araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Cytogenetic Study of Ocular Melanoma

Summary: Patients who are diagnosed with choroidal melanoma and undergo I-125 plaque or enucleation surgery consent to participate in the study. A tumor sample taken during surgery is studied in the lab for genetic features. These features and features of subjects' clinical course are recorded. Analysis of the data may identify genetic features that are indicative of prognostic factors including risk of metastasis.

Detailed description: The Jules Stein Eye Institute Ocular Melanoma Research Group is conducting cytogenetic studies of choroidal melanoma to improve the screening of biopsy samples of choroidal melanoma through cytogenetic analysis. Our goal is to identify molecular probes that specifically target regions of chromosomes that undergo changes characteristic of metastatic choroidal melanoma.

Eligibility: Inclusion Criteria:
  1. Patient with diagnosis of ocular melanoma
  2. Patient with local treatment plan for ocular melanoma- plaque brachytherapy or enucleation
  3. Patient 18 years of age or older
  4. Archival enucleation specimens with diagnosis of ocular melanoma
  Exclusion Criteria:
  1. Patient who refuses local melanoma treatment
  2. Patient who refuses to participate in this study

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Melanoma Biomarker Study

Summary: The purpose of this study is to measure the level of a specific protein, CXCL1, in the blood of patients with untreated, metastatic (Stage IV) melanoma. These levels will be compared to blood levels in normal controls. If the levels are elevated in metastatic melanoma, further studies to determine if this correlates with presence and extent of disease will be pursued.

Detailed description: Malignant Melanoma has rapidly increased in incidence over the past thirty years, at a rate of roughly 3% per year. In 2005, approximately 59,000 new cases of melanoma were diagnosed with 8000 deaths. While the majority of early melanomas can be surgically cured, advanced melanoma has an extremely poor prognosis. Current chemotherapy and immunotherapy options for advanced melanoma still offer response rates of only 10-20%. Thus, the elucidation of biomarkers in melanoma, both diagnostic and prognostic, is an important area for investigation.
  CXCL1 is a chemokine whose expression is upregulated in melanoma. We postulate that CXCL1 plays an important role in the progression of melanoma to invasive disease. Our hypothesis states that serum CXCL1 levels correlate with the presence of melanoma.
  Aims:
  1. To measure serum levels of CXCL1 in untreated, metastatic melanoma patients and to compare to serum CXCL1 levels in normal controls.
  2. To measure and compare centrally and peripherally collected serum CXCL1 levels in untreated, metastatic melanoma.
  Blood will be collected from metastatic melanoma patients on one occasion, both peripherally and centrally. Control will have blood collected peripherally on one occasion. The blood will be processed and then tested in a blinded, batched fashion.

Eligibility: Inclusion Criteria:
  1. Histologic diagnosis of melanoma; primary may be cutaneous, mucosal or ocular.
  2. Evidence of metastatic disease based on standard AJCC staging.
  3. Willing to give written informed consent.
  4. Willing and able to comply with protocol procedures.
  5. At least 18 years of age.
  6. No prior chemotherapy, immunotherapy, or radiotherapy.
  7. Are able to safely donate 50 mL of blood.
  8. Have a central venous catheter in place (this will not be placed for participation in this trial)
  Exclusion Criteria:
  1. Known diagnosis of a chronic inflammatory disease, ie: Rheumatoid Arthritis, Systemic Sclerosis, Inflammatory bowel disease
  2. Known diagnosis of NYHA class 3 or 4 Congestive Heart Failure
  3. Are unable to safely donate 50 mL blood
  4. Known HIV, Hepatitis B, or Hepatitis C infection.
  5. Any malignancy within 5 years, other than melanoma (for patients); Have any malignancy within the past 5 years including melanoma (for normal controls). Basal cell and squamous cell skin cancers are permitted in all participants.

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Safety Study of PLX4032 in Patients With Solid Tumors

Summary: The primary objective of this FIH study is to assess the safety and pharmacokinetics of PLX4032 in patients with solid tumors. The secondary objective is to assess the pharmacodynamic activity in paired biopsy specimens obtained from patients with malignant melanoma who have the V600E BRAF oncogenic mutation.

Detailed description: Activating mutations of the BRAF gene have been observed in a variety of cancers, including 55-68% of malignant melanomas. In general, oncogenic mutations of BRAF correlate with a poor outcome. PLX4032 is a compound that selectively inhibits oncogenic B-Raf kinase.
  Two extension cohorts of patients with confirmed V600E mutations will be recruited, consisting of advanced melanoma and metastatic colorectal carcinoma.

Eligibility: Inclusion Criteria:
  -  Solid tumors confirmed histologically whose tumors are refractory to standard therapy, or for whom standard or curative therapy does not exist
  -  Patients from whom paired melanoma biopsies are planned must have a V600E+ BRAF mutation confirmed prior to the administration of PLX4032
  -  Previous chemotherapy, immunotherapy, or radiation therapy must have been completed at least 2 weeks prior to starting PLX4032 therapy, and all associated toxicity must be resolved prior to administration of PLX4032
  -  Patients in the Extension cohorts (melanoma or adenocarcinoma of the colon or rectum) must have both a V600E+ BRAF mutation and measurable disease (by RECIST V 1.0 criteria) prior to the administration of PLX4032. All patients enrolled must provide archival or fresh melanoma tumor biopsy for confirmation of V600E+ BRAF mutation status by TaqMan assay
  -  ECOG performance status 0 or 1
  -  Life expectancy ≥ 3 months
  -  Adequate hematologic, hepatic, and renal function
  Exclusion Criteria:
  -  Brain metastases that are progressing or have been documented to be stable for less than 3 months, or for which systemic corticosteroids are required
  -  Investigational drug use within 28 days of the first dose of PLX4032
  -  Uncontrolled intercurrent illness
  -  Refractory nausea and vomiting, malabsorption, or significant bowel resection that would preclude adequate absorption

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Study to Test Genetic Alterations Among Different Dermoscopic Types of Melanocytic Nevi.

Summary: This project is a multicenter study in which we will investigate a dual concept of nevogenesis. Study location is the Department of Dermatology at the Medical University of Graz in collaboration with centers in Austria (Vienna), Italy (Naples, Benevento, Modena), Spain (Barcelona) and the United States (New York).
  The hypothesis is that small congenital melanocytic nevi (CMN), "early" acquired melanocytic nevi in childhood (AMN) and dermal nevi, all dermatoscopically characterized by globular pattern, belong to the same spectrum of genetically determined melanocytic proliferations that develop due to endogenous pathways, in contrast to "true" acquired melanocytic nevi, dermatoscopically showing reticular pattern, that develop due to exogeneous factors such as UV-exposure.

Detailed description: The investigations to this study will verify whether small CMN, "early" AMN and dermal nevi, characterized by globular pattern differ in their genetic alterations compared to reticular typed nevi. It will be expected that globular typed nevi and eventually dermal nevi lack B-RAF mutations whereas reticular nevi show alterations in the B-RAF gene. Study location: Graz

Eligibility: Inclusion Criteria:
  -  Healthy individuals aged 9 to 80 years showing one or more dermoscopically benign nevi with either uniform globular-cobblestone pattern or reticular pattern or a combination of both types
  Exclusion Criteria:
  -  Children under the age of 9 years
  -  Pregnant woman
  -  Patients with atypical nevi (i.e., melanoma cannot be clinically ruled out)
  -  Patients with immunosuppression
  -  Patients with sun exposure 4 weeks before enrollment

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Study of Families With Melanoma

Summary: RATIONALE: A study that evaluates patients' lifestyle, skin, and blood and tissue samples may help doctors understand the risk factors for melanoma relapse.
  PURPOSE: This clinical trial is studying the risk factors for melanoma in families with melanoma.

Detailed description: OBJECTIVES:
  Primary
  -  Determine what lifestyle factors and which genes govern relapse from melanoma.
  Secondary
  -  Compare sun exposure and genes that cause melanoma in patients with melanoma vs healthy participants.
  -  Assess how unusual moles relate to sun exposure and genes that cause melanoma.
  OUTLINE: This is a multicenter, cohort study.
  Patients and healthy participants complete lifestyle questionnaires by mail and telephone. Some patients* and healthy participants undergo a skin examination to count moles and classify skin type (e.g., degree of freckling and wrinkling indicative of sun damage).
  NOTE: *Patients diagnosed with primary invasive melanoma after September 2005 do not need to consent to a skin examination.
  Patients and healthy participants also undergo blood collection for lymphocyte analysis, DNA extraction, and the measurement of minerals, vitamins, and beta carotene. Tissue samples from original diagnosis are examined by immunohistochemistry for gene expression and mutations, including CDKN2A and CDK4.
  Patients and healthy participants are followed annually.
  Peer reviewed and funded or endorsed by Cancer Research UK
  PROJECTED ACCRUAL: A total of 3,700 patients and healthy participants will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Meets 1 of the following criteria:
  -  Newly diagnosed primary invasive melanoma (patient group)
  -  Lentigo maligna malignant melanoma allowed
  -  Rare variants of melanoma allowed, including any of the following:
  -  Acral lentiginous
  -  Subungual
  -  Ear, nose, and throat
  -  Oropharyngeal
  -  Perineal
  -  Vaginal
  -  Vulval
  -  Rectal
  -  Nodal with no known primary
  -  Patients undergoing sentinel node biopsy are eligible
  -  No in situ melanoma, melanocytic intraepidermal neoplasia, or ocular melanoma
  -  Healthy participant meeting either of the following criteria (control group):
  -  Relative of a patient who was diagnosed with melanoma after September 2005
  -  Healthy volunteer who is age- and sex-matched for patients who were diagnosed with melanoma before October 2005
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: High-resolution Magnetic Resonance Imaging (MRI) Scans to Look for Spread of Melanoma to Nearby Lymph Nodes

Summary: The study is designed to see if a high-resolution MRI scan of lymph node areas near where a melanoma has been removed from the skin can pick up the spread of melanoma to those lymph nodes with a high degree of accuracy.

Detailed description: When a melanoma of the skin is diagnosed, there is some chance it can spread to nearby lymph nodes, and from there to other parts of the body. Currently, patients with melanoma at low risk for spreading to lymph nodes do not get the lymph nodes assessed except by a physical exam. Those at high risk for spreading to lymph nodes get one or more lymph nodes removed surgically to check for melanoma spread. But physical exam alone will often miss small areas of melanoma in lymph nodes; removal of lymph nodes by surgery is painful and can cause complications. Neither assessment tool is optimal.
  This study is designed to see if use of very high-resolution contrast-enhanced MRI scans of lymph node areas near the primary melanoma site in the skin can accurately detect small areas of melanoma spread to those lymph nodes. If this turns out to be the case, in the future, MRI scans could potentially be an alternative for assessing lymph nodes, compared to physical exams alone or surgical removal of the lymph nodes.
  In this study, patients with low risk melanoma will receive very high-resolution MRI scans of nearby lymph nodes every 6 months for 5 years of follow-up. If the MRI looks abnormal, the lymph nodes will be biopsied, and results from the biopsy compared to the results from the MRI.
  Patients with high risk melanoma will get a baseline MRI of the nearby lymph nodes, and then one or more lymph nodes will be removed (usually by sentinel lymph node biopsy) regardless of the MRI results. Again, results from the biopsy will be compared to the results from the MRI. MRI's will still be repeated every 6 months to assess whether lymph nodes not removed at surgery develop any changes.
  We plan to enroll 200 patients on this study and by the end of the study will have a measure of the sensitivity and specificity of high-resolution MRI scans in the detection of melanoma involvement of regional lymph nodes.

Eligibility: Inclusion Criteria:
  -  history of invasive cutaneous melanoma stages 1-3 within 2 years of treatment of the melanoma by primary excision
  -  eligible whether or not a sentinel lymph node biopsy or regional lymph node dissection has been performed
  -  adequate renal function (creatinine 2 or less)
  -  life expectancy 2 years of more
  Exclusion Criteria:
  -  history of severe claustrophobia precluding MRI scans
  -  known hypersensitivity or other contraindication to gadolinium contrast
  -  known presence of metastatic melanoma at sites beyond regional lymph nodes (stage 4)

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Health Behaviors, Surveillance, Psychosocial Factors, and Family Concerns

Summary: The purpose of this study is to examine the health behaviors of melanoma survivors. We want to know about their thoughts and concerns. Melanoma is a type of skin cancer. The number of people being diagnosed with melanoma is growing. Many people who are diagnosed with melanoma are young. Little research has been done to find out how melanoma survivors feel years after they have been treated.

Detailed description: The rapidly rising incidence and mortality rates of melanoma, the most fatal form of skin cancer, are among the greatest increases of all preventable cancers over the past decade. However, because of recent advances in early detection, secondary prevention efforts, and treatment, the number of melanoma survivors is increasing. Little research has been conducted on melanoma survivors and important opportunities exist for research in this understudied population. Understanding recurrence and second primary cancer risk, cognitive characteristics, behaviors, surveillance patterns, economic sequelae, and family issues of melanoma survivors is imperative from a public health standpoint to promote the health and well-being of this cohort. The objectives of this study are to: 1) conduct focus groups to enhance our understanding of the behaviors of melanoma survivors, and 2) conduct a pilot survey study based on the results of the focus groups to further describe the behavioral and psychosocial issues in melanoma survivors. This will be among the first studies that explores behavioral and psychosocial issues in melanoma survivors. The study findings will inform a large-scale melanoma survivorship grant proposal to the National Cancer Institute or other federal/private sources of funding.

Eligibility: Inclusion Criteria:
  For the focus group recruitment (Specific Aim 1) - Patients with melanoma (invasive primary cutaneous melanoma, stages 1-III), who have been treated at MSKCC from 1996-2005
  For the survey group recruitment (Specific Aim 2):
  patients with melanoma (invasive primary cutaneous melanoma, stages 1-III), who have been treated at MSKCC from 2001-2011• Ability to sign informed consent which indicates the psychosocial, behavioral, epidemiological nature of this study
  • Age ≥ or = to 18 years and fluent in the English language
  Exclusion Criteria:
  -  Patients with intraepithelial (in situ) melanoma
  -  Patients with stage IV melanoma
  -  Patients with nodal or visceral melanoma without a documented primary lesion
  -  Patients with prior malignancies For the focus group recruitment (Specific Aim 1): (patients treated at MSKCC from 1996-2005) who have a diagnosis >10 years ago from treatment. For the survey group recruitment (Specific Aim 2): patients treated at MSKCC from 2001-2011)who have a diagnosis >10 years ago from treatment.
  -  Patients with a recent diagnosis of melanoma, <12 months
  -  Patients who are one year or more post diagnosis and are still receiving treatment for their melanoma

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: Riluzole in Treating Patients With Stage III or Stage IV Melanoma That Can Be Removed by Surgery

Summary: RATIONALE: Riluzole may stop or slow the growth of tumor cells and may be an effective treatment for melanoma.
  PURPOSE: This early phase I trial is studying how well riluzole works in treating patients with stage III or stage IV melanoma that can be removed by surgery.

Detailed description: OBJECTIVES:
  Primary
  -  To evaluate the potential effects of glutamate receptor blockade on cellular pathways important in the genesis and progression of melanoma in patients with stage III or IV melanoma undergoing surgical resection.
  -  To determine whether treatment with riluzole alters expression of activated PLC and ERK in lysates from tumor tissue biopsies.
  Secondary
  -  Determine if treatment with riluzole affects the overall metabolic activity of melanoma tumors as measured by pre- and post-treatment PET scanning, pre- and post-treatment tumor mitotic rate evaluation, and pre- and post-treatment immunohistochemical staining for Ki-67.
  OUTLINE: Patients receive oral riluzole twice daily for 14 days. Within 24 hours after the final dose of riluzole, patients undergo standard surgical resection.
  Patients undergo tumor tissue sample collection at baseline and during surgery for laboratory studies. Samples are analyzed by routine histology, immunohistochemistry, western blotting, and RT-PCR for Grm1 expression, - RAS and B-raf mutations, PLC and MAP kinase activity, Ki-67 staining, and mitotic rate. Patients also undergo blood sample collection periodically for pharmacokinetics studies.
  PET scans are obtained before and after treatment to evaluate the overall metabolic activity of the tumor and how this activity changes with inhibition of the Grm1 pathway.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically or cytologically confirmed melanoma
  -  Stage III or IV disease
  -  Must have at least two resectable tumors or a tumor large enough to undergo pre-treatment core needle biopsy
  -  Must be eligible for resection of disease with curative or palliative intent
  PATIENT CHARACTERISTICS:
  -  ECOG performance status 0 or 1
  -  ANC ≥ 1,000/mm³
  -  Platelet count ≥ 50,000/mm³
  -  AST/ALT ≤ 3 times upper limit of normal (ULN)
  -  Total bilirubin normal
  -  Calculated creatinine clearance ≥ 50 mL/min
  -  INR ≤ 25% of ULN
  -  Not pregnant or nursing
  -  Negative pregnancy test
  -  Fertile patients must use effective contraception during and for 48 hours after completion of study treatment
  -  No history of allergic reaction to riluzole or similar compounds
  -  No known history of hepatitis B or C
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: PEAK: Panitumumab Plus mFOLFOX6 vs. Bevacizumab Plus mFOLFOX6 for First Line Treatment of Metastatic Colorectal Cancer (mCRC) Patients With Wild-Type Kirsten Rat Sarcoma-2 Virus (KRAS) Tumors

Summary: The primary objective of this study is to estimate the treatment effect on progression-free survival (PFS) of panitumumab relative to bevacizumab in combination with mFOLFOX6 chemotherapy as first-line therapy in patients with tumors expressing wild-type KRAS, unresectable mCRC.


Eligibility: Inclusion Criteria:
  -  Histologically or cytologically-confirmed adenocarcinoma of the colon or rectum in patients with unresectable metastatic (M1) disease
  -  Patients with at least 1 uni-dimensionally measurable lesion of at least 10 mm per modified Response Evaluation Criteria in Solid Tumors (RECIST) guidelines
  -  Wild-type KRAS tumor status confirmed by an Amgen approved central laboratory or an experienced laboratory (local laboratory) per local regulatory guidelines using a validated test method
  -  Eastern Cooperative Oncology Group (ECOG) score of 0 or 1
  -  Men or women 18 years of age or older
  -  Adequate hematologic, renal, hepatic, metabolic, and coagulation function
  Exclusion Criteria:
  -  History of prior or concurrent central nervous system (CNS) metastases
  -  Prior chemotherapy or other systemic anticancer therapy for treatment of metastatic colorectal carcinoma
  -  Clinically significant cardiac disease
  -  Clinically significant peripheral sensory neuropathy
  -  Active inflammatory bowel disease
  -  Recent gastroduodenal ulcer to be active or uncontrolled
  -  History of interstitial lung disease
  -  Recent pulmonary embolism, deep vein thrombosis, or other significant venous event
  -  Pre-existing bleeding diathesis and/or coagulopathy with exception of well-controlled anticoagulation therapy
  -  Recent major surgical procedure, open biopsy, or significant traumatic injury not yet recovered from prior major surgery.

Relevance to patient case: not relevant
Patient case: 32-year-old male with melanoma; genetic feature: NRAS (Q61H)

Clinical trial: NKTR-102 Versus Irinotecan in Patients With Second-Line, Irinotecan-Naïve, KRAS Mutant, Colorectal Cancer

Summary: This study will evaluate whether NKTR-102, an investigational drug has an anti-tumor effect in patients with colorectal cancer. This study will also evaluate how the safety and anti-tumor activity of NKTR-102 compares with irinotecan, a cancer drug that is approved for use in the US for treatment of patients with certain types of colorectal cancer.


Eligibility: Inclusion Criteria:
  -  metastatic colorectal cancer
  -  tumor with k-ras mutation
  Exclusion Criteria:
  -  More than 1 prior regimen for treatment of metastatic disease

Relevance to patient case: not relevant