araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

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: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Study Of Sumatriptan Succinate Injection Kit In Patients With Migraine or Cluster Headache In Japan

Summary: This study will be conducted to collect cases treated by self-injection of sumatriptan 3mg kit product for the treatment of migraine or cluster headache attacks in clinical settings, to demonstrate the efficacy, and to examine patient acceptability (simplicity and usefulness) and rate of successful self-injection.


Eligibility: Inclusion criteria:
  -  Diagnosis of migraine (with or without aura) or cluster headache according to the International Classification of Headache Disorders, Version 2 (ICHD-II)
  -  History of migraine or cluster headache persisting for at least 6 months
  -  Migraine: One to 6 attacks of moderate or severer headaches per month during the 2 months prior to enrollment
  -  Cluster Headache: Each attack persisting for at least 45 minutes
  -  Written informed consent obtained from the patient. When a patient is a minor, written informed consent from his/her proxy consenter (e.g., person with parental authority) will also be required.
  Exclusion criteria:
  -  History of hypersensitivity to any of the ingredients of 5-HT1B/1D receptor antagonists (e.g., triptans) or serious AE due to treatment with these drugs
  -  History of serious adverse event attributable to treatment with Imigran® Injection 3
  -  History of myocardial infarction, current or previous history of ischemic heart disease or its symptoms/signs, or current history of atypical variant angina (coronary arteriospasm)
  -  Previous history of cerebrovascular disorder or transient cerebral ischemic attack
  -  Current or previous history of peripheral angiopathy (including Raynaud's syndrome)
  -  Systolic blood pressure (SBP) >160 mmHg or diastolic blood pressure (DBP) >95 mmHg at the start of treatment period
  -  Current familial hemiplegic migraine, basilar migraine, or sporadic hemiplegic migraine
  -  Current abuse of ergotamine- or dihydroergotamine-containing preparations or triptans
  -  Pregnant women, lactating mothers, women who may be pregnant, or women of childbearing potential using no appropriate contraceptive measures.
  -  Epilepsy or organic cerebral disorder which may lead to convulsion
  -  Previous history of hypersensitivity to sulfonamides
  -  Known drug allergy or idiosyncrasies
  -  Known drug dependency or alcoholism

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Study of XL647 in Subjects With Non-Small-Cell Lung Cancer

Summary: The purpose of this phase II study is to determine the safety, tolerability, and activity of XL647 in previously untreated subjects with non-small cell lung cancer (NSCLC). XL647 is a small molecule that potently inhibits multiple receptor kinases, including EGFR, VEGFR2 (KDR), ErbB2, and EphB4. Sensitivity to EGFR inhibitors has been linked to specific EGFR mutations and associated with certain clinical characteristics in patients with NSCLC (eg, female, minimal and remote smoking history, and adenocarcinoma histology).


Eligibility: Inclusion Criteria:
  -  Subject has NSCLC with a histologically confirmed diagnosis of adenocarcinoma with measurable disease (stage IIIB, with malignant pleural effusion, and stage IV) and either has a demonstrated activating mutation of the EGF receptor in tumor tissue or meets one of three criteria: asian, female, and minimal or no smoking history.
  -  Measurable disease defined according to RECIST
  -  ECOG performance status of 0 or 1
  -  Normal organ and marrow function
  -  No other malignancies within 5 years, except for non-melanoma skin cancer
  Exclusion Criteria:
  -  Radiation to ≥25% of bone marrow within 30 days of XL647 treatment
  -  Prior systemic anticancer therapy, including cytotoxic chemotherapy, anti-VEGF, anti-VEGFR, or anti-EGFR agents or investigational drug
  -  Subject has not recovered to ≤ grade 1 or to within 10% of baseline values from adverse events due to other medications administered > 30 days before study enrollment
  -  Receiving anticoagulation therapy with warfarin (low-dose warfarin < 1 mg/day, heparin and low molecular weight heparins are permitted)
  -  The subject meets any of the following cardiac criteria:
  -  Corrected QT interval (QTc) of > 460 msec
  -  Family history of congenital long QT syndrome or unexplained sudden death
  -  History of sustained ventricular arrhythmias
  -  Has a finding of left bundle branch block
  -  Has an obligate pacemaker
  -  Has important bradycardia defined as a heart rate of < 50 bpm due to sinus node dysfunction
  -  Has uncontrolled hypertension
  -  Has symptomatic congestive heart failure, unstable angina, or a myocardial infarction within the past 3 months
  -  Has a serum potassium or serum magnesium level that falls outside the normal range
  -  The subject has progressive symptomatic or hemorrhagic brain or leptomeningeal metastases
  -  Uncontrolled intercurrent illness
  -  Subject is pregnant or breastfeeding
  -  Known HIV

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

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: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

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: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Evaluation of Diagnostic Value of Molecular Markers in Renal Cancer

Summary: Renal cancer is frequent and its diagnosis mainly dependant on imaging. More than 50% of renal tumors are currently diagnosed without symptoms. However, 20% of small solid tumors are benign and this percentage is much higher in atypical cystic tumors Bosniak II and III, where 76% and 59% are benign respectively. Determining the malignancy by imaging in these cases is difficult and sometimes impossible. The fine needle aspiration (FNA) cytology or biopsy is necessary. The diagnostic sensitivity and specificity with biopsy are high, but the potential tumor contamination is a major risk. The FNA cytology is simple and safe, but its sensitivity is about 50%. We are conducting a multicentric prospective study to add the molecular markers in FNA cytology as a new diagnostic method in imaging-indeterminate renal tumors.
  Four molecular markers including MN/CA9, vimentin, KIT, and S100A1 will be studied. These four markers have been reported to have a differential diagnostic value in renal tumors. MN/CA9 and vimentin are often found in conventional renal cancers. KIT is frequently expressed in renal oncocytomas and chromophobe renal cancers. S100A1 may further distinguish renal oncocytoma from chromophobe renal cancer. These markers will be analyzed by real time polymerase chain reaction (RT-PCR).
  The aim of this study is to evaluate the diagnostic performance of the association cytology-molecular markers in imaging-indeterminate renal tumors (small solid tumors and cystic tumors ≥ Bosniak III). About 156 patients will be included in five French clinical centers including Saint-Etienne, Marseille, Grenoble, Toulouse, and Nancy.
  The expected results will improve the preoperative diagnostic accuracy in renal tumors.


Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of kidney tumor < 4 cm
  -  Cystic kidney tumor (Bosniak > IIF)
  -  Consent signed
  Exclusion Criteria:
  -  Benign tumor confirmed
  -  Impossibility to do abdominal pelvic ultra-sound or abdominal thoracic scanner
  -  Contraindication for renal puncture

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Testing of INSTI™ HIV-1 Antibody Test Kit in Volunteer Subjects at Risk for HIV Infection

Summary: Each year up to 22 million persons in the US are tested for HIV. Currently available "rapid" tests do not provide test results for at least 30 minutes from the collection of serum and plasma from the subject. Providing accurate test results in less than a minute would make it easier to make timely decisions about treatment and counselling.
  This study will compare results of an experimental rapid test to existing standards to determine if the test can reliably and accurately diagnose HIV in less than one minute.

Detailed description: The primary objective is to determine if INSTI™ performed with finger-stick whole blood, venous whole blood, and plasma demonstrates at least 98.0% sensitivity and specificity compared to an FDA-approved HIV testing algorithm.
  The study will have two parts. The first part of the study will be conducted in institutions where HIV testing is routinely performed and where HIV counseling is offered [i.e. point of care (POC) centers]. The second part of the study will be conducted in a central laboratory that routinely conducts laboratory-based HIV testing using an FDA-licensed HIV-1 ELISA and Western blot test.
  Geographically diverse POCs will be selected in the USA. Approximately 15-20 POCs are planned. Approximately 2,500 subjects will participate in the study including 1,500 subjects with unknown HIV status and 1,000 seropositive subjects. Across these POC sites, voluntary testing of 1500 subjects with unknown HIV status is planned with at least 500 of these subjects being high risk. Samples will be obtained from consenting subjects in the voluntary testing population including high-risk and known HIV 1 seropositive individuals.
  Each subject is to receive an INSTI™ on finger-stick blood and parallel HIV testing of EDTA-treated venous whole blood and plasma samples will be conducted at a central laboratory.
  The results of INSTI™ will not be given to the subject. The subject will be given the results of the POC HIV test only, per their standard of care procedures. Subsequent subject care decisions will NOT be based on the results of INSTI™.

Eligibility: Inclusion Criteria:
  -  Unknown HIV status who are undergoing voluntary testing for HIV infection in a POC clinic setting or known HIV seropositive subjects willing to be re-tested.
  -  Ability to give proper informed consent, or have legal parent or guardian provide consent.
  -  Willingness to participate in a POC standard of care HIV counseling and testing program and receive POC standard of care test results
  -  Willingness to provide the necessary volume of whole blood collected through venous blood draw and finger stick (approximately 10 ml)
  Exclusion Criteria:
  -  Subject self-report of history of multiple myeloma
  -  Subject self-report of history of long-term anti-retroviral therapy with known low or non-existent antibody titre (sero-inversion)

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Trial of Dacarbazine With or Without Genasense in Advanced Melanoma

Summary: This study is being performed to prospectively determine whether dacarbazine plus Genasense is significantly better than dacarbazine plus placebo in chemotherapy-naive patients with advanced melanoma and low baseline LDH (LDH less than or equal to 0.8 times the upper limit of normal). LDH is a biomarker strongly associated with improved outcomes in a recent trial of dacarbazine plus Genasense.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed diagnosis of melanoma
  -  Progressive disease that is not surgically resectable, or metastatic Stage IV
  -  Low-normal LDH, defined as ≤ 0.8 times the upper limit of normal
  -  No prior chemotherapy
  -  Measurable disease
  -  ECOG performance status ≤ 1
  -  At least 4 weeks and recovery from effects of major prior surgery or other therapy, including immunotherapy, radiation therapy, or cytokine, biologic or vaccine therapy
  -  Prior immunotherapy allowed
  -  Adequate organ function
  Exclusion Criteria:
  -  Prior cytotoxic chemotherapy, including regional perfusion, or prior Genasense treatment
  -  Primary ocular or mucosal melanoma
  -  Bone-only metastatic disease
  -  History or presence of brain metastasis or leptomeningeal disease
  -  Significant medical disease other than cancer
  -  Organ allograft

Relevance to patient case: not relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Kinase Genotyping of Gastro Intestinal Stomach Tumors (GISTs) From Patients Enrolled in Pfizer A6181112 Phase IIIb Trial

Summary: The purpose of this study is to determine the genetic makeup of gastro intestinal stomach tumors (GISTs) from patients enrolled in the A6181112 phase IIIb trial. Tumor samples will be screened for mutations and this information will be used to determine whether the progression-free survival of patients being treated with the cancer medication sunitinib is related to the underlying genotype of their GIST.

Detailed description: In this companion study, we will analyze the genomic DNA from the GIST tumor specimens of patients enrolled in the in the A6181112 phase IIIb trial at participating U.S. and ex-U.S. medical centers. Specifically, GIST samples will be screened for mutations in KIT gene exons 9, 11, 13 and 17, and PDGFRA gene exons 12, 14 and 18, to determine the primary kinase genotype. Subset analyses will be performed and compared with the overall PFS rates observed in patients with primary and secondary imatinib resistance. Based on data from a previous phase I/II trial, our hypothesis is that patients with either primary or secondary imatinib resistance having a KIT exon 9-mutant or WT GIST will have a longer PFS when treated with sunitinib than patients with exon 11-mutant GIST. We further hypothesize that this difference will be observed among patients treated with high-dose imatinib.

Eligibility: Inclusion Criteria:
  -  Patients enrolled in Pfizer A6181112
  Exclusion Criteria:
  -  Patients who do not consent for analysis of their tumor in this companion study

Relevance to patient case: not relevant