal, ≤3.0x the upper limit of normal if the patient has Gilbert's Syndrome.
  -  Alkaline phosphatase ≤2.0x the upper limit of normal.
  -  AST and ALT ≤2.0x the upper limit of normal.
  -  Serum creatinine ≤ 1.5x the upper limit of normal.
  Exclusion Criteria:
  -  Uveal melanoma as primary.
  -  Concurrent chemotherapy, immunotherapy, or radiotherapy.
  -  Prior treatment with a RAF inhibitor. Other prior chemotherapy, immunotherapy, or radiotherapy will be allowed including prior treatment with a MEK inhibitor Patients must have had complete recovery from any adverse events or toxicities of prior cancer-directed therapies.
  -  Pregnant or lactating women.
  -  A second active malignancy. Prior malignancy will be allowed as long as the patient is known to be free of disease for at least 2 years. Patients with indolent B-cell malignancies will not be eligible.
  -  QTc interval > 500 msec.

Relevance to patient case: not relevant