araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

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
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Family and Personal History of Malignancy in Intraductal Papillary Mucinous Neoplasm (IPMN)

Summary: This is a retrospective observational study to determine the proportion of patients with a family history of pancreatic cancer and other malignancies among patients who have intraductal papillary mucinous neoplasm (IPMN).
  The investigators will be reviewing the demographic, clinical, radiologic, pathologic, and follow-up information from the Pancres Center database. The investigators will also conduct a chart review to collect information recorded by clinicians on each subject's family history of malignancy and personal history of malignancy. Results of this database and chart review will be incorporated into a datasheet in which all patient identifiers have been removed.
  The primary outcome will be the percentage of IPMN patients with at least one first-degree relative with pancreatic cancer or IPMN, or at least two first or second degree relatives with pancreatic cancer, IPMN, or malignancies related to pancreatic cancer syndromes, including colorectal, gastric, breast, ovarian, and melanoma neoplasms. Secondary outcomes will be the relative risk of IPMN subtypes of higher malignant potential (main duct or mixed type location), more advanced histology (carcinoma in situ or invasive carcinoma), and recurrence following surgical resection amongst subjects with a family history.

Detailed description: Intraductal papillary mucinous neoplasm (IPMN) is a cyst-like cancer of the pancreas that is increasingly being identified in medical practice, including during the screening of individuals at high risk of pancreatic cancer. It has been established that 10 to 20% of pancreatic cancers are familial. In comparison, there has been little research into the importance of genetic risk in IPMN incidence. The investigators will perform a retrospective chart review of patients with IPMN who were evaluated for surgical intervention at our tertiary referral center. The investigators are interested in determining the proportion of IPMN patients with a family history of pancreatic and other cancers. In addition, the investigators will assess if familial cancer risk is associated with increased risk for malignant IPMN and recurrence, relative to those patients without an inherited predisposition.

Eligibility: Inclusion Criteria:
  -  Tissue-confirmed diagnosis of intraductal papillary mucinous neoplasm or imaging suspicious for IPMN
  -  Seen in consultation for IPMN at Columbia-Presbyterian Medical Center between 2002 and 2008
  Exclusion Criteria:
  -  Not meeting the inclusion criteria.

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Stool Testing for Pancreatic Cancer

Summary: The purpose of this study is to determine if pancreatic cancer/pre-cancer can be detected in early stages through the molecular analysis of stool samples. Investigators hypothesize that analysis of stool samples using digital melt curve (DMC) analysis, can be used as a sensitive and specific method to detect the common genetic abnormalities present in pancreatic cancers and pre-cancerous lesions of the pancreas.

Detailed description: Pancreatic ductal adenocarcinoma (PDC) remains the fourth leading cause of cancer-related death in the United States. This is largely due to the fact that most patients present with advanced, unresectable disease, highlighting the critical need for a screening test for this disease. Stool testing is an approach that has not been explored for use in PDC screening. With the advent of stool-based DNA tests, it may be possible to target genetic abnormalities that have been recently characterized in PDC tumorigenesis.
  Aim: The aim of this study is to determine if deoxyribonucleic acid (DNA) alterations present in pancreatic cancer and precancerous intrapapillary mucinous neoplasms (IPMN) can be reliably recovered in matched stool.
  Methods: This is a case-control prospective study to determine the utility of a stool-based digital melt curve (DMC) assay in PDC screening. A total of 30 patients (18 with pancreatic cancer, 12 with IPMN) who will be undergoing pancreatic resection will be enrolled. Pancreatic neoplastic tissue will be isolated from their surgical specimens and the genes most commonly mutated in PDC will be sequenced from extracted DNA. In addition, hypermethylation at common promoter sites will be assessed by methylation-specific PCR. The genetic and epigenetic alterations isolated in pancreatic tissue will be utilized as the targets for stool DMC assay. Blinded technicians will process stool specimens from control patients as well as a matched control. The primary outcomes of this study will be the sensitivity and specificity of the stool DMC assay in detecting genetic mutations present in tumor or IPMN lesions.

Eligibility: Inclusion Criteria:
  -  18 years of age and older.
  -  Tissue-confirmed or radiological evidence of either pancreatic adenocarcinoma or intrapapillary mucinous neoplasm(IPMN).
  -  Scheduled for surgical resection of the adenocarcinoma or IPMN.
  -  Able to give informed consent
  Exclusion Criteria:
  -  History of colorectal, gastric cancer, esophageal, or head-and-neck cancer.
  -  Endoscopic procedure conducted less than 1 week prior to enrollment.
  -  Unwillingness or inability to sign informed consent.

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: First-in-Man, Dose-escalation Trial of c-Met Kinase Inhibitor EMD 1204831 in Subjects With Advanced Solid Tumors

Summary: EMD Serono has closed enrollment into this trial prior to determination of maximum tolerated dose (MTD). EMD Serono has decided not to pursue the development of EMD 1204831 in patients with advanced solid tumors for reasons other than safety.

Detailed description: This is a an open-label, dose-escalation, first-in-man (FIM) study designed to explore the safety, tolerability, pharmacokinetics, and clinical activity of an investigational drug, EMD 1204831, in patients with advanced solid tumors who have not responded to previous therapies or for whom no other therapies are available. Subjects will receive EMD 1204831 twice a day (BID) during each 21-day cycle until disease progression or unacceptable toxicity.

Eligibility: Inclusion Criteria:
  Main Inclusion Criteria
  1. Histologically or cytologically confirmed solid tumor, either refractory standard therapy or for which no effective standard therapy is available
  2. Measurable or evaluable disease, as defined by RECIST 1.0
  3. Men or women aged ≥ 18 years
  4. ECOG performance status of 0 to 2
  5. Adequate hematological function: Hemoglobin ≥ 9.0 g/dL; Neutrophils > 1.5 x 109/L; Platelets ≥ 100 x 109/L
  6. Adequate liver function: Total bilirubin ≤ 1.5 x ULN; AST/ ALT ≤ 2.5 x ULN
  7. For subjects with liver metastases: Total bilirubin ≤ 1.5 x ULN; AST/ALT ≤ 5 ULN
  8. Adequate renal function: Serum creatinine < 1.5 x ULN, and/or Calculated creatinine clearance > 60 mL/min
  9. Resolution of all acute chemotherapy, radiotherapy or surgery-related AEs to Grade ≤1, except for alopecia
  10. Recovery from any surgical intervention
  11. Subjects enrolling after the MTD has been determined must present specific c-Met alterations (overexpression, amplification, mutation)
  Exclusion Criteria:
  Main Exclusion Criteria
  1. Received chemotherapy, immunotherapy, hormonal therapy (except subjects with prostate cancer), biologic therapy, or any other investigational agent or anticancer therapy within 28 days (or five half-lives for non-cytotoxics, whichever is shorter), of Day 1 of trial treatment (six weeks for nitrosureas or mitomycin C)
  2. Received extensive prior radiotherapy on more than 30% of bone marrow
  3. Symptomatic primary tumors or metastasis of brain and/or central nervous system, uncontrolled with antiepileptics and requiring high doses of steroids
  4. Medical history of liver fibrosis/ cirrhosis
  5. Medical history of surgery within six weeks prior to enrollment
  6. Neuropathy Grade ≥ 2
  7. Requires concurrent treatment with a non-permitted drug
  8. Absence or abnormal pupillary reflex

Relevance to patient case: possibly relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Cyclooxygenase-2 Inhibitor for Adjuvant Anticancer Effect in Patients With Biliary-pancreas Cancer

Summary: In extrahepatic bile duct cancer and pancreatic cancer, we will treat postoperatively with COX2 inhibitor and assess survival rate and recurrent rate.

Detailed description: Patients : total 220 patients
  -  Extrahepatic bile duct cancer : 55 patients for administration of COX2 55 patients for control group
  -  Pancreas cancer : 55 patients for administration of COX2 55 patients for control group
  Indication
  -  After operation of extrahepatic bile duct cancer or pancreas cancer
  -  Age : 19 - 70 years old
  -  The patients who agree to consent sheet.
  Contraindication
  -  Impossible of administration due to severe postoperative morbidities (bleeding, bowel obstruction, pancreatic fistula, biliary fistula)
  -  Preexisting heart disease: Ischemic heart disease, Heart failure. Severe uncontrolled hypertension (systolic BP>160)
  -  Renal insufficiency: CCR < 50 or serum creatinin >3.0
  -  Hepatic insufficiency: Liver cirrhosis or active hepatitis
  -  Preexisting allergic reaction history for NSAIDs or Sulfonamide
  -  Current drug intake: Warfarin. Lithium, Fluconazole, Aspirin, Celecoxib
  -  Preexisting Asthma. Especially aspirin-sensitive asthma.
  -  Contraindications to aspirin, clopidogrel or celecoxib
  -  The patients who refuse trial
  -  The patients who has Psychogenic problem
  Allocation
  -  We will allocate patients randomly, to administration group or control group
  Methods
  -  From postoperative third day, administration will be started
  -  celecoxib 200mg bid for 6 months for administration group
  -  Follow up and assess recurrence rate and survival rate

Eligibility: Inclusion Criteria:
  -  The patients who underwent operation for extrahepatic bile duct cancer or pancreas cancer
  -  Between 19 and 70 years old
  -  Agreed to consent sheet
  Exclusion Criteria:
  -  The patients cannot administration of drug due to severe postoperative morbidities.
  -  Preexisting heart disease: Ischemic heart disease, Heart failure. Severe uncontrolled hypertension (systolic BP>160)
  -  Renal insufficiency: CCR < 50 or serum creatinin >3.0
  -  Hepatic insufficiency: Liver cirrhosis or active hepatitis
  -  Preexisting allergic reaction history for NSAIDs or Sulfonamide
  -  Current drug intake: Warfarin. Lithium, Fluconazole, Aspirin, Celecoxib
  -  Preexisting Asthma. Especially aspirin-sensitive asthma.
  -  Contraindications to aspirin, clopidogrel or celecoxib
  -  When patients refused
  -  Patients has psychological problem

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: An Investigational Drug, Crizotinib (PF-02341066), Is Being Studied In Tumors, Except Non-Small Cell Lung Cancer, That Are Positive For Anaplastic Lymphoma Kinase (ALK)

Summary: This is a Phase 1 trial evaluating the safety and efficacy of crizotinib in patients with tumors except non-small cell lung cancer that are positive for ALK.


Eligibility: Inclusion Criteria:
  -  histologically or cytologically proven diagnosis of malignancy other than NSCLC
  -  positive for translocation or inversion event involving the ALK gene locus
  -  positive for ALK amplification events
  -  positive for ALK activating point mutations
  Exclusion Criteria:
  -  mutations of amplifications involving the c-Met gene but not the ALK gene
  -  concurrent treatment on another therapeutic clinical trial
  -  prior therapy specifically directed against ALK

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Frequency of Methods of Local Invasion of Pancreatic Adenocarcinoma

Summary: Pancreatic cancer often spreads through local invasion into local structures, including fat, blood vessels, nerves, and nearby organs (stomach, duodenum, spleen, bile duct). Local microscopic invasion is associated with recurrence of pancreatic cancer after pancreatic resection, such that even if the original cancer is surgically removed, microscopic areas of cancer often remain. Data on the patterns of local invasion by pancreatic cancer have not been published. In this study, The investigators hope to investigate the frequency of the various methods of local invasion of pancreatic adenocarcinoma. This would help the investigators better understand how pancreatic cancer spreads, and determine what cancers are not resectable.

Detailed description: Pancreatic cancer is the eighth most common malignancy, and the fifth leading cause of cancer-related death, in the United States. Unfortunately, patients often present late in the course of the disease. Accordingly, the 1- year survival rate is approximately 20%, and the 5-year survival rate is less than 4%. Even in patients with local disease who are surgical candidates, survival at five years remains only 10-25%. Staging for pancreatic adenocarcinoma typically utilizes the TNM classification, where "T" represents tumor size, "N" represents regional lymph node metastasis, and "M" represents distant metastasis. This type of staging can usually only be done after operative resection. Unfortunately, up to 25% of patients are found to be unresectable at the time of surgical exploration. This is most often due to local invasion or metastatic disease. Local microscopic invasion is associated with recurrence of pancreatic cancer after pancreatic resection. Comprehensive data on the patterns of local invasion by pancreatic cancer have not been published. The investigators believe that it would be beneficial to investigate the frequency of the various methods of local invasion of pancreatic adenocarcinoma. A clearer understanding of the natural history of local invasion could potentially lead to a better determination of what constitutes unresectability.

Eligibility: Inclusion Criteria:
  -  Tissue confirmed diagnosis of pancreatic adenocarcinoma.
  -  Underwent surgical resection for adenocarcinoma at the Columbia University Medical Center between 2001-2009.
  Exclusion Criteria:
  -  Did not undergo surgery.

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Viokase 16, Viokase16 Plus Nexium and Nexium Alone

Summary: Our primary hypothesis is that the addition of Nexium to Viokase 16 will decrease the chronic abdominal pain in patients with small duct chronic pancreatitis in a superior fashion compared to Viokase 16 plus placebo or to Nexium alone. A secondary hypothesis would be an increase in quality of life. Our objective is to elucidate the role of Nexium in the control of pancreatic pain, quality of life, and narcotic usage alone or when added to Viokase 16. Our endpoints are the reduction of abdominal pain, decreased pain medication usage, decreased ER visits and decreased hospital admissions for abdominal pain.


Eligibility: Inclusion Criteria:
  1. Males and females age 18 to 75 years inclusive. Female subjects of child bearing potential or less than two years post-menopausal must use a medically acceptable form of birth control or barrier method and have a negative pregnancy test prior to entry into study.
  2. History of abdominal pain associated with chronic pancreatitis
  3. Evidence of chronic pancreatitis as manifested by an abnormal secretin test, calcification of the pancreas on plain film, an abnormal CT showing a dilated pancreatic duct and/or atrophy, an abnormal Endoscopicretrogradecholangeopancreatography (ERCP), or diffuse changes on Endoscopic Ultrasound (EUS), fecal elastase > 100ug/g stool, or serum trypsinogen > 20ng/ml
  Exclusion Criteria:
  1. Subjects on enzyme therapy within the last 14 days, proton pump inhibitor (PPI)within the last 7 days, or octreotide within 48 hours.
  2. Subjects with known hypersensitivity to pork or exogenous or pancreatic enzymes.
  3. Female subjects who are pregnant or lactating
  4. Subject use of enzyme therapy other than that called for in this study
  5. Subject use of therapeutic amounts of antacids or H2 receptor antagonists during the course of the study.
  6. Past history of documented steatorrhea by 72 hour fecal fat determination or current history consistent with steatorrhea -

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Biomarkers in Tissue Samples From Patients With Breast Cancer Treated With Bevacizumab

Summary: RATIONALE: DNA analysis of tumor tissue may help doctors predict how well patients will respond to treatment.
  PURPOSE: This research study is studying biomarkers in tissue samples from patients with breast cancer treated with bevacizumab.

Detailed description: OBJECTIVES:
  Primary
  -  To demonstrate that vascular endothelial growth factor-A (VEGFA) haplotypes that are associated with an increased VEGFA expression will predict superior outcome for patients with metastatic breast cancer receiving bevacizumab in ECOG-E2100 (but not for the control arm).
  -  To demonstrate that candidate single nucleotide polymorphisms (SNPs) will further improve the predictive capacity of outcome (efficacy and toxicity) in patients enrolled in ECOG-E2100.
  -  To demonstrate that tumor VEGFA amplification or borderline amplification (estimated 14% frequency) will predict superior outcome for patients with metastatic breast cancer receiving bevacizumab on ECOG-E2100 whereas those with VEGFA deletion (estimated 11% frequency) will predict inferior outcome.
  -  To demonstrate that VEGFA amplification/deletion will not predict outcome in the control arm of ECOG-E2100.
  Secondary
  -  To demonstrate that tumor VEGFA amplification will predict increased protein expression as ascertained by IHC.
  -  To demonstrate that a combined algorithm calculated from tumor-specific variability (VEGFA amplification/deletion) and host-specific variability (SNPs) will optimally predict outcome (efficacy) with bevacizumab in patients enrolled on ECOG-E2100.
  OUTLINE: This is a multicenter study.
  Previously collected tumor-derived DNA is analyzed for VEGFA amplification/deletion and haplotype as biomarkers for outcome after bevacizumab treatment. Gene expression, polymorphism, protein expression analysis, and IHC are performed on the samples.

Eligibility: DISEASE CHARACTERISTICS:
  -  Enrolled on ECOG-E2100
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 48-year-old male with Pancreatic cancer. Genetic variant: CDK6 Amplification. Other conditions: None.

Clinical trial: Trial Comparing Two Techniques of Celiac Plexus Neurolysis for Treatment of Pain in Carcinoma Pancreas

Summary: Coeliac plexus neurolysis (CPN) is a management option for pain control in carcinoma pancreas.CPN is conventionally performed by percutaneous technique with fluoroscopic guidance. Endoscopic ultrasound (EUS) is increasingly used for CPN as it offers a better visualization of the plexus. There are limited data comparing the two modalities.The patients are on follow-up for 6 months post neurolysis.

Detailed description: Carcinoma pancreas patients with abdominal pain requiring daily analgesics for more than 4 weeks were included.we are randomising about 100 patients into two groups to undergo either of the two procedures, i.e. celiac plexus neurolysis by percutaneous technique or by endoscopic ultrasound guided technique.The pain scores have been recorded by visual analogue scale for an average follow-up of 6 months.

Eligibility: Inclusion Criteria:
  -  all patients with carcinoma pancreas
  Exclusion Criteria:
  -  patients below 18 years of age and who have not given consent

Relevance to patient case: not relevant