araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: The Aging Endocrine Pancreas: Characterization of the Entero-insular Axis Physiology in the Elderly

Summary: Like most endocrine axes, the entero-insular axis is expected to go through an age-related physiological deterioration, what might contribute to special features of the elderly onset type 2 diabetes in comparison to middle-age.
  Twenty four NGT volunteers will be evaluated by a meal tolerance test (MTT) for incretin hormone measurements, and by the hyperglycemic clamp followed by an arginine test for assessing the beta-cell function and the acute insulin response. Others parameters as body composition and basic biochemistry will be also evaluated at Laboratory of Investigation on Metabolism and Diabetes - LIMED / State university of Campinas, Brazil.
  The characterization of the glucagon-like peptide-1 (GLP-1) production, dipeptidyl peptidase IV (DPP-IV) activity and/or endocrine pancreas incretin-response at aging, might be an interesting evidence to reinforce an incretin-based therapeutic approach for elderly onset type 2 diabetes.


Eligibility: Inclusion Criteria:
  -  Stable weight (< 5% variation) within the last three months
  -  Age: 35 to 50 years old for middle-age group, and 65 to 80 years old for elderly group.
  -  BMI: 20 to 29.9 kg/m2
  -  Normal glucose tolerance (NGT) for groups Elderly and Middle-age
  Exclusion Criteria:
  -  Use of estrogen, progestogen or systemic corticosteroids.
  -  Hepatic cirrhosis, renal failure or any clinical condition with impaired insulin sensitivity
  -  Smoking
  -  Obesity
  -  Uncontrolled systemic or debilitating diseases

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Genetic Risk Factors and Acquired Oncogenic Mutations of Melanoma

Summary: Though it is generally accepted that exposure to sunlight is a major causative factor for skin cancer, the risk for developing melanoma is not directly linked to sun exposure such as in non-melanoma skin cancer. Therefore, a dual pathway has been proposed, distinguishing melanoma that develops on skin that is chronically exposed to sunlight from those that occur on skin that is normally protected. The risk for each type of melanoma is believed to be determined in part by genetic factors. To define these markers reproducibly, the investigators plan to establish a large cohort with comprehensive information regarding sun sensitivity (skin type), history of experienced sun exposure, skin pigmentation phenotypes, total number of nevi, and other types of skin tumors in a central European population. The investigators will obtain blood from all participants for DNA as well as serum analyses. Based on the finding that genetic variants of the melanocortin-1 receptor (MC1R) gene, associated with red hair and fair skin, have been shown to be associated with increased risk for melanoma, particularly those harboring BRAF mutations, the investigators will now focus on the study of recently discovered genetic variants associated with pigmentation. Furthermore, the investigators will study the relation of these variants with oncogenic mutations of melanoma in BRAF, RAS and c-Kit. The study of other genetic variants will follow, once a sufficiently large cohort has been established to reveal an independent genetic risk factor in a multivariate analysis including potential covariates as mentioned above. The identification of genetic risk factors for melanoma will not only help identify individuals with increased risk but also improve our understanding of the molecular background of the development of melanoma.


Eligibility: Inclusion Criteria:
  -  patients with or without melanoma
  Exclusion Criteria:
  -  HIV and Hepatitis C positive individuals.

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Trial of Imatinib (Gleevec®) in Selected Patients With Metastatic Melanoma

Summary: This study is a single-armed, open-label, single-center phase II trial of signal transduction inhibitor number 571 (STI-571) systemic therapy in selective patients with metastatic melanoma, and aims to study the efficacy and safety. The primary endpoint is progression-free survival (PFS) and the second endpoints are overall response rate (ORR), overall survival (OS), 1-year OS and safety.

Detailed description: Only patients who meet the inclusion and exclusion criteria will be enrolled. The estimated recruitment duration is 1 year. Imatinib will be given in the dose of 400 mg orally each day unless disease progression or intolerance. The follow-up is 12 months.
  Forty-eight subjects will be recruited for this study. This sample size is justified by the number of patients required to establish an improvement in PFS with statistical significance compared to historical control.
  The standardized RECIST (Response Evaluation Criteria in Solid Tumors) method of unidimensional tumor assessment will be employed to evaluate tumor lesion size per 2 months in the determination of response rate and progression free survival. Repeated radiographic assessment at 4 week intervals is consistent with general oncological practice associated with computerized tomography (CT) or magnetic resonance imaging (MRI) scan testing. All efficacy endpoints will be evaluated by the investigator.
  Safety will be characterized in terms of the incidence, timing, severity, and relatedness of adverse events and laboratory abnormalities. Severity will be graded according to the NCI CTCAE Version 3.0.

Eligibility: Inclusion Criteria:
  1. Histologically confirmed melanoma with metastases and has no received any systemic treatment within 1 month
  2. Evidence of mutations and/or copy number increases of KIT with laboratory examination documented from either primary or metastatic tumor site
  3. ECOG performance status 0, 1, or 2
  4. Estimated life expectancy of 6 months or greater
  5. Age 18 years or older, male of female
  6. At least one measurable site of disease
  7. Adequate organ function
  8. Willingness and ability to comply with scheduled visits, treatment plans, laboratory tests, and other study procedures
  Exclusion Criteria:
  1. Melanoma from primary sites other than acral or mucosal melanoma
  2. Received systemic anti-cancer therapy within 1 month before enrollment for metastatic disease
  3. Diagnosis of any second malignancy within the last 5 years, except for adequately treated basal cell carcinoma, squamous cell skin cancer, or in situ cervical cancer
  4. Severe and/or uncontrolled concomitant medical diseases
  5. pregnant or childbreeding women
  6. Known hypersensitivity to imatinib
  7. Current treatment on another clinical trial

Relevance to patient case: possibly relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Identification of Gene Biomarkers in Aging Skin

Summary: This study is a blinded, prospective, single-center, clinical study conducted in Japanese female subjects between the ages of 20-75 years. This design uses skin biopsy samples from environmentally exposed areas and unexposed (control) areas within the same subjects to assess the gene expression profile from three different age groups.

Detailed description: The primary objective of the skin aging study is to investigate changes in gene expression patterns that occur during the aging process.

Eligibility: Inclusion Criteria:
  -  Individuals who are willing to read and sign an informed consent form prior to participating in the study.
  -  Individuals who have a temperature of less than or equal to 100 degrees F at the time of biopsy collection.
  -  Individuals who had not applied any sunless tanning product on the arms within the past year.
  -  Individuals with no prior history of alcoholism (or who consume fewer than 2 to 3 alcoholic beverages per day).
  -  Individuals who have not consumed any anti-aging nutritional supplements (multivitamins and multiminerals are acceptable) or aspirin, NSAIDS, or other pain medication in the last 48 hours before biopsy.
  Exclusion Criteria:
  -  Male gender
  -  Individuals who did not fit the 'inclusion criteria' above.

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: OX-40 Protein Expression in the Sentinel Lymph Nodes of Patients With Cancer

Summary: RATIONALE: Studying protein expression in sentinel lymph node tissue from patients with cancer in the laboratory may help doctors identify and learn more about biomarkers related to cancer. It may also help the study of cancer in the future.
  PURPOSE: This laboratory study is evaluating OX-40 protein expression in the sentinel lymph nodes of patients with cancer.

Detailed description: OBJECTIVES:
  -  Determine the qualitative and quantitative expression of OX-40 and related markers in sentinel lymph nodes previously removed from patients with cancer.
  -  Determine the qualitative and quantitative expression of OX-40 and related markers in sentinel lymph nodes freshly removed from patients with cancer.
  -  Correlate the expression of OX-40 and related markers in sentinel lymph node tissue with expression in nonsentinel tissue from primary tumors and nonsentinel lymph nodes, tumor stage, and patient outcomes.
  OUTLINE: Sections of primary tumors, nonsentinel lymph nodes, and sentinel lymph nodes will be analyzed for expression of OX-40 by immunohistochemistry. Sections of negative (no tumor metastases) lymph nodes will be used as internal controls. Fresh tissue and blood will be tested for marker analysis and in vitro assays of immune function.
  PROJECTED ACCRUAL: A total of 100 specimens from sentinel lymph nodes previously removed from cancer patients and 100 specimens from sentinel lymph nodes freshly removed from cancer patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically or cytologically confirmed cancer, including, but not limited to, the following:
  -  Melanoma
  -  Breast cancer
  -  Invasive squamous cell cancer
  -  Other cancers for which patients underwent or will undergo the following:
  -  Adequate archived paraffin-embedded tissue for making slides for immunostaining
  -  Adequate freshly removed sentinel lymph node (and primary tumor, if available) tissue for laboratory assays
  -  Clinical data and date of last follow-up on tumor stage and status must be available
  -  Hormone receptor status not specified
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Pilot Study of Infrared Imaging of Cutaneous Melanoma

Summary: Design: this is a pilot study of infrared imaging of cutaneous lesions in patients and volunteers with and without clinically detectable melanoma, and with one or more palpable cutaneous lesions eligible for this imaging study. Participants will be evaluated with infrared camera imaging at cutaneous sites with known melanoma deposits, suspected melanoma deposits that are to be biopsied, or at cutaneous sites with other lesions, including other skin cancers, benign inflammatory lesions, benign neoplastic lesions (lipomas, epidermal cysts, dermatofibromas, scar, healing wound, etc.).


Eligibility: Inclusion Criteria:
  -  Patients or volunteers with or without a history of melanoma.
  -  One or more palpable skin or subcutaneous lesions for which at least one of the following is true:
  -  A tissue diagnosis has been made for the lesion(s) in question, by prior cytologic or histologic evaluation (Category A1).
  -  A tissue diagnosis will be obtained for the lesion(s) in question by cytologic or histologic evaluation (Category A2).
  -  A tissue diagnosis is not available, but a clinical diagnosis of melanoma or benign lesion is available with a high degree of confidence. Examples are hemangiomas, skin tags, seborrheic keratoses, dermatofibromas, lipomas, or growing pigmented skin lesions that are comparable to other cutaneous metastases of melanoma in the same patient (Category B).
  -  All patients must have the ability and willingness to give informed consent and must be age 18 years or older at the time of study entry.
  Exclusion Criteria:
  -  Known or suspected allergy to the adhesive skin markers or water-soluble ink used for the labeling of lesions.
  -  Very fragile skin that may be susceptible to injury from adhesive markers.
  -  Patients in whom there is a medical contraindication or potential problem in complying with the requirements of the protocol, in the opinion of the investigator.

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: International Melanoma Algorithm Training Study - IMATS

Summary: This is an international, multicenter, prospective, non controlled, non randomized, clinical study to collect electrical impedance data of potentially malignant pigmented nevi and histological diagnoses (International Melanoma Algorithm Training Study [IMATS]). The study objective is to collect data for training and optimization of an algorithm that can classify skin lesions using electrical impedance, i.e., to identify malignant melanomas.


Eligibility: Inclusion Criteria:
  -  Men and women of any ethnic group
  -  Lesion located on normal healthy skin
  -  Maximum number of eight lesions per patient
  -  etc.
  Exclusion Criteria:
  -  Lesion under finger and toe nails
  -  Lesion located on eczema, psoriasis areas or similar
  -  Lesion located on scars
  -  etc.

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Study of Tumor Tissue Samples From Patients With Stage I, Stage II, or Stage III Malignant Melanoma

Summary: RATIONALE: Studying the genes expressed in samples of tumor tissue from patients with cancer may help doctors identify biomarkers related to cancer.
  PURPOSE: This research study is looking at tumor tissue samples from patients with stage I, stage II, or stage III malignant melanoma.

Detailed description: OBJECTIVES:
  -  Determine the genetic profile of primary melanomas with and without synchronous regional nodal involvement by examining for 1) activating mutations B-Raf and N-Ras associated with melanoma development, and 2) allelic imbalances across the genome.
  -  Compare the genetic profile of primary melanomas from patients with and without lymph node involvement.
  -  Determine the combinations of genetic lesions that correlate with nodal metastasis by adopting a statistical machine learning approach to build a lesion-based classifier for nodal metastasis.
  OUTLINE: Laser capture microdissection is performed on the archived tissue samples to isolate melanoma cells. DNA is then purified from the samples and amplified using PCR. Matrix-assisted laser desorption/ionization (MALDI)-time of flight mass spectrometry technology is used to detect mutations of B-Raf and N-Ras. Single nucleotide polymorphism arrays are also performed.
  Information about the patient's demographics (e.g., TNM staging, sex, age, and tissue collection dates) will be gathered by chart review or from the Multidisciplinary Melanoma Conference at University Hospitals tumor conference report in order to match cases.

Eligibility: Inclusion Criteria:
  -  Node positive Group (experimental group)
  -  Primary melanoma > 2 mm in depth
  -  Metastasis must be > 0.1 mm and detectable by IHC or hematoxylin and eosin (H&E) to be considered node positive
  -  Slides and block for primary and node must be archived in UH dermatopathology
  -  Node Negative Group (control group)
  -  Primary melanoma > 2 mm in depth
  -  A negative sentinel lymph node must be negative by IHC and H&E
  -  No stage IV disease
  -  No acral and mucosal histology
  -  No history of prior invasive melanoma
  -  Underwent primary excision and sentinel lymph node biopsy within 3 months of each other
  -  Archived tissue available
  -  Slides and block for primary tumor and node biopsy must be archived in University Hospitals Case Medical Center (UH) dermatopathology
  Exclusion Criteria:
  -  Acral and mucosal histology
  -  Previous diagnosis of invasive melanoma
  -  previous chemotherapy or immunotherapy
  -  patients who are found to have stage IV disease during workup

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Efficacy and Safety Study of PEG-rIL-29 Plus Ribavirin to Treat Chronic Hepatitis C Virus Infection

Summary: Interleukin 29 (IL-29) is a substance that is produced in the body to help fight viral infections. The purpose of this study is to evaluate the safety and antiviral effects of several different doses of PEG-rIL-29 (a man-made form of IL-29) when it is given in combination with daily oral doses of ribavirin (an antiviral drug) to subjects with hepatitis C infection who have received no prior treatment for this disease.

Detailed description: PEG-rIL-29 (also known as PEG-interferon lambda) is a unique Type III interferon molecule that has demonstrated antiviral activity when administered weekly for 4 weeks to treatment-relapsed and treatment-naive subjects with genotype 1 hepatitis C virus (HCV) infection. Because PEG-rIL-29 binds to a unique receptor with a more limited distribution than the receptor for interferon (IFN)-α, it may have the potential to treat HCV without some of the treatment-limiting side effects associated with IFN-α-based therapies. The purpose of this Phase 2a/b randomized, controlled, multicenter study is to compare the safety and efficacy of PEG-rIL-29 and peginterferon alfa-2a, both administered subcutaneously weekly for up to 48 weeks in combination with daily oral ribavirin, in treatment-naive subjects with chronic genotype 1, 2, 3, or 4 HCV infection. The initial part of the study (Phase 2a) will be conducted as an open-label study; the second part of the study (Phase 2b) will be conducted as a blinded study. The above information provided in this listing is specific to the Phase 2b portion of the study. In addition, two small open-label substudies will be conducted to evaluate the efficacy of 24-week treatment with PEG-rIL-29 and ribavirin in subjects with HCV genotype 1 who have a particular genetic polymorphism associated with favorable response (n=60) and to evaluate the efficacy of 16-week treatment with PEG-rIL-29 and ribavirin in subjects with HCV genotype 2 or 3 (n=30).

Eligibility: Inclusion Criteria:
  -  No prior therapy for chronic HCV, other than up to 2 weeks of single-agent therapy with a direct-acting antiviral agent, including but not limited to, a protease or polymerase inhibitor
  -  HCV genotype 1, 2, 3, or 4
  -  HCV RNA ≥100,000 IU/mL
  -  ALT and AST ≤5.0 × ULN
  -  Documented absence of cirrhosis
  -  Able to comprehend the investigational nature of this study and sign an informed consent form
  Exclusion Criteria:
  -  Mixed genotype HCV infection
  -  Current or prior history of decompensated liver disease
  -  Received any investigational drug, including a direct-acting antiviral agent, within 60 days prior to receiving study drug
  -  Positive test for hepatitis B surface antigen, human immunodeficiency virus (HIV)-1, or HIV2 antibody at screening
  -  Active substance abuse, such as alcohol, or inhaled or injected drugs, within 6 months
  Additional inclusion and exclusion criteria are specified in the protocol.

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: The Identification of Novel Prognostic Markers in Melanoma

Summary: The purpose of this project is to analyze tumour tissue from a group of subjects with malignant melanoma, who have been treated at the Royal Marsden Hospital.

Detailed description: Background - The Royal Marsden Hospital and the Institute of Cancer Research constitute the largest comprehensive cancer centre in Europe. In addition to an in-house drug development program, phase I - phase III clinical trials of novel anti-cancer agents are hosted. In order to investigate the optimal use of novel molecularly targeted agents, access to clinical tumour samples is needed in order to determine which particular cancer type expresses a molecular "signature" that may indicate potential therapeutic utility. Understanding such signatures should accelerate the registration of new drugs for routine cancer therapy; offering the potential of selecting those patients with tumour types most likely to benefit from therapy. Furthermore, new insights into disease biology may be gained.
  Main research question/ objective - Are there features of primary melanoma or lymph node metastases that predict subsequent clinical outcome better than existing markers?

Eligibility: Inclusion Criteria:
  -  Diagnosis of melanoma
  -  Adequate paraffin-embedded material available for analysis.
  -  Adequate clinical follow-up information
  -  Written informed consent where applicable
  Exclusion Criteria:
  -  Inadequate paraffin-embedded material available
  -  Inadequate clinical follow-up information.

Relevance to patient case: not relevant
Patient case: 62-year-old female with melanoma; genetic feature: KIT (K642E)

Clinical trial: Survey Study - Sensitivity Comparison Between MelaFind and Physician Group

Summary: This survey study purposes to determine and compare the biopsy/referral sensitivity and specificity of MelaFind to the average biopsy/referral sensitivity and specificity of dermatologists. 241 subjects logged into system but only 183 signed consents and completed the intake survey. Out of these 183, 155 were accounted for in the data analysis after exclusions were removed from the pool of subjects.

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. Studies have demonstrated that the diagnostic accuracy of physicians 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 biopsy the lesion. Primary care physicians (PCPs) are often expected to screen for melanoma and only refer to dermatologists when there is a high clinical suspicion of melanoma. However, if PCPs are not adept at diagnosing melanoma, then opportunities for early diagnosis and treatment could be missed. Conversely, the morphology of benign pigmented lesions can often mimic that of early melanomas, resulting in potentially unnecessary dermatology referrals, biopsies, and patient anxiety. Studies have indicated that there is great variability in the ability of PCPs to make a correct decision to biopsy/refer a pigmented lesion (1.5 times greater than dermatologists) as well as for diagnosing melanoma (over 2.5 times greater than dermatologists). To aid in detection of early melanomas, new technologies are being developed.
  One such technology is MelaFind, an investigational device that has been developed to give a recommendation for biopsy (or not) of pigmented skin lesions to rule out melanoma. Our hypothesis is that MelaFind will have equal or better sensitivity than pigmented lesion experts in making an appropriate recommendation for biopsy (i.e., MelaFind will be at least as accurate as dermatologists in recommending biopsy for melanomas).

Eligibility: Inclusion Criteria:
  -  Board Certified physicians or equivalent
  Exclusion Criteria:
  -  Did not participate in EOS Protocols 20061 or 20081

Relevance to patient case: not relevant