araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 65-year-old female with melanoma; genetic feature: KIT (L576P)

Clinical trial: Development of Tuberculosis Diagnostic Kit

Summary: Pulmonary tuberculosis is one of the most important infectious diseases in human with high mortality.
  Early diagnosis followed by antibiotic treatment is the only way for control of the disease. However, most of commercial tuberculosis diagnostic kits are of moderate sensitivity. Oncoprobe Inc. recently developed a tuberculosis diagnostic kit (HR-103) based on detection of antibody against Mycobacterium tuberculosis in serum. The main purpose of this project is to evaluate the sensitivity and specificity of the kit in detection of pulmonary tuberculosis from saliva, urine, pleura and serum samples.Capilia TB assay and another Immunochromatographic assay such as ESAT-6 and CFP-10 based or other PCR based immunochromatographic assay will be tried to detection tuberculous disease.

Detailed description: Sputum samples from 200 patients with chest or respiratory problems will be collected. Presence of M.
  tuberculosis in the samples will be checked by acid-fast stain and bacterial culture and identification methods.
  At the same time, saliva, urine, and serum samples from these 200 patients and 50 healthy volunteers will be collected. The tuberculosis diagnostic kit (HR-103) from Oncoprobe Inc. or capilia TB assay or another Immunochromatographic assay such as ESAT-6 and CFP-10 based or other PCR based immunochromatographic assay will be used to detect tuberculosis disease from these samples. By comparing the results with the stain and identification results of sputum samples from the 200 patients, the sensitivity and specificity of the kit in detection of pulmonary tuberculosis from saliva, urine,pleura and serum samples, as well as from combination of these samples, will be obtained. In addition to pulmonary tuberculosis, M. tuberculosis causes pleural tuberculosis. Diagnosis of pleural tuberculosis involves determination of activities of adenosine deaminase and interferon-gamma in pleural effusion, which is tedious. We also plan to collect pleural effusion samples from 100 patients, and examined by the tuberculosis diagnostic kit (HR-103) from Oncoprobe Inc. By comparing the results with the adenosine deaminase and interferon-gamma activities of the same samples, the sensitivity and specificity of the kit in detection of pleural tuberculosis from pleural effusion samples will be obtained.

Eligibility: Inclusion Criteria: clinical suspicious of tuberculosis
  Exclusion Criteria:
  -  HIV

Relevance to patient case: not relevant
Patient case: 65-year-old female with melanoma; genetic feature: KIT (L576P)

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: 65-year-old female with melanoma; genetic feature: KIT (L576P)

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: 65-year-old female with melanoma; genetic feature: KIT (L576P)

Clinical trial: Study of XL820 Given Orally Daily to Subjects With Solid Tumors

Summary: The purpose of this study is to assess the safety and tolerability of the KIT inhibitor XL820 when given orally daily to adults with advanced solid tumors.


Eligibility: Inclusion Criteria:
  -  Subject has a histologically confirmed solid tumor that is metastatic or unresectable for which known effective measures do not exist or are no longer effective, and there are no known therapies to prolong survival
  -  Subject is at least 18 years old
  -  Subject has ECOG performance status ≤ 2
  -  Subject has a life expectancy of > 3 months
  -  Subject has adequate organ and marrow function
  -  In the adrenocorticotropic hormone (ACTH) stimulation test, the subject has a serum cortisol level ≥ 20 ug/dL (552 nmol/L) 30-90 minutes after injection of ACTH
  -  Subject has given written informed consent
  -  Sexually active subjects (male and female) must use accepted methods of contraception during the course of the study.
  -  Female subjects of childbearing potential must have a negative pregnancy test at screening.
  Exclusion Criteria:
  -  Subject has received anticancer treatment within 30 days before the first dose of XL820, or has not recovered to grade ≤ 1 from adverse events due to agents administered more than 30 days earlier
  -  Subject has received radiation to ≥ 25% of his/her bone marrow within 30 days of XL820 treatment
  -  Subject has received an investigational agent within 30 days of the first dose of XL820
  -  Subject has known brain metastases
  -  Subject has known uncontrolled intercurrent illness
  -  Subject is pregnant or lactating
  -  Subject is known to be positive for HIV
  -  Subject has a known allergy or hypersensitivity to any of the components of the XL820 formulation

Relevance to patient case: not relevant
Patient case: 65-year-old female with melanoma; genetic feature: KIT (L576P)

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: 65-year-old female with melanoma; genetic feature: KIT (L576P)

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: 65-year-old female with melanoma; genetic feature: KIT (L576P)

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: 65-year-old female with melanoma; genetic feature: KIT (L576P)

Clinical trial: Hyperbaric Therapy and Deep Chemical Peeling

Summary: To evaluate whether treatment with Hyperbaric oxygen can accelerate skin recovery after deep peeling, and decrease frequency and severity of local side effects and complications.
  20 post peel patients will recieve 5 daily hyperbaric treatments, starting from day 7 to peel.Patient's followup will include self- filling questionnaire and photographs

Detailed description: The study will include 40 post-deep peel women (exoderm), older than 18 years old, treated by the same dermatologist.
  The treatment group will recieve 5 consecutive daily hyperbaric treatments, 1 hours long each, at 2 ATF, starting from day 7 to peel. Prior to treatment, each patient will be signed on informed consent and will have complete physical examination.
  The control group will be matched by the following parameters: age, skin color and type, and indication for peeling, and will be picked up by the dermatologist.
  Patients will be excluded if they have known middle ear disease, chronic lung disease or claustrophobia.
  Follow -up:
  The same dermatologist will follow-up, on regular dates: the follow-up examination will start at day 1 to mask\occlusive dressing removal (equivalent to day 7 post-peel), and at days 7, 28, and after 3 months. All follow-up examinations will take place at noon (04-08 pm) regularly.
  Efficacy parameters:
  All patients will be asked to fill up a daily questionnaire on the first week after peel, and score the severity of pain, pruritus and tightness of facial skin (1 to 5). They will also mention the daily analgesic usage.
  Parameters that will be evaluated by the dermatologist during the study will be: tightness of the skin, pain/burning, pruritus/stinging, swelling/edema, erythema, crusting, and scaling, assessed on a 4-point severity scale (0- best, 3- worst).
  Photographs:
  Photographs of the patients in 5 angles views will be taken on the day of peel, day of mask removal (7), day 28 and after 3 months.

Eligibility: Inclusion Criteria:
  -  The study will include 40 post-deep peel women (exoderm), older than 18 years old, treated by the same dermatologist (dr. Landau).
  -  The treatment group will receive 5 consecutive daily hyperbaric treatments, 1 hours long each, at 2 ATF, starting from day 7 to peel. Prior to treatment, each patient will be signed on informed consent and will have complete physical examination.
  -  The control group will be matched by the following parameters: age, skin color and type, and indication for peeling, and will be picked up by the dermatologist.
  Exclusion Criteria:
  -  Patients will be excluded if they have known middle ear disease, chronic lung disease or claustrophobia

Relevance to patient case: not relevant
Patient case: 65-year-old female with melanoma; genetic feature: KIT (L576P)

Clinical trial: Evaluation of Pigmented Skin Lesions With MelaFind(R) System

Summary: The purpose of this clinical trial is to demonstrate that MelaFind®, a new instrument that uses machine vision for non-invasive early detection of cutaneous pigmented malignant melanoma, is safe and effective. MelaFind® acquires digital images of the lesion with illumination in different spectral bands, from visible to near infrared, and automatically analyzes these images. Diagnostic accuracy of MelaFind® and that of study dermatologists will be evaluated. The reference standard will be final interpretation of lesions by central dermatohistopathology.


Eligibility: Inclusion Criteria:
  -  The lesion is pigmented (i.e., melanin, keratin, blood)
  -  Clinical management of the lesion by the examining dermatologist is either biopsy of the lesion in toto, or 3-month follow-up of the lesion
  -  The diameter of the pigmented area is between 2 and 22 millimeters
  -  The lesion is accessible to the MelaFind hand-held imaging device
  -  The patient, or a legally authorized representative, has consented to participate in the study and has signed the Informed Consent Form
  Exclusion Criteria:
  -  The patient has a known allergy to isopropyl alcohol
  -  The lesion has been previously biopsied, excised, or traumatized
  -  The skin is not intact (e.g., open sores, ulcers, bleeding)
  -  The lesion is within 1 cm of the eye
  -  The lesion is on mucosal surfaces (e.g., lips, genitals)
  -  The lesion is on palmar hands
  -  The lesion is on plantar feet
  -  The lesion is on or under nails
  -  The lesion is located on or in an area of visible scarring
  -  The lesion contains foreign matter (e.g., tattoo, splinter, marker)

Relevance to patient case: not relevant
Patient case: 65-year-old female with melanoma; genetic feature: KIT (L576P)

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