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

Clinical trial: Genome Wide SNP Array-based Approach to Detect Micro-cytogenetic Lesions and KIT Mutation to Improve Treatment Outcomes in Patients With Core-binding Factor Positive Acute Myeloid Leukemia

Summary: Core binding factor (CBF) positive acute myeloid leukemia (AML) consist of 15% of patients in overall AML, expected to harbor a favorable prognosis. However, around a half of cases relapses. Accordingly, more sophisticated classification in CBF positive AMLs is essential to achieve further improvement in the treatment outcome. The current study is designed to evaluate CBF positive AML patients with genome-wide SNP array and KIT mutation study in CBF positive AML patients diagnosed at the Samsung Medical Center and Hwasun Chonnam National University Hospital, Korea between 1994 and 2008.
  1. Construction of the CBF positive AML patient cohort: clinical database establishment (including treatment outcomes and prognosis) and extraction/storage of tumor cell DNAs from marrow samples, then processing of Affymetrix SNP array 6.0.
  2. Construction of prognostic predictive model using pharmacogenomics with the results of genotypes and copy number variations (CNVs).
  3. Detection of hidden microscopic cytogenetic lesions with SNP array technique, and correlation with clinical outcomes in CBF positive AML.
  4. Detection of KIT, FLT3/ITD, and NPM1 gene mutation and its correlation with clinical outcomes in CBF positive AML.
  The current study attempts to analyze genetic data of core binding factor (CBF) positive acute myeloid leukemia (AML) using genome wide SNP array technique with tumor DNAs collected at the time of diagnosis.
  1. To detect microcytogenetic lesions and will analyze its prognostic significance
  2. To analyze genome-wide genotypes and copy number variations (CNVs) using pharmacogenetic approach and will construct a prognostic predictive model
  3. To detect KIT, FLT3/ITD and NPM1 mutation and evaluate its prognostic significance. The present study will establish individualized therapy for CBF positive AML, will provide a basis for molecular marker guided clinical trial in CBF positive AML.


Eligibility: Inclusion Criteria:
  -  patients with core binding factor positive acute myeloid leukemia
  -  18 years or older
  -  patients were treated with standard chemotherapy
  -  patients with available medical record and stored bone marrow specimen at time of diagnosis
  Exclusion Criteria:
  -  no definive criteria

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

Clinical trial: SciBase International Melanoma Pivotal Study

Summary: The purpose of this clinical investigation was to determine the safety and effectiveness of the SciBase III device (Test) designed to help distinguish between malignant melanoma and benign lesions, using electrical impedance spectroscopy (EIS) relative to the histological gold standard (Reference).
  The purpose of the study is to collect data to support a Pre-market Application(PMA) to obtain Food and Drug Administration(FDA) approval to market the SciBase III Electrical Impedance Spectrometer.


Eligibility: Inclusion Criteria
  For inclusion in the study, all subjects had to fulfill all of the following criteria:
  -  Men or women of any ethnic group aged ≥18 years
  -  Primary lesions (i.e., not metastases or recurrent lesions) that the physicians choose to excise.
  -  Lesion ≥ 2 mm in diameter and ≤ 20 mm in diameter
  -  In subjects with multiple skin lesions, all lesions destined for excision must be identified for purposes of study participation. Note: a subject may only be entered into the study once.
  -  The subject is willing and able to read, understand and sign the study specific informed consent form.
  Exclusion Criteria:
  Subjects were excluded from the study if they fulfilled any of the following criteria:
  -  Skin surface not measurable, e.g. lesion on a stalk
  -  Skin surface not accessible, e.g. inside ears, under nails
  -  Lesion located on acral skin, e.g. sole or palms.
  -  Lesion located on areas of scars, crusts, psoriasis, eczema or similar skin conditions.
  -  Lesion on hair-covered areas, e.g. scalp, beards, moustaches or whiskers.
  -  Lesion located on genitalia.
  -  Lesion located in an area that has been previously biopsied or subjected to any kind of surgical intervention or traumatized.
  -  Lesion located on mucosal surfaces.
  -  Skin is not intact (measurement area) e.g. bleeding or with clinical noticeable ulceration.
  -  Lesion with foreign matter, e.g. tattoo, splinter
  -  Lesion and/or reference located on acute sunburn.

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

Clinical trial: Sorafenib for Imatinib/Sunitinib-failed GIST

Summary: With discovery of KIT (CD117) mutations and the advent of KIT tyrosine kinase inhibitor imatinib, there has been substantial improvement in overall survival in patients with advanced and/or metastatic gastrointestinal tumors (GIST). Recently, sunitinib showed activity as second-line therapy in GIST patients after failure with imatinib. However, virtually all patients will eventually progress or become intolerable after imatinib and sunitinib. In preclinical models, sorafenib inhibits KIT activity and cell growth of imatinib-resistant tumors. The objective of this multi-center, non-randomized phase II study is to evaluate the safety and activity of sorafenib given as third-line therapy for GIST.

Detailed description: This is a non-randomized, open-label, multi-center, phase II study recruiting patients with advanced GIST who are pretreated with both imatinib and sunitinib. The current study will provide an estimate of the activity and safety of sorafenib in GIST. The primary study endpoint is the disease control rate (DCR), defined as complete or partial response or stable disease of at least 24 weeks of sorafenib therapy. Secondary endpoints include PFS, OS and safety.
  Patients with advanced (unresectable and/or metastatic) GIST who failed after previous therapy involving both imatinib and sunitinib will be eligible. Failure to imatinib and sunitinib is defined as disease progression regardless of intervening response during therapy, or intolerance. There is no limit to the number of prior therapies a patient may have received (e.g., patients may have received therapy with nilotinib, other TKIs, or chemotherapy in addition to imatinib or sunitinib).

Eligibility: Inclusion Criteria:
  -  age over 18 years
  -  advanced GIST
  -  failed (progressed and/or intolerable) after prior treatments for GIST
  -  ECOG performance status of 0~2
  -  resolution of all toxic effects of prior treatments
  -  no prior radiotherapy within 1 month before registration
  -  measurable lesion as defined by RECIST
  -  adequate marrow, hepatic, renal and cardiac functions
  -  provision of a signed written informed consent
  Exclusion Criteria:
  -  severe co-morbid illness and/or active infections
  -  pregnant or lactating women
  -  history of other malignancies
  -  active CNS disease not controllable with radiotherapy or corticosteroids
  -  active and uncontrollable bleeding from gastrointestinal tract
  -  prior history of sorafenib use
  -  gastrointestinal obstruction or malabsorption syndrome

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

Clinical trial: Study of Nilotinib in Metastatic Melanoma With KIT Aberrations

Summary: Major response was observed to imatinib mesylate in KIT-mutated metastatic rectal melanoma (Hodi FS et al, J Clin Oncol 26:2046-2051, 2008). In the ASCO annual meeting in 2009ar, KIT mutations were reported to be present in 23% of acral and 15.2% of mucosal melanomas (Heinrich MC et al, J Clin Oncol 26:2008 abstr 9016). Nilotinib is a novel tyrosine kinase inhibitor (TKI) targeting KIT, PDGFR, and Bcr-Abl and inhibiting the proliferating of both imatinib-sensitive and imatinib-resistant cells in vitro. Phase I study of nilotinib alone and in combination with imatinib in patients with imatinib-resistant gastrointestinal stromal tumors (GIST) demonstrated significant activity (72% stable disease for nilotinib alone and 56% for nilotinib/imatinib combination) (Blay JY et al, J Clin Oncol 26:2008, abstr 10553).
  Thus, we propose to conduct a phase II study of nilotinib in metastatic melanoma with KIT mutations.


Eligibility: Inclusion Criteria:
  1. Histologically or cytologically proven melanoma with stage IV or unresectable stage III disease
  2. Documented KIT aberration
  3. Adequate organ function as defined by the following criteria:
  -  Serum aspartate transaminase (AST); serum glutamic oxaloacetic transaminase (SGOT)) and serum alanine transaminase (ALT); serum glutamic pyruvic transaminase (SGPT)) ≤ 2.5 x local laboratory upper limit of normal (ULN), or AST and ALT less than or equal to 5 x ULN if liver function abnormalities are due to underlying malignancy
  -  Total serum bilirubin ≤ 1.5 x ULN
  -  Absolute neutrophil count (ANC) ≥ 1500/µL
  -  Platelets ≥ 100,000/µL
  -  Hemoglobin ≥ 9.0 g/dL (may be transfused or erythropoietin treated)
  -  Serum calcium ≤ 12.0 mg/dL
  -  Serum creatinine ≤ 1.5 x ULN
  4. Patients with CNS metastasis must have stable neurologic function without evidence of CNS progression within 8 weeks
  5. May have previous adjuvant therapy with interferon, vaccines or therapy with IL-2, chemotherapy
  6. At least one measurable lesion by RECIST criteria
  7. ECOG PS 0-2
  Exclusion Criteria:
  1. Major surgery or radiation therapy within 4 weeks of starting the study treatment.
  2. History of or known carcinomatous meningitis, or evidence of symptomatic leptomeningeal disease on screening CT or MRI scan.
  3. Ongoing cardiac dysrhythmias of NCI CTCAE grade ≥ 2.
  4. QTc > 470 msec on baseline EKG.
  5. Pregnancy or breastfeeding.

Relevance to patient case: possibly relevant
Patient case: 65-year-old female with melanoma; genetic feature: KIT (L576P)

Clinical trial: Early Diagnosis of Malignant Transformation of Pigmentary Skin Lesions

Summary: Malignant Melanoma is a deadly skin cancer that can be cured if diagnosed early. To date atypical pigmented skin lesions are diagnosed by appearance alone and many moles and lesions are excised unnecessarily and on the other hand malignant lesions are missed and diagnosed too late. In this study a protein conjugated to a florescent dye is spread on a suspicious pigmented lesion, the hypothesis is that this protein binds to malignant cells only and thus with a special camera that picks up the dye we can find pigmented lesions with early malignant transformation.


Eligibility: Inclusion Criteria:
  -  pigmented lesion indicated for surgical excision
  -  over 18 years of age
  Exclusion Criteria:
  -  pregnancy

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

Clinical trial: A Safety and MORAb-028 Dose Determination Study in Subjects With Metastatic Melanoma

Summary: The purpose of this study is to evaluate whether therapy with MORAb-028 is safe, effective, and to determine the appropriate dose of MORAb-028 in the treatment of metastatic melanoma.

Detailed description: Melanoma is a serious form of skin cancer. If untreated, the melanoma can spread beyond the original affected tissue and invade distant tissue and organs. Treatment for metastatic melanoma includes medical treatments (chemotherapy or immunotherapy), surgery, or radiation therapy. MORAb-028 is a recombinant human immunoglobulin M (IgM) monoclonal antibody that recognizes a cell surface diacyl ganglioside named disialoganglioside (GD2). GD2 is overexpressed in tumors of neuro-ectodermal origin such as melanomas, neuroblastomas, small-cell lung carcinomas, and many sarcomas, while absent in most normal tissues. GD2 expression has been demonstrated in human melanoma and small cell lung cancer by thin layer chromatography and radiolabeled anti-GD2 antibody detection. It is hypothesized that one mode of action of MORAb-028 is complement-dependent cytotoxicity. Complement-dependent cytotoxicity is a mechanism for killing tumor cells in which an antibody bound to the target cell surface fixes complement, which results in assembly of the complement membrane attack complex that punches holes in the target cell membrane resulting in subsequent cell lysis. IgMs strongly bind to C1Q and robustly activate complement-dependent cytotoxicity. MORAb-028 is being developed as a potential therapy for GD2-positive tumors.

Eligibility: Inclusion Criteria:
  -  Measurable metastatic melanoma that has failed standard therapy
  -  Males and females greater than or equal to 18 years of age
  -  Life expectancy of greater than or equal to 3 months
  Exclusion Criteria:
  -  Significant cardiovascular impairment
  -  Clinically significant illness, medical condition, surgical history, or laboratory abnormality that could affect the safety of the subject or negatively impact the study results
  -  Chemotherapy, radiotherapy, or immunotherapy within 3 weeks prior to administration to MORAb-028

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

Clinical trial: Liver-PILP First-in-Man

Summary: The purpose of this study is to determine whether the PILP-kit can be safely used, within specific performance parameters, to isolate and perfuse the liver with a chemotherapeutic drug for the treatment of patients with unresectable liver metastases.

Detailed description: The objective of this Medical Device Study, is to demonstrate the feasibility of the liver PILP intervention.
  The liver PILP intervention will be considered feasible if the procedure is demonstrated to be safe and the liver PILP kit performs according to specifications.

Eligibility: Inclusion Criteria:
  1. Subjects with ECOG (Eastern Cooperative Oncology Group) stages 0 or 1
  2. Unresectable metastatic disease predominant in the liver
  Exclusion Criteria:
  1. More than 60 % tumor involved liver tissue
  2. Abnormal vascular anatomy
  3. Severe atherosclerosis
  4. Dissection and/or thrombotic occlusion and/or aneurysm of the aorta, iliac or hepatic arteries
  5. Short suprahepatic vena cava segment (< 1.5 cm)
  6. One or both jugular veins are occluded
  7. Other severe, concomitant diseases regarding the subject status

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

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

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

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

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