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

Clinical trial: Home Usage of Conception Kit Instructions

Summary: Patients will use the Conception Kit in their home and fill out a 22 question questionnaire in order to demonstrate their knowledge of the method of usage as described in the instructions and on the website: www.conceptionkit.com.

Detailed description: Patients will be given a Conception Kit and take the Kit home and read the instructions and if needed consult the website. The patient will then complete a 22 question questionnaire in order to demonstrate their knowledge of the method of use.
  All Components have 510K clearance. This study is a validation of the instructions for use (IFU) only.
  OPK Class I Device 21CFR 862.1485, Conception Cap K993953, Pregnancy Test Kit K974059, Semen Collection Device K902936 (21CFR 884.5300),
  Conception Kit has CE Marked by GMED. (Certificate 2037)
  Conceivex is an ISO 13485: 2003 company

Eligibility: Inclusion Criteria:
  -  Women who are actively trying to become pregnant
  Exclusion Criteria:
  -  Women who are contraindicated for a pregnancy

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

Clinical trial: Molecular Mechanisms and Diagnosis of Mastocytosis

Summary: Mastocytosis is a disorder characterized by presence of excessive numbers of mast cells in skin, bone marrow and internal organs. It can affect both children and adults, males and females and individuals from all ethnic backgrounds, although precise demographic information about the affected populations is not available as it is a rare disorder. Mastocytosis in children is generally limited to the skin and follows a self limited course, while it is a disorder of the hematopoietic stem cell associated with somatic mutations of the c-kit gene in most patients with adult-onset of disease. There is no known curative therapy for most patients with systemic mastocytosis. Recent research studies identified several subtypes of disease with distinct clinical and pathologic features, however, a precise understanding of the incidence as well as molecular pathology of different disease subtypes is lacking. This study aims to examine molecular and cellular pathological aspects of disease in patients with mastocytosis and correlate findings with clinical presentation and prognosis. Patients will undergo a routine history and physical examination, and diagnostic tests will be ordered as dictated by each patient's clinical presentation. Blood and bone marrow will be obtained for diagnostic and research purposes. Genetic analysis of the c-kit gene regulating mast cell growth and differentiation will be performed. It is hoped that findings obtained from this study will help to design novel therapies for mastocytosis and other disorders in which mast cells play a critical role.


Eligibility: Inclusion Criteria:
  -  Confirmed or suspected diagnosis of mastocytosis.
  -  Ability to give informed consent (by the patient or legal guardian if minor)
  Exclusion Criteria:
  -  Inability or not willing to provide informed consent.

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

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

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

Clinical trial: Characterization of the Melanoma-Specific Immune Response

Summary: The aim of this study is to study T-cells. Blood will be collected and the samples will be used to generate T cell clones. Two separate blood draws will be required at the maximum.

Detailed description: The aim of the study is to in-vitro characterize and expand T cells specific for melanoma-derived antigens. Peripheral blood with be collected from 20 volunteers with biopsy proven melanoma and 10 age matched controls. Blood will be collected prior to the initiation of chemotherapy. There will be no more than two blood draws per patient. Most patients will receive a single blood draw; however, some participants may be asked to return for a single additional blood draw if investigators were unable to isolate melanoma-specific immune cells after the first blood draw. Two separate blood draws will be the maximum. The interval between these blood draws will be a minimum of 3 months apart. Blood samples will be used to determine the patient's HLA haplotype via PCR and DNA sequencing. After the patient's haplotype has been established melanoma-specific T cell clones will be generated from the peripheral blood samples and expanded in-vitro. These clones will then be assayed for specificity against commercially available melanoma cell lines. The T cell clones will also be assayed for reactivity to melanocyte differentiation antigens such as MART-1 and gp100. If the volunteer requires a palliative resection of a melanoma tumor then the patient's own tumor cells may also be used to test the specificity of the isolated T cell clones. All experiments will be conducted in-vitro.

Eligibility: Inclusion Criteria:
  -  Biopsy diagnosis of malignant melanoma
  -  Have had a biopsy diagnosis of malignant melanoma in the past
  Exclusion Criteria:
  -  Patients taking immunosuppressive medications

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

Clinical trial: Efficacy of Albumin Interferon Alfa-2b With Ribavirin Compared With Peg-IFN Alfa-2a With Ribavirin in IFN Naive Patients

Summary: This is a phase 3, randomized, multi-center study to evaluate the efficacy and safety of albumin interferon alfa 2b (alb-IFN)in combination with ribavirin compared with peginterferon alfa-2a (PEGASYS or PEG-IFNa2a) in combination with ribavirin in subjects with chronic hepatitis C, genotype 1 who are IFNa treatment naive.


Eligibility: Key Inclusion Criteria:
  -  Diagnosis of chronic hepatitis C.
  -  Liver biopsy performed within 2 years of Day 0 or during screening.
  -  Infected with hepatitis C virus genotype 1.
  -  Interferon alfa treatment naïve (ie, have never been treated with an interferon product).
  -  Subjects are eligible to enter the study if they (or their partners) are not pregnant or nursing, are sterile, or of non childbearing potential, or are willing to practice abstinence or use appropriate birth control methods during the study and for 7 months after the last dose of ribavirin.
  -  Have compensated liver disease.
  Key Exclusion Criteria:
  -  Decompensated liver disease including those subjects with a past history or presence of ascites, bleeding varices or hepatic encephalopathy.
  -  History of moderate, severe or uncontrolled psychiatric disease, especially depression, including a history of hospitalization or prior suicidal attempt.
  -  Positive for human immunodeficiency virus (HIV-1) or hepatitis B surface antigen (HBsAG).
  -  Clinical diagnosis of other causes of chronic liver disease including but not limited to hepatitis B, autoimmune hepatitis, primary biliary cirrhosis, alcoholic liver disease, hemochromatosis, Wilson's Disease, or alpha 1-antitrypsin deficiency.
  -  A history of immunologically mediated disease (eg, rheumatoid arthritis, inflammatory bowel disease, moderate/severe psoriasis, sarcoidosis, systemic lupus erythematosus).
  -  Active seizure disorder within the last 2 years.
  -  Organ transplant other than cornea and hair transplant.
  -  Clinically significant hemoglobinopathy (eg, thalassemia, sickle cell anemia).
  -  Cancer within the last 5 years(with the exception of adequately treated basal cell carcinoma of the skin or in situ carcinoma of the uterine cervix).
  -  Drug or alcohol addiction within the last 6 months. Subjects in a supervised methadone treatment program may be enrolled in the study.
  -  Received any experimental agent within 28 days prior to Day 0.

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

Clinical trial: Imatinib in Patients With Mucosal or Acral/Lentiginous Melanoma

Summary: The purpose of this study is to evaluate how effective imatinib (Gleevec) is in treating acral/lentiginous and mucosal melanoma which has spread to other parts of the body in patients who's disease carries a c-kit mutation. Imatinib is a protein-kinase inhibitor. It is believed that imatinib may be effective in blocking signals on certain cancer cells which allow the malignant cells to multiply and spread.

Detailed description: OBJECTIVES:
  Primary
  -  To determine the response rate of patients with metastatic mucosal, acral/lentiginous, or chronically sun damaged melanomas to treatment with of imatinib.
  -  To determine the time to progression.
  Secondary
  -  To correlate c-kit mutational status with response to therapy.
  -  To evaluate the use of FDG-PET scanning in determining early biologic response to therapy.
  -  Tolerability of imatinib.
  -  To assess amplification of c-kit status through quantitative PCR and/or FISH and other related molecular pathway targets.
  -  To correlate c-kit amplification status with response to therapy.

Eligibility: Inclusion Criteria:
  -  Melanomas that arise on chronically sun damaged skin and have pathologic evidence of solar elastosis
  -  History of primary mucosal or acral/lentiginous melanoma
  -  Histologically documented stage IV metastatic melanoma
  -  ECOG performance status 0,1, or 2
  -  Estimated life expectancy of 6 months or greater
  -  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
  -  C-kit mutation documented from either primary or metastatic tumor site
  -  > 4 weeks from prior chemotherapy or investigational drug
  -  At least one measurable site of disease as defined by at least 1 cm in greatest dimension
  Exclusion Criteria:
  -  Severe and/or uncontrolled medical disease
  -  Pregnant or nursing mothers
  -  Any other significant medical, surgical, or psychiatric condition that my 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 brain metastasis
  -  Known chronic liver disease
  -  Known diagnosis of HIV infection
  -  Previous radiotherapy to > 25% of the bone marrow
  -  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 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: 39-year-old female with melanoma; genetic feature: KIT (N822Y)

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

Clinical trial: MicroRNA Expression and Function in Cutaneous Malignant Melanoma

Summary: Spectrophotometric intracutaneous analysis (SIAscopy) is a new technique for imaging pigmented skin lesions and for diagnosing melanoma and non-melanoma skin cancer. The SIAscope is a portable system comprising of a laptop computer connected to a small handheld skin probe equipped with a light source. The skin lesion is interrogated with light of different wavelengths and the reflection spectra analysed by proprietary algorithms showing distribution, position and quantity of melanin, blood and collagen within the papillary dermis (the SIAgraphs). Earlier studies generated promising results and documented >80% specificity and sensitivity of SIAscopy for melanoma diagnosis. It has been suggested that this technique could be used for the initial screening and selection of pigmented lesion for excision. In this work we addressed the usefulness of SIAscopy for the clinical diagnosis of pigmented malignant melanoma in a prospective, blinded design.


Eligibility: Inclusion Criteria:
  -  Pigmented lesion
  Exclusion Criteria:
  -  No pigmented lesion

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

Clinical trial: A Pilot Study to Evaluate Optical Spectroscopy of Pigmented Skin Lesions

Summary: The incidence of malignant melanoma has increased dramatically in recent decades. In 1930, the lifetime risk of an individual in the United States developing melanoma was 1 in 1,500. This has been exponentially increasing over the years with the risk estimated to be 1 in 75 in 2000 . According to the American Cancer Society, approximately 59,580 new cases of melanoma will be diagnosed in the United States in 2005 and about 7,770 people are expected to die of the disease.

Detailed description: The researcher ucan use special imaging devices to obtain information about a typical mole and melanoma and use this information to determine the different between malignant and benign melanized lesions. The imaging devices are, Modified Two Layer Diffuse Optical Spectroscopy,multi-spectral imaging, and Spatially Modulated Quantitative Spectroscopy can use to measure atypical moles and melanoma and correlate the results of the biopsy tissue histology.
  The imaging devices can quantify melanin, oxy and deoxy hemoglobin concentration, water, lipid and reduced scattering coefficients and can compare results to histopathologic. Atypical moles and melanoma have a different optical profile based on physiological parameters compared to benign nevus.

Eligibility: Inclusion Criteria:
  -  18 years or older.
  -  Have atypical mole/s and melanoma
  Exclusion Criteria:
  -  Age less than 18 years old.
  -  have NO atypical mole/s and melanoma

Relevance to patient case: not relevant