araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: A Study of Pegylated Liposomal Doxorubicin and Cyclophosphamide in Her2-negative Stage I and II Breast Cancer Patients

Summary: Primary objective:
  -  To evaluate the disease-free survival (DFS) in the two randomized arms after therapy with LC vs. EC in chemo-naive Her2-patients with stage I or II breast cancer
  Secondary objectives:
  -  To assess the overall survival (OS)
  -  To establish the safety profile by assessing the toxicities and tolerability
  -  To assess the quality of life (QoL)
  -  To evaluate survival correlation with biomarkers expression.


Eligibility: Inclusion Criteria:
  -  histologically confirmed invasive, but non-inflammatory, breast adenocarcinoma with stage I or II (if N0, T must be >1cm) disease
  -  Her2-negative on fluorescence in situ hybridization (FISH) study
  -  performance status of ECOG 0, 1
  -  female, age between 20 and 70 years
  -  life expectancy of at least one year
  -  ability to understand and willingness to sign a written informed consent document
  Exclusion Criteria:
  -  Her2 3+ over-expression on immunohistochemistry (IHC), or Her2 amplification on fluorescence in situ hybridization (FISH) study
  -  previous or current systemic malignancy with the exception of curatively treated non-melanoma skin cancer or cervical carcinoma in situ, unless there has been a disease-free interval of at least 5 years
  -  Patients who have received prior chemotherapy
  -  inadequate hematological function defined as absolute neutrophil count (ANC)less than 1,500/mm3, and platelets less than 100,000/mm3
  -  inadequate hepatic function defined as: serum bilirubin greater than 1.5 times the upper limit of normal range (ULN) alanine aminotransferase (ALT) or aspartate aminotransferase (AST) greater than 2.5 times the ULN
  -  inadequate renal function defined as serum creatinine greater than 1.5 times the ULN
  -  left ventricular ejection fraction (LVEF) < 50% confirmed by multiple-gated acquisition (MUGA) scan or echocardiogram
  -  concomitant illness that might be aggregated by chemotherapy or interfere study assessment. For examples, active, non- controlled infection (such as hepatitis B and hepatitis C, HIV, infectious tuberculosis) or other active, non-controlled disease such as congestive heart failure, ischemic heart disease, uncontrolled hypertension or arrhythmia, unstable diabetes mellitus, and active peptic ulcer
  -  patients who are presence of liver cirrhosis or are HBV/HCV carrier
  -  participation in another clinical trial with any investigational drug within 30 days prior to entry
  -  pregnant or breast feeding women
  -  fertile women of child-bearing potential unless using a reliable and appropriate contraceptive method throughout the treatment period and for three months following cessation of treatment

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: A Study of the Effect of Food on the Pharmacokinetics of Single Dose RO5185426 And the Safety And Efficacy of Continuous Administration in Patients With BRAF V600E Mutation-Positive Metastatic Melanoma

Summary: This randomized, open-label, two period crossover study will evaluate the effect of food on the pharmacokinetics of a single dose of RO5185426 and the efficacy and safety of continuous administration in patients with BRAF V600E mutation-positive metastatic melanoma. Patients will be randomized to receive in a crossover design single oral doses of RO5185426 with or without food, with a 10-day washout period between doses. Following the crossover periods, patients will receive RO5185426 orally twice daily on a continuous basis until disease progression or unacceptable toxicity occurs.


Eligibility: Inclusion Criteria:
  -  Adult patients, >/= 18 years of age
  -  Histologically confirmed metastatic melanoma (Stage IV, American Joint Committee on Cancer)
  -  Positive BRAF V600E mutation result determined by Cobas 4800 BRAF V600 Mutation Test
  -  Previously treated patients must have failed at least one prior treatment regimen; if patients have received prior systemic treatments for metastatic melanoma, the time elapsed from previous therapy must be >/= 28 days; patients must have recovered fully from toxicities of all prior therapy
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0 or 1
  -  Evaluable disease (measurable for disease progression according to RECIST criteria)
  -  Adequate hematological, renal and liver function
  Exclusion Criteria:
  -  Active CNS lesions
  -  History of or known spinal cord compression or carcinomatous meningitis
  -  Anticipated or ongoing administration of anti-cancer therapies other than those administered in this study
  -  Previous malignancy within the past 5 years except for basal or squamous cell carcinoma of the skin, melanoma in-situ and carcinoma in-situ of the cervix
  -  Previous treatment with BRAF inhibitor (sorafenib allowed) or MEK inhibitor
  -  Refractory nausea or vomiting, malabsorption, external biliary shunt, or history of any type of gastrointestinal surgery that would preclude adequate absorption of study drug

Relevance to patient case: possibly relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Use of High Cost Monitoring During Letrozole Ovulation Induction

Summary: The purpose of this study is to investigate monitoring methods during ovulation induction cycles with letrozole and their effect on pregnancy rates. Monitoring ovulation induction cycles with letrozole can be done with a variety of methods, the two most commonly utilized are home-based urinary LH kits (or ovulation predictor kits) and office-based midcycle follicular ultrasound. Letrozole coupled with follicular monitoring by ultrasound may add extra cost per cycle with no improvement in fecundability (pregnancy rates per cycle).

Detailed description: The study will be a randomized controlled trial of adult women with primary and secondary infertility seen at the University of Michigan Health System undergoing ovulation induction (OI) with letrozole as part of their standard clinical care. Patients who are undergoing OI with letrozole as per standard clinical care will be randomized to urinary luteinizing hormone (LH) ovulation predictor kit use versus mid-cycle ultrasound with administration of hCG when appropriate for timing of intercourse or intrauterine insemination. Patients who have been prescribed letrozole as per routine clinical care will be approached to determine willingness to participate in this study. Study period involves up to three ovulation induction cycles or until pregnancy occurs.

Eligibility: Inclusion Criteria:
  -  Women ages 21-39 undergoing letrozole ovulation induction (as part of routine clinical care) at a single academic-infertility center.
  -  Normal uterus and evidence of at least tubal patency on one side (as assessed by saline-infusion sonography or hysterosalpingogram per clinical care).
  Exclusion Criteria:
  -  Current pregnancy
  -  Nursing mothers
  -  Prior hypersensitivity to hCG preparations
  -  Primary ovarian failure or menopausal levels of FSH (>12 mIU/mL)
  -  Patients with abnormal uterine bleeding of undetermined origin or ovarian cyst of undetermined origin, sex-hormone dependent tumors, documented bilateral tubal obstruction, uncorrected uterine anomalies,
  -  Previous letrozole or gonadotropin use and/or previous treatment with in vitro fertilization
  -  Other uncorrected medical condition that would be a contraindication to attempting elective ovulation induction (e.g., uncontrolled diabetes, intracranial lesion, thyroid or adrenal disease).

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: A Phase 3 Study to Compare Efficacy and Safety of Masitinib to Dacarbazine in the Treatment of Patients With Non-Resectable or Metastatic Stage 3 or Stage 4 Melanoma Carrying a Mutation in the Juxta Membrane Domain of C-Kit

Summary: Masitinib is a novel TKI that potently inhibits wild type (WT) c-kit and its activated form, mutated in the juxtamembrane region (JM c-kit) PDGFRs, the intracellular kinase Lyn, and to a lesser extent fibroblast growth factor receptor 3 (FGFR3).
  Pre-clinical data suggest that masitinib is a strong candidate for the treatment of patients with advanced melanoma carrying a c-kit JM mutation.


Eligibility: Inclusion Criteria:
  -  Patient with histologically or cytologically confirmed non-resectable or metastatic stage 3 (non-resectable IIIB or IIIC, AJCC TNM staging system 7th edition) or stage 4 melanoma
  -  Patient with detectable c-kit JM mutation confirmed by DNA or RNA sequencing, which is expected to be mainly found after screening of mucosal or acral melanoma or melanoma on skin with chronic sun-induced damages (defined by a microscopically marked elastosis involving the skin surrounding their primary melanoma)
  -  Patient with measurable disease according to RECIST
  -  Patient with ECOG ≤ 2
  Exclusion Criteria:
  -  Patient with other malignancies from which the patient has been continuously disease-free for < 3 years, with the exception of melanoma, cervical carcinoma in situ, basal cell or squamous cell skin cancer, ductal or lobular carcinoma in situ of the breast
  -  Patient with active brain metastases are not eligible. Patients with treated brain metastases are eligible if :
  -  presence of 3 brain lesions or less
  -  lesion(s) diameter is ≤ 2 cm
  -  radiation therapy (gamma knife) was completed ≥ 4 weeks prior to baseline
  -  surgery was completed ≥4 weeks prior to baseline
  -  lesions assessed by follow-up scan (or MRI if MRI performed before brain therapy) ≥ 1 month after brain therapy are considered under control at baseline
  -  Patient refractory to dacarbazine defined as patient presenting a disease progression after 3 months of dacarbazine therapy.
  -  Prior treatment with a tyrosine kinase c-kit inhibitor

Relevance to patient case: possibly relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Interferon Alfa Sensitivity in HIV/HCV Persons Before and After HIV Meds

Summary: The chief purpose of this research is to evaluate interferon alpha sensitivity and cell type specific levels of interferon receptor and interferon stimulated genes and proteins in HIV/ HCV (hepatitis C virus) coinfected persons before and after administration of HIV medications (antiretroviral therapy).

Detailed description: We plan to perform liver biopsy by microlaparoscopy on previously untreated HIV/HCV coinfected persons, then give them a dose of peginterferon alfa 2b. HCV and HIV kinetics will be studied. Afterward, HIV will be treated using antiretroviral therapy and the procedure will be repeated.

Eligibility: Inclusion Criteria:
  -  Adult Human
  -  Able to provide written informed consent
  -  HIV antibody positive
  -  HIV viral load positive
  -  HIV treatment naive
  -  Hepatitis C antibody positive
  -  Hepatitis C viral load positive
  -  Hepatitis C treatment naive
  -  Approved to take HIV medications for minimum 9 months
  -  Willing to use contraception, Life expectancy greater than 2 years
  Exclusion Criteria:
  -  Significant opportunistic infections within 12 month
  -  Hepatitis B positive
  -  Evidence of liver cirrhosis
  -  Decompensated liver disease
  -  Chronic alcohol abuse
  -  Allergy to raltegravir, tenofovir, and/or emtricitabine
  -  Active or suspected malignancy
  -  Sarcoidosis
  -  Active TB
  -  Coronary artery disease
  -  Uncontrolled seizures
  -  Untreated thyroid disease
  -  Untreated diabetes
  -  Weight greater than 125 kg
  -  Severe depression or severe psychiatric disorder
  -  Ongoing alcohol or illicit drug use
  -  Pregnant, nursing, pr planning to become pregnant
  -  Allergy to interferon

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Detection of Choroidal Nevus Cells in Vitrectomy Fluid

Summary: The purpose of this study is to determine if the investigators can detect the presence of choroidal nevi cells in the vitreous fluid of humans, as this may improve the diagnosis and classification of choroidal nevi and melanomas in the future.

Detailed description: Approximately 7% of the population has a choroidal nevus, or "freckle," in the back of the eye. Like a nevus on the skin, there is potential for malignant change to a melanoma. Dermatologists have the ability to quickly and easily biopsy suspicious skin lesions while ophthalmologists currently have no way of determining the malignant potential of choroidal nevi other than a fine needle aspiration (which is invasive and has the potential complications of bleeding and retinal detachment). This study's sole aim is to see if choroidal nevi cells are present in the inside fluid of the eye. The investigators plan to analyze the fluid of the eye, which is routinely removed during retina surgery, to detect any nevus cells. If the investigators are able to detect these cells, then future studies may allow us to better classify choroidal nevi for potential malignant change.

Eligibility: Inclusion Criteria:
  -  Patients with a choroidal nevus who are undergoing routine vitrectomy surgery for another indication (such as epiretinal membrane or macular hole repair).
  Exclusion Criteria:
  -  Patients without a choroidal nevus
  -  Children under the age of 18
  -  Pregnant and nursing females

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Study to Evaluate the Safety and Efficacy of BA058 (Abaloparatide) for Prevention of Fracture in Postmenopausal Women

Summary: The purpose of this study is to determine whether BA058 (abaloparatide), a parathyroid hormone-related peptide, is effective in preventing fractures in postmenopausal women with severe osteoporosis who are at risk of fractures.

Detailed description: This is a randomized, double-blind, placebo-controlled, comparative Phase 3, multicenter international study to evaluate the efficacy and safety of BA058 (abaloparatide) 80 µg in the prevention of fracture in otherwise healthy ambulatory postmenopausal women with severe osteoporosis.

Eligibility: Inclusion Criteria:
  -  Healthy ambulatory postmenopausal (≥ 5 years) women from 50 to 85 years of age (inclusive) with a diagnosis of osteoporosis
  -  The women are to have a bone mineral density (BMD) T score ≤ -2.5 and > -5.0 at the lumbar spine or hip (femoral neck) by dual energy x-ray absorptiometry (DXA) and radiological evidence of 2 or more mild or one or more moderate lumbar or thoracic vertebral fractures, or history of low trauma forearm, humerus, sacral, pelvic, hip, femoral, or tibial fracture within the past 5 years. Postmenopausal women older than 65 who meet the above fracture criteria but have a T score ≤ -2.0 and > -5.0 may be enrolled. Women older than 65 who do not meet the fracture criteria may also be enrolled if their T score is ≤ -3.0 and > -5.0
  -  Normal physical exam, vital signs, electrocardiogram (ECG) and medical history
  -  Laboratory tests within the normal range including serum calcium, PTH(1-84), serum phosphorus and alkaline phosphatase
  Exclusion Criteria:
  -  History of more than 4 mild or moderate spine fractures or any severe fracture
  -  Abnormality of the spine or hip that would prohibit assessment of bone mineral density (BMD)
  -  Unexplained elevation of serum alkaline phosphatase, history of bone disorders (such as Paget's disease) or a diagnosis of cancer within the last 5 years (with the exception of basal cell or squamous cancer of the skin)
  -  History of thyroid, parathyroid, or adrenal disorders, or malabsorptive syndromes or any chronic or recurrent diseases or disturbances that would interfere with the interpretation of study data or compromise the safety of the patient
  -  Prior treatment with parathyroid hormone (PTH) or parathyroid hormone-related peptid (PTHrP)
  -  Prior treatment with bisphosphonates, fluoride, or strontium within the past five years or treatment with androgens, anabolic steroids, corticosteroids or selective estrogen receptor modulators within the past 12 months (except hormone replacement therapy)
  -  Prior treatment with an investigational drug within the past 12 months
  -  History of nephrolithiasis or urolithiasis within the past five years, or history of osteosarcoma at any time

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: A Study of Vemurafenib in Metastatic Melanoma Participants With Brain Metastases

Summary: This open-label, single-arm, multicenter study will evaluate the efficacy and safety in participants with metastatic melanoma who developed brain metastases. Participants may or may not have received prior systemic treatment for metastatic melanoma [except treatment with v-raf murine sarcoma viral oncogene homolog B (BRAF) or mitogen-activated protein kinase (MEK) inhibitors]. Participants will receive oral doses of 960 mg vemurafenib twice daily until disease progression, unacceptable toxicity or consent withdrawal.


Eligibility: Inclusion Criteria:
  -  Adult participants, >/= 18 years of age
  -  Histologically confirmed metastatic melanoma (Stage IV, American Joint Committee on Cancer) with BRAF V600 mutation (cobas 4800 BRAF V600 Mutation Test)
  -  Measurable brain metastases, defined as lesions that were accurately measured in at least one dimension (longest diameter to be recorded) as ≥0.5 cm in the brain MRI with contrast, treated or untreated
  -  Participants may or may not have received prior systemic therapy for metastatic melanoma and either a) have received no prior treatment for brain metastases or b) have received prior treatment for brain metastases and have progressed
  -  Participants may or may not have symptoms related to their brain metastases
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0-1
  -  Participants must have recovered from all side effects of their most recent systemic or local treatment for metastatic melanoma
  Exclusion Criteria:
  -  Increasing corticosteroid dose during the 7 days prior to first dose of study drug
  -  Leptomeningeal involvement in participants with no prior treatment for brain metastases
  -  Previous malignancy requiring active treatment within the past 2 years, except for treated and controlled basal or squamous cell carcinoma of the skin, or carcinoma in-situ of the cervix
  -  Concurrent administration of any anticancer therapies other than those administered in the study
  -  Treatment with any cytotoxic, investigational drug or targeted therapy 4 weeks prior to first dose of study drug. Radiation therapy ≤1 week prior to first administration of vemurafenib; and stereotactic radiotherapy ≤1 day prior to prior to first administration of vemurafenib
  -  Prior treatment with BRAF or MEK inhibitors
  -  Clinically significant cardiovascular disease or event within the 6 months prior to first dose of study drug

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Ph I Ipilimumab Vemurafenib Combo in Patients With v-Raf Murine Sarcoma Viral Oncogene Homolog B1 (BRAF)

Summary: Treatment of subjects who have metastatic melanoma that expresses an activated mutant form of the BRAF oncogene (V600E) with a combination of the specific BRAF inhibitor, Vemurafenib, and the Cytotoxic T Lymphocyte Antigen 4 (CTLA-4) inhibitor mAb Ipilimumab will be safe and feasible and will show preliminary evidence of anti-tumor efficacy and survival in comparison to historical results following treatment with either agent alone.


Eligibility: For more information regarding BMS clinical trial participation, please visit www.BMSStudyConnect.com.
  Inclusion Criteria:
  -  Metastatic melanoma with activating V600 BRAF mutation
  -  Measurable Tumor
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status (PS) 0-1
  Exclusion Criteria:
  -  Autoimmune disease
  -  Active Brain Metastasis (must be stable after radiation for at least one month)
  -  Prior therapy with immune stimulating agents

Relevance to patient case: not relevant
Patient case: 66-year-old female with melanoma; genetic feature: KIT amplification

Clinical trial: Safety and Efficacy of OsmoPrep® Tablets Versus HalfLytely® and Bisacodyl Tablet Bowel Prep Kit for Colon Cleansing

Summary: The purpose of this study is to compare the safety and efficacy of OsmoPrep tablets versus HalfLytely and Bisacodyl Tablet Bowel Prep Kit in subjects who are undergoing colonoscopy.


Eligibility: Inclusion Criteria:
  -  Between 18 and 70 years of age, inclusive
  -  Scheduled for colonoscopy within 21 days of the screening visit
  -  Able to swallow tablets the size of a multivitamin without difficulty
  Exclusion Criteria:
  -  History of biopsy-proven acute phosphate nephropathy
  -  Known allergy or hypersensitivity to treatment arms
  -  History of gastric stapling or bypass procedure or history of gastric retention
  -  History of any other sodium phosphate preparation within 6 months prior to colonoscopy

Relevance to patient case: not relevant