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

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 mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Ultraviolet Light Exposure and Immunosuppression in Cutaneous Melanoma

Summary: This project seeks to understand differences in the serum vitamin D levels and immune status in cutaneous malignant melanoma patients with different UV exposure histories in New Mexico.

Detailed description: It is well established that ultraviolet radiation (UV) exposure is related to the development of melanoma. There is also evidence that immune reactions are altered after UV exposure in the skin (locally) and perhaps throughout the body (systemically). Additionally, while the role of vitamin D and melanoma development has not been fully established, UV-B exposure is essential for vitamin D production in the skin. Increased sun exposure is also related to the presence of solar elastosis, which might protect (1) or improve survival from melanoma. Thus, melanoma represents a unique model for studying UV exposure, the immune system, and vitamin D. Malignant melanoma is an antigenic cancer; therefore, the role of UV exposure-induced immunosuppression and vitamin D production in the recognition, destruction and growth inhibition of cancerous melanocytes is worth further study.
  To underscore the importance of this project, the Scientific Advisory Committee of the Melanoma Research Foundation and the Steering Committee of the Society of Melanoma Research have indicated a need to collect more human data on the host immune response mechanisms in melanoma and also to focus on the skin as a whole microenvironment, moving away from only in vitro experiments.

Eligibility: Inclusion Criteria:
  -  Resident of New Mexico
  -  Age between the 1 and 95
  -  Newly diagnosed with cutaneous invasive melanoma; any stage permitted (ICDO C44.0-9) between September 1, 2008 and December 31, 2011.
  -  SSM (superficial spreading melanoma) and NM (nodular melanoma) histological subtypes are allowed
  -  Access to a telephone or be able to participate in a personal interview at the clinic
  -  Physically and mentally competent to complete a 1-hour telephone or personal interview
  Exclusion Criteria:
  -  Ocular melanoma, LMM (lentigo maligna melanoma) or ALM (acral lentigo melanoma), and mucosal melanoma cases.
  -  No access to a telephone or is not able to meet with the interviewer.

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

Clinical trial: A Study of AMNN107 in the Treatment of Metastatic and/or Inoperable Melanoma Harboring a c-Kit Mutation

Summary: The purpose of this study is to determine whether nilotinib is efficacious in the treatment of metastatic and/or inoperable melanoma harboring a c-Kit mutation.

Detailed description: This trial began as a multi-center, randomized, Phase III, controlled trial for nilotinib vs (DTIC) dacarbazine to assess the efficacy and safety of nilotinib (400 mg bid) in patients with c-Kit mutated metastatic and/or inoperable melanoma. The study was open to patients with mucosal or acral melanoma.
  Due to substantial difficulties identifying and recruiting eligible patients, the trial design was altered from a randomized, two-arm, Phase III study to a single-arm, Simon two-stage Phase II study with protocol Amendment 2 (27-Jul-2011). While the original protocol required the recruitment of 120 patients, this amendment required the study to recruit only 41 patients (patients randomized to nilotinib prior to Amendment 2 were to be counted in this total, but those randomized to dacarbazine ( DTIC ) DTIC were not). Patients randomized to DTIC were allowed to cross-over to nilotinib, either immediately or at the time of progression.

Eligibility: Inclusion Criteria:
  1. Histologically confirmed mucosal or acral 2. Presence of a c-Kit mutation of exon 9, 11 or 13, or mutations Y822D and mutations D820Y, Y823D of exon 17, as confirmed by the central laboratory 3. Stage III unresectable or stage IV disease 4. The presence of one or more measurable lesions as detected by radiological or photographic methods and assessed according to RECIST 1.0. Lesions must have a size of at least 10mm at longest diameter (using a slice thickness of 5 mm)or double the slice thickness to be considered a target lesion. Target lesions should not be selected in previously irradiated fields unless there is clear evidence of progression 5. WHO performance status 0 - 2
  Exclusion Criteria:
  1. C-Kit mutation of exons 17(except mutations D820Y, Y822D or Y823D) or any other exon not allowed by the inclusion criteria
  2. Patients with c-Kit amplifications only and no mutation
  3. Patients with any history of brain metastases
  4. Patients who have had any prior treatment with TKIs
  5. Patients receiving medications or herbal extracts which interfere with nilotinib metabolism which are not discontinued by the time of the baseline visit
  6. Acute or chronic liver or renal disease considered unrelated to melanoma
  Other protocol-defined inclusion/exclusion criteria may have applied.

Relevance to patient case: possibly relevant
Patient case: 62-year-old female with mucosal melanoma; genetic feature: KIT (L576P), KIT amplification

Clinical trial: Safety and Pharmacokinetic Study of C13-URA in Healthy Volunteers

Summary: The purpose of this study is to evaluate the safety and establish the pharmacokinetic (PK) profile of C13-URA in healthy volunteers

Detailed description: The C13-URA Breath Test Kit is intended to be used as a diagnostic tool to identify rapid and/or delayed gastric emptying in patients who have upper GI symptoms such as stomach pain, fullness, early satiety, vomiting, etc., and who have suspected gastric emptying abnormalities such as gastroparesis or dumping syndrome.
  This study will be a double-blind, placebo-controlled, 3-period safety and PK study of 13C-uracil administered as a single oral dose of 50 mg at step 1 (Period 1), 100 mg at step 2 (Period 2), and 200 mg at step 3 (Period 3) in the form of a semi-solid meal to subjects following at least a 10-hour fast from food and 2-hour fast from water. Dosing will be followed by a 6-hour fast from food and a 4-hour fast from water. There will be a washout of at least 7 days between doses.
  The objectives of this study are as follows;
  1)to evaluate the safety of 13C-uracil in a semi-solid meal in healthy volunteers, 2)to establish the pharmacokinetic profile of 13C-uracil in a semi-solid meal in healthy volunteers, 3)to assess the correlation between plasma concentration of 13C-uracil and urinary excretion of 13C-uracil, 4)to evaluate the reproducibility (intra/inter-individual variance) of the breath test, 5)to determine the dose for 13C-uracil that facilitates adequate Δ13C in breath expired by healthy volunteers

Eligibility: Inclusion Criteria:
  -  Body mass index [range is 18.5 to 29.9 kg/m2]
  -  In good health, determined by no clinically significant findings from medical history, physical examination, 12-lead ECG, and vital signs
  Exclusion Criteria:
  -  Significant history or clinical manifestation of any significant metabolic, allergic, dermatological, hepatic, renal, hematological, pulmonary, cardiovascular, gastrointestinal, neurological, or psychiatric disorder (as determined by the investigator)
  -  History of significant hypersensitivity, intolerance, or allergy to any drug compound, food, or other substance, unless approved by the investigator
  -  History of stomach or intestinal surgery or resection that would potentially alter absorption and/or excretion of orally administered drugs (except that appendectomy, hernia repair, and/or cholecystectomy will be allowed)
  -  History or presence of an abnormal ECG, which, in the investigator's opinion, is clinically significant

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

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

Clinical trial: Tesetaxel as Second-line Therapy for Patients With Advanced Melanoma and Normal Serum LDH

Summary: Tesetaxel is an orally administered chemotherapy agent of the taxane class. This study is being undertaken to evaluate the efficacy and safety of tesetaxel administered as second-line therapy to patients with advanced melanoma and normal serum lactate dehydrogenase (LDH).


Eligibility: Primary inclusion criteria:
  -  Histologically confirmed diagnosis of melanoma
  -  Progressive disease that is not surgically resectable, or metastatic Stage IV disease
  -  Measurable disease (revised RECIST; Version 1.1)
  -  Serum LDH not more than 1.1 times the upper limit of normal
  -  Eastern Cooperative Oncology Group performance status 0 or 1
  -  Treatment with 1 prior regimen (including cytotoxic chemotherapy, immunotherapy, radiation therapy, or cytokine, biologic, or vaccine therapy) as first-line treatment for metastatic disease (Administration of interleukin-2 or interferon as adjuvant therapy is allowed and is not to be considered in determining the 1 prior treatment regimen administered as first-line treatment for metastatic disease.)
  -  Adequate bone marrow, hepatic, and renal function, as specified in the protocol
  -  At least 3 weeks and recovery from effects of prior surgery or other therapy with an approved or investigational agent
  -  Ability to swallow an oral solid-dosage form of medication
  Primary exclusion criteria:
  -  History or presence of brain metastasis or leptomeningeal disease
  -  Primary ocular or mucosal melanoma
  -  Significant medical disease other than cancer
  -  Organ allograft
  -  Presence of neuropathy > Grade 1 (National Cancer Institute Common Toxicity Criteria [NCI CTC]; Version 4.0)
  -  Prior treatment with a taxane or other tubulin-targeted agent (eg, indibulin) other than a vinca alkaloid
  -  Need to continue any regularly-taken medication that is a potent inhibitor or inducer of the CYP3A pathway or P-glycoprotein activity

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

Clinical trial: Randomized Trial of Vaginal Self Sampling for Human Papillomavirus (HPV)

Summary: Up to 30% of Canadian women do not participate in Pap smear screening for cervical cancer prevention despite many being members of family practices and having access to family physicians. One reason is reluctance to undergo pelvic examination.
  The investigators purpose is to determine whether the offer of vaginal self sample collection for oncogenic human papillomavirus (HPV) testing increases participation in cervical cancer screening compared to repeat reminder for Pap smear testing among female family practice members who have not previously responded to invitations for Pap testing.

Detailed description: Pap smear screening for cervical cancer precursors has substantially reduced the incidence of invasive cervical cancer in Canada. While regular Pap screening can give up to 90% protection against cervical cancer, about 30% of Canadian women do not participate in regular screening.
  Pap screening in Ontario is opportunistic. There are women who have family doctors and regularly present for other medical issues at their physician's office but forego Pap smear testing.
  Numerous studies have shown that women are able to self collect vaginal samples, and that these samples can be tested for the presence of oncogenic human papillomavirus. A recent meta-analysis showed that HPV testing through physician collected samples had a sensitivity of 80%-90% for detection of cervical intraepithelial neoplasia (CIN) 2 or worse, and a specificity of 86%-95%. In comparison, a meta-analysis of self collected vaginal samples tested for HPV showed a sensitivity of 74% and a specificity of 88%.
  Studies have reported that women find self collection acceptable. However, we have found that many women are more comfortable if a health care professional is available to help if needed, and so this option should be provided for self-testing.
  We are proposing a randomized controlled trial to see whether (a) the offer of a vaginal self collection kit together with a second reminder for Pap testing will increase cervical screening participation amongst "never-screened" and "hard to reach" women, as compared to (b) a second reminder letter alone.

Eligibility: Inclusion Criteria:
  -  members of consenting family physicians identified through OSCAR EMR
  -  overdue for Pap smear testing
  -  have not presented for Pap smear screening after 1 reminder letter
  Exclusion Criteria:
  -  currently attending colposcopy clinic
  -  institutionalized
  -  without a cervix

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

Clinical trial: Pancreatic Cancer Genetics

Summary: The aim of this study is to determine the frequency of the three most common BRCA1 and BRCA2 genetic mutations that are commonly found in Ashkenazi Jewish patients with pancreatic cancer. Testing for BRCA1 and BRCA2 mutations in relatives of hereditary pancreatic cancer patients may have a significant impact; allowing for early screening, treatment, and resection of pre-malignant tissue or malignant lesions.

Detailed description: Pancreatic cancer is the fourth leading cause of death from malignancy in the United States. Up to 15% of pancreatic cancers have a hereditary component. Several gene mutations and cancer syndromes have been identified that are frequently found in greater frequency in individuals with pancreatic cancer, including the breast ovary cancer syndrome (BRCA1/BRCA2 mutations). No studies adequately describe the epidemiology of inherited pancreatic cancer and genetic risk factors that may modify the penetrance of BRCA1/BRCA2 mutations. The primary aim of this study is to determine the frequency of BRCA1 (185delAG,5382insC) and BRCA2 (6174delT) mutations in Ashkenazi Jewish pancreatic cancer patients. Secondary endpoints will include determining the individual frequency of these mutations and other disease-modifying mutations, death from any cause, disease-free survival, and stage of disease at time of presentation, differences in tissue pathology, risk factors, treatment decisions and development of metachronous malignancies.
  The investigator plan to study about 100 patients, which will enable the true frequency of the mutation to be estimated. Although the impact of BRCA1/BRCA2 mutations will be initially studied in the Ashkenazi population, these data will be widely applicable to other pancreatic cancer patients carrying BRCA1/BRCA2 mutations. Testing for BRCA1 and BRCA2 mutations in relatives of hereditary pancreatic cancer patients may allow early screening, treatment, and resection of pre-malignant tissue or malignant lesions.

Eligibility: Inclusion Criteria:
  -  Patients diagnosed with pancreatic cancer.
  -  Patients are of Ashkenazi Jewish descent.
  -  Patients have been Columbia Pancreatic Cancer Prevention Program Registry and Tissue Bank for High-Risk Individuals (IRB-AAAA6154).
  Exclusion Criteria:
  -  Inability to provide informed consent.
  -  Under the age of 18 years old.

Relevance to patient case: not relevant