araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Analysis of Respiratory System Mechanics and Inflammatory Response During Orthotopic Liver Transplantation (SPPLIT Trial)

Summary: During orthotopic liver transplantation (OLT), respiratory system function may be severely impaired for several reasons including anaesthesia effects, hyperdynamic volume state with fluid overload and ischemia reperfusion injury. In particular, reperfusion syndrome is characterised by the release of several inflammatory mediators such as cytokines and oxygen free radicals which may contribute to alveolar endothelial barrier dysfunction. The object of this study is to investigate the respiratory system mechanics impairment in its partitioning between lung and chest wall.
  We hypothesize that impairment of respiratory system mechanics (of both lung and chest wall) occurs after reperfusion phase of liver. This impairment is associated with the systemic inflammatory response following liver reperfusion.


Eligibility: Inclusion Criteria:
  -  orthotopic liver transplantation
  -  valid informed consent
  Exclusion Criteria:
  -  Age < 18 yrs

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: A Phase II, Single Arm Study of BGJ398 in Patients With Advanced Cholangiocarcinoma

Summary: This is a multi-center, open label, single arm phase II study evaluating BGJ398 anti-tumor activity in advanced or metastatic cholangiocarcinoma patients with FGFR genetic alterations.

Detailed description: Adult patients with histologically or cytologically confirmed advanced or metastatic cholangiocarcinoma with FGFR2 gene fusion/ translocation or other FGFR genetic alteration who have evidence of radiologic progression following a cisplatin-and gemcitabine-containing regimen for advanced disease or a gemcitabine-containing regimen for those who are considered intolerant to cisplatin will be enrolled. Approximately 55 adult patients over age 18, both male and female will be enrolled. Of these 55 patients, 40 patients will have cholangiocarcinoma with identified FGFR2 gene fusions and up to 15 patients may have other FGFR genetic alterations. All patients will receive oral BGJ398, once daily, on a three weeks on (21 days), one week off (7 days) schedule. One treatment cycle will consists of 28 days.

Eligibility: Inlcusion criteria:
  - Adult patients with histologically or cytologically confirmed cholangiocarcinoma at the time of diagnosis.
  Patients with cancers of the gallbladder or ampulla of Vater are not eligible.
  - Patients must have received at least one prior regimen containing gemcitabine with or without cisplatin for advanced/ metastatic disease. Patient should have evidence of progressive disease following prior regimen, or if prior treatment discontinued due to toxicity must have continued evidence of measurable or evaluable disease.
  Exclusion criteria:
  -  Prior or current treatment with a MEK or selective FGFR inhibitor
  -  insufficient organ function
  -  ANC < 1,000/mm3 [1.0 x 109/L]
  -  Platelets < 75,000/mm3 [75 x 109/L]
  -  Hemoglobin < 109.0 g/dL
  -  Total bilirubin > 1.5x ULN
  -  AST/SGOT and ALT/SGPT > 2.5x ULN (AST and ALT > 5x ULN in the presence of liver metastases)
  -  Serum creatinine > 1.5x ULN and a calculated or measured creatinine clearance < 45 mL/min
  -  Inorganic phosphorus outside of normal limits
  -  Total and ionized serum calcium outside of normal limits
  Other protocol-defined inclusion/exclusion criteria may apply.

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Testing BRCA 1/2 Mutation Using Next Generation Sequencing

Summary: Testing BRCA 1/2 mutation is important for patients with breast cancer, and Sanger sequencing is a standard method to identify BRCA 1/2 mutation. Next generation sequencing (NGS) is a high-throughput parallel sequencing that can provide genetic information with high accuracy. NGS is a faster and cost-effective method to detect gene mutations compared to Sanger sequencing. In this study, we evaluated the clinical role of NGS testing for BRCA 1/2 compared to Sanger sequencing.


Eligibility: Inclusion Criteria:
  -  Age > 18
  -  Breast or ovarian cancer history in 2nd degree family members
  -  Male breast cancer
  -  Bilateral breast cancer
  -  Patient with breast cancer under 40 year of age
  -  Simultaneous breast and ovarian cancer
  -  Patients with epithelial ovarian cancer
  -  Breast cancer with other simultaneous extramammary malignancy
  Exclusion Criteria:
  -Patients who do not agree with testing BRCA 1/2 mutation

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Prostate Cancer Screening in Men With Germline BRCA2 Mutations

Summary: The purpose of this study is to determine the incidence of prostate cancer in men with the BRCa2 gene mutation as an independent indicator for prostate cancer screening.

Detailed description: This is a cohort screening study to prospectively identify the incidence of prostate cancer in a population of BRCA2 carriers. All men identified to have a BRCA2 mutation as part of the Yale Cancer Genetic Counseling Program will be approached and offered participation in the study via our program newsletter, BRCA listserv, Facebook page and a targeted mailing.
  Standard of care screening at the Yale Cancer Center for men with a normal prostate cancer risk consists of a PSA test and prostate physical examination beginning at age 50 years and if either is abnormal an MRI of the prostate followed by Fusion-targeted biopsy of the prostate is performed.

Eligibility: Inclusion Criteria:
  -  All men ≥30 years of age with at least a ten-year life expectancy
  -  A known BRCA2 mutation
  -  Ability to have an MRI
  -  Able to give informed consent will be approached to participate in the study
  Exclusion Criteria:
  -  If a man has received or is currently receiving treatment for prostate cancer

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Treatment for Bile Duct Cancer in the Liver

Summary: The current standard treatment of inoperable intrahepatic cholangiocarcinoma (bile duct cancer in the liver) is chemotherapy, which is of limited efficacy. The use of selective internal radiotherapy treatment (SIRT-Y90) is proven efficacious in patients with intra-heptic tumor. Previous experience with SIRT is safe in patients with intrahepatic cholangiocarcinoma. This study aims to study the benefits of sequential administration of SIRT followed by standard chemotherapy for treatment of inoperable intrahepatic cholangiocarcinoma.


Eligibility: Inclusion Criteria:
  -  Age>18 years
  -  Histological or cytological diagnosis of cholangiocarcinoma
  -  Disease not amenable to surgery
  -  Predominant disease load in the liver (in case of extra-hepatic involvement, only patients with lymph nodes metastases are allowed)
  -  Naïve to locoregional or systemic treatment (but patients who develop recurrent disease after surgery are suitable)
  -  ECOG PS 0-1
  -  At least one measurable disease lesion according to RECIST v 1.1
  -  Life expectancy of 12 weeks or longer
  -  Adequate hematological, renal and hepatic function
  -  Platelet ≥100 x 109
  -  ANC ≥ 1.5 x 109
  -  Bilirubin ≤ 30µmol/L
  -  Albumin ≥ 30g/L
  -  ALT ≤ 3 ULN
  -  INR ≤ 1.5
  -  Serum creatinine ≤ 1.5 x ULN
  Exclusion Criteria:
  -  Prior malignancy except cervical carcinoma-in-situ or treated basal cell carcinoma. Any cancers treated curatively > 5 years prior to study entry are permitted.
  -  Patients with extra-hepatic disease other than regional lymph node metastases.
  -  Evidence of ascites or cirrhosis, as determined by clinical or radiologic assessment
  -  Biliary obstruction with no possibility of drainage
  -  Non-malignant disease that would render the patient unsuitable for treatment according to the protocol
  -  Prior treatment of chemotherapy for the cholangiocarcinoma
  -  Prior radiation therapy to the upper abdomen
  -  Complete thrombosis of the main portal vein
  -  Tumor volume > 50% of the normal liver volume
  -  Allergy to non-ionic contrast agents

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Safety Study of Liver Transplantation for Hilar Cholangiocarcinoma

Summary: Hilar cholangiocarcinoma is a highly malignant tumor. Surgical resection or simple liver transplantation leads to poor prognosis accompanied by high recurrence rate and low survival rate. The newly proposed neoadjuvant therapy with liver transplantation strategy shows promising clinical application, which once reported 5-year survival rate 82%. However, transplantation centers conducting this kind of research are limited due to its complexity and long-term. The investigators would like to conduct a clinical trial for only unresectable hilar cholangiocarcinoma patients who should take neoadjuvant brachytherapy and chemoradiotherapy followed by orthotopic liver transplantation.

Detailed description: The enrolled patients should be prescribed with several examinations when admitted to hospital consisting of CT, MRI, MRCP, ECT, PET/CT and other laboratory tests. All preoperative examinations must indicate that enrolled individuals should be diagnosed as unresectable hilar cholangiocarcinoma. In addition, repetitive ERCP manipulations are needed in order to obtain positive results by brush cytology. Of course, all enrolled patients should be adherent to the fundamental principles of liver transplantation.
  We employed I-125 radioactive plastic stents (patent No: ZL 201610116321.3) to conduct brachytherapy. Each stent composed of a drainage tube with a stab at both ends that had a stabilizing effect. Two opposite channels were made in the wall of stents paralleling the drainage lumen, with irradiation window in the lateral wall of the channel. The diameter of the channel is a bit smaller than that of the radioactive seeds, so as is the length and width of irradiation windows. The stents are so designed to immobilize seeds and radiate properly. The radioactive I-125 seeds were 4.5 mm long and 0.8 mm thick, and their half-life was 60.1 days. The nasobiliary radiography was performed to determine the length of involvement of bile duct.Corresponding radioactive seeds are then put in appropriate location with biliary stents by ERCP procedure.
  About a month later, external beam radiotherapy was administrated to a target dose of 30Gy in 30 fractions, 1.5Gy twice per day. Concomitantly, Intravenous capecitabine was given at 1.0g bid for two weeks, which is repeated after 14 days until transplantation.
  Immunosuppressive therapy was provided with tacrolimus, mycophenolate and corticosteroids. Corticosteroids were withdrawn a week later. Chemotherapy was continued 1 month after OLT with expected 3 courses.

Eligibility: Inclusion Criteria:
  unresectable hilar cholangiocarcinoma tumor diameter less than 3 cm adherence to liver transplantation requirements
  Exclusion Criteria:
  intrahepatic cholangiocarcinoma uncontrolled infection intrahepatic or extrahepatic metastasis distant lymph node metastasis

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Next Generation Sequencing in Intrahepatic Cholangiocarcinoma

Summary: The aim of the present study is to perform a comprehensive molecular characterization of intrahepatic cholangiocarcinoma (ICC) in patients exposed to well-known or putative risk factors (such as asbestos) for this malignancy, in order to identify possible "molecular signatures" associated to such different risk factors.

Detailed description: Exposure to distinct risk factors of the enrolled ICC patients will be assessed by modified ReNaM questionnaire. Molecular characterization of ICC tissue samples will be carried out by RNAseq. Briefly, after surgical resection tissue samples will be immediately suspended in RNAlater. RNAseq analysis will be performed on the Illumina HiScanSQ platform. Any possible mutations identified by RNAseq will be validated by Sanger sequencing. Putative identified fusion transcripts will be confirmed by RT-PCR, using specific primers pairs located on the sequences from the exons of the two putative fusion genes. Variations in gene expression will be validated by the real-time PCR. The bioinformatic analysis will be made by using CentOS5 Server. For evaluation of asbestos fibers in tumor tissues, samples embedded in paraffin will be incinerated and then analyzed in a scanning electron microscope and by EDS spectroscopy.

Eligibility: Inclusion Criteria:
  -  patients having a confirmed diagnosis of ICC resected;
  -  patients who have signed the informed consent;
  -  patients (males or females) who are at least 18 years old.
  Exclusion Criteria:
  -  patients who have been treated with any medical treatment (chemotherapy or experimental standard) or with radiotherapy during the last 5 years.

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Preliminary Results for the Double-dose Adenovirus-mediated Adjuvant Therapy Improving Outcome of Liver Transplantation in Patients With Advanced Hepatocellular Carcinoma

Summary: HCC patients with tumors >5 cm in diameter, regardless of involvement in the intrahepatic and extrahepatic portal branches participated in the study. Patients were randomized allocated in liver transplantation (LT) only group and LT plus ADV-TK therapy group. All patients received orthotopic liver transplantation; in the LT plus ADV-TK group, ADV-TK therapy was delivered to patients twice.


Eligibility: Inclusion Criteria:
  -  18～70 years of age (Male and Female).
  -  Clinical diagnosis of advanced hepatocellular carcinoma who could accept liver transplantation
  -  Patients who had unresectable HCC >5 cm and no metastasis in lungs and bones were eligible to participate in this study. Tumor involvement in the intrahepatic and extrahepatic portal branches was not considered to be an exclusion criterion.
  -  No prior chemotherapy, radiation therapy, targeted therapy or other kind of biological treatment within 4 weeks.
  -  Provide written informed consent
  Exclusion Criteria:
  -  Metastasis in lungs and bones
  -  Invasion in main vescular.
  -  Contraindications of liver transplantation
  -  Contraindications of operation of other organ system
  -  Hypersensitivity to adenovirus, GCV or similar drugs
  -  Accept clinical trials of other drugs
  -  Immunological deficit
  -  Active pregnancy
  -  Unable or unwilling to sign informed consents

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Pancreatic Cancer Early Detection Program

Summary: Early detection testing is recommended for individuals at elevated risk for the development of Pancreatic Cancer. This Protocol will define sufficiently elevated risk as either equal to or greater than five times the general population risk, or five times the average risk (1.5%) of developing pancreatic cancer by age 70; that is a 7.5% lifetime risk. Our inclusion criteria has a strong focus on the risk for pancreatic cancer imparted by the presence of hereditary cancer genes, as well as by family history. Enrolled subjects will undergo Endoscopic Ultrasound (EUS) alternating with Magnetic Resonance Imaging (MRI), every six to 12 months, for up to 5 years.

Detailed description: Interested individuals can be referred by physicians, or by family or friends.
  Individuals are informed that the purpose of this study is to collect outcome data following early detection testing based upon our criteria for elevated risk.
  Consent is obtained by any of the co-investigators. Consent is obtained for the primary PCEDP, and also obtained to allow for data to be used by our Cancer Program.
  We have a weekly review of all calls made and of all enrollments.
  We have a monthly meeting to review all proceeding regarding the study.
  Our IRB routinely reviews the proceedings of the study
  Our institution has a monthly Clinical research Committee meeting.

Eligibility: Inclusion Criteria: Any of the following:
  1. Known carrier of either the BRCA2 or CDKN2A mutation;
  2. Known carrier of any of the following mutations (BRCA1, MLH1, MSH2, PMS2, MSH6, EPCAM , P53, PALB2, APC, or ATM) PLUS first or second degree relative affected with pancreatic cancer;
  3. Individual with Peutz-Jeghers Syndrome;
  4. Familial Pancreatic Cancer, defined as at least two affected relatives with Pancreatic Cancer, who are first degree relatives with each other, and at least one of those affected must be first degree relative to the study subject;
  5. Both parents affected, any age:
  6. Any first degree relative diagnosed with pancreatic cancer under age 50;
  7. Chronic Pancreatitis Syndrome, defined by either PRSS1 or SPINK1 mutations AND appropriate clinical and family history
  Exclusion Criteria:
  1. Any medical condition that contraindicates endoscopy or biopsy
  2. Any medical condition that contraindicates MRI
  3. Status post partial or complete resection of the pancreas
  4. History of pancreatic cancer, either endocrine or exocrine
  5. Clinical suspicion of pancreatic cancer, or any previous radiographic or histologic diagnosis of a pre-malignant finding, including IPMN (Intraductal papillary mucinous neoplasm) and PanIN (Pancreatic intraepithelial Neoplasm).
  6. diagnosis of dementia
  7. Uncontrolled, current illness
  8. Renal insufficiency with serum creatinine greater than 2.0 mg/dl

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Radioactive Stents for Treatment of Unresectable Biliary Tract Cancer

Summary: The purpose of this study is to determine whether radioactive stents and common used plastic stents are effective and safety in the treatment of unresectable biliary tract cancer.

Detailed description: Patients with unresectable biliary tract cancer (intrahepatic or extrahepatic cholangiocarcinoma, or ampullary carcinoma) were enrolled and placed with a stent loaded with radioactive seeds (irradiation stent group) or a conventional plastic stent (traditional stent group). After stent placement, the outcomes were compared in terms of tumor response, progression-free survival, overall survival time, and complications related to the procedures.

Eligibility: Inclusion Criteria:
  -  Patients were eligible if they had received a histopathological or cytologic diagnosis of nonresectable, recurrent, or metastatic biliary tract carcinoma (intrahepatic or extrahepatic cholangiocarcinoma,or ampullary carcinoma)
  -  Patients aged between 18 and 80 years
  -  an estimated life expectancy of more than 3 months
  -  Disease had to be measurable by computed tomography scan (as assessed by Response Evaluation Criteria in Solid Tumors (RECIST) 1.0 criteria
  -  TNM stage III-IV
  -  no evidence of cancer of another organ.
  -  no prior chemotherapy for advanced disease was allowed, but adjuvant/neoadjuvant therapy was allowed
  -  Karnofsky index of ≥60%
  -  ECOG index ≥2
  -  previous technically successful stenting or ENBD derange
  -  Accept of informed consent
  Exclusion Criteria:
  -  Clinically significant cardiovascular disease
  -  coagulation disorders
  -  contraindication of Endoscopic
  -  pregnant or breastfeeding women
  -  known sensitivity sensitivity to investigated agents or components
  -  recent invasive procedure
  -  prior chemotherapy or radiotherapy for biliary cancer
  -  refusal of informed consent

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Triple Negative Breast Cancer and Germline Hereditary Breast and Ovarian Cancer Mutation Carrier Registry

Summary: PROGECT is a registry for patients with Triple Negative breast cancer (TNBC) or patients who have an identified germline mutations (such as a mutation on the BRCA1 or BRCA2 genes).

Detailed description: This study is being done to collect cancer-related information from patients with triple negative breast cancer and patients with hereditary genetic mutations. This information will help us better understand the link between genetic changes and cancer outcome in patients with triple negative breast cancer.

Eligibility: Inclusion criteria include:
  Triple Negative Breast Cancer
  -  ER/PR <10% and HER negative per current ASCO/CAP guidelines
  -  Stages I-IV
  -  Any age at diagnosis
  -  Patient must be within 5 years of diagnosis
  -  Eligible regardless of genetic testing status
  -  Genetic testing recommended for patients meeting NCCN and Medicare guidelines
  AND/OR
  Germline mutation Carriers
  -  Patients with deleterious or uncertain mutations in HBOC genes (BRCA, PTEN, P53, -PALB2 etc) are eligible regardless of type/site of cancer
  -  Healthy patients harboring mutations also eligible
  -  There is no time limit from the time of diagnosis of cancer and enrollment.
  -  Eligible regardless of personal history of cancer
  Exclusion Criteria include:
  Triple Negative Breast Cancer -Patient is not within five years of diagnosis
  Germline mutation Carriers:
  -Patient only carries a HBOC mutation that is classified as "polymorphism" of "favor polymorphism"

Relevance to patient case: not relevant
Patient case: 72-year-old male with Cholangiocarcinoma. Genetic variant: BRCA2. Other conditions: Diabetes.

Clinical trial: Pancreatic Cancer Screening of High-Risk Individuals in Arkansas

Summary: 100 subjects who have a family history of pancreatic cancer (PC), or known genetic syndromes associated with increased risk of pancreatic cancer, will be followed for five years. This data will be used to determine the pancreatic cancer and precancerous lesion detection rate in High Risk Individuals (HRIs). Subjects may agree to annual imaging and annual biomarkers or to biomarkers only.


Eligibility: Inclusion Criteria:
  -  Have a family history of PC as listed below or who have one of the following syndromes: Peutz-Jeghers syndrome - STK11; BRCA 1 and 2; PALB2; ATM; FAMMM / P16; HNPCC (Lynch) / MMR genes; Hereditary pancreatitis - PRSS1
  -  Individuals with three or more affected blood relatives (1st, 2nd or 3rd degree)
  -  Individuals with two or more affected blood relatives with PC, with at least one affected FDR, should be considered for screening.
  -  Patients with a history of Peutz-Jeghers syndrome should be screened, regardless of family history of PC.
  -  Patients with a known p16 (FAMMM syndrome) with one affected 1st or 2nd degree relative will be considered for screening.
  -  Patients with a known BRCA1 or BRCA2 mutation with one affected 1st or 2nd degree relative should be considered for screening.
  -  Patients with a known PALB2 mutation with one affected family member should be considered for screening.
  -  Patients with a known Mismatch-repair gene-mutation carriers (Lynch syndrome) with one affected family member should be considered for screening.
  Exclusion Criteria:
  -  Not candidates for surgery

Relevance to patient case: possibly relevant