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

Clinical trial: Targeted Next-generation Sequencing Panel for Identification of Germline Mutations in Early Onset Cancers With Sporadic or Hereditary Presentation

Summary: Despite relevant clinical and/or familial presentations suggesting a hereditary predisposition (early-onset, multiple primary tumors, familial aggregation), targeted genomic analysis based on the phenotype are often non contributive. As somatic cancer genes are limited, the hypothesis is that the targeted next-generation sequencing of 200 genes, selected for their implications in cancers may contribute to the understanding of many selected patients' presentation by the identification of germline deleterious mutations, and may identified phenotype overlapping and/or mosaicisms. The focus will be put on early-onset breast, ovarian, colorectal cancer or pediatric cancers and multiple primary tumors.


Eligibility: Inclusion Criteria :
  -  Older than 18 or parental agreement in case of children.
  For patient with early-onset breast cancer :
  -  Invasive breast cancer, regardless of histological type or stage, diagnosed before 31 years.
  -  Sporadic or familial presentation
  -  No genomic alterations of BRCA1, BRCA2 or TP53
  For patient with early-onset ovarian cancer :
  -  Invasive ovarian cancer, regardless of histological type or stage, diagnosed before 41 years.
  -  Sporadic or familial presentation
  -  No genomic alterations of BRCA1, BRCA2
  Patient with early-onset colorectal cancer :
  -  Invasive colorectal cancer diagnosed before 31 years.
  -  Sporadic or familial presentation
  -  No genomic alteration of MSH2, MLH1 or MSH6 in case of HNPCC presentation
  -  No genomic alteration of APC, MUTYH, SMAD4, BMPR1A, PTEN or STK11 in case of adenomatous polyposis or hamartoma presentation
  Patient with pediatric cancer :
  -  Non haematological tumour diagnosed before 16 years, with Li-Fraumeni presentation.
  -  No genomic alteration of TP53
  Patient with Multiple primary malignant tumours :
  -  Multiple synchronous or metachronous primary malignant tumors with early-onset
  -  No syndromic presentation
  Exclusion Criteria:
  -  Any already known deleterious mutations according to the patient's phenotype

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

Clinical trial: Biliary Cancer in Italy: a Study on Cholangiocarcinoma cAUSEs and Risk Factors

Summary: Multi-centric, observational, prospective study, designed for pts with diagnosis of all-stages cholangiocarcinoma, including rare and crossing-over histological types, and excluding gallbladder cancer and ampullary carcinoma.

Detailed description: Patients will undergo basal blood sample exams regarding blood cell count, renal and liver function, tumor markers, inflammatory and metabolic state, along with a screening (and, if needed, a more in-depth laboratory analysis) for viral hepatitis infections. Information will be collected about radiological, clinical and pathological features of the neoplasm at time of diagnosis, as well, at a later time, about its natural history. A two-step data analysis will be performed: Task-1 analysis will define the risk factors landscape, Task-2 analysis will examine the influence of etiology on clinical outcomes. Anonymized data will be stored in a central database, kept at the Leading Centre.

Eligibility: Inclusion Criteria:
  -  voluntary, written, dated and signed informed consent;
  -  age ≥ 18 years;
  -  histologically documented diagnosis of cholangiocarcinoma (including histological variants and mixed forms). Neoplasms under investigation do not include gallbladder cancer and ampullary carcinoma.
  Exclusion Criteria:
  -  Dementia or altered mental status leading to inability to understand or render the informed consent.
  -  Patients who already underwent a systemic treatment (chemotherapy and/or targeted therapy) may be enrolled but will not be subject to data collection about BI-CAUSE - Study Protocol Version 1.0 Oct 18th, 2015 10 blood laboratory tests (with the exception of viral screening) and natural history, and will not be factored in the data analysis of prognostic factors. Performance status, life expectancy, tumour staging, tumour site (distal or hilar extrahepatic, intrahepatic), previous surgical resection, previous biliary stenting, previous radiotherapy are not part of inclusion/exclusion criteria.

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

Clinical trial: Radiofrequency Ablation Using Octopus Electrodes for Treatment of Focal Liver Malignancies

Summary: The purpose of this study is to evaluate the clinical feasibility and short-term outcome of switching monopolar RFA using a separable cluster electrode in patients with primary and secondary liver malignancies.

Detailed description: Radiofrequency ablation (RFA) is one of minimal invasive treatment methods and it has been showing comparable overall survival with surgery in early or small hepatocellular carcinomas (HCCs) and better cost-effectiveness. However, it is suffering from high local tumor progression (LTP) rate. To reduce LTP rate, creation of large ablative zone has been attempted in various strategies. A separable cluster electrode is a new type of RFA electrode. It consists of three individual applicators and the applicators can be incorporated as a single handle such as a cluster electrode, and can be separated as three electrodes, depending on operators' needs. It allows high flexibility to operators and the preclinical results were promising. Herein, we want to evaluate the clinical feasibility of the electrodes by observing major complication rates, technical success rate and 12-months LTP rate.

Eligibility: Inclusion Criteria:
  -  Hepatic malignancies diagnosed on biopsy OR
  -  Typical imaging features of hepatocellular carcinoma (HCC) on computed tomography (CT) or magnetic resonance imaging (MRI) according to AASLD guideline
  -  Typical imaging feature of metastasis on CT or MRI AND
  -  1~5 tumors equal to or smaller than 5cm in the liver
  -  no direct contact with or invasion into the hepatic hilar structures or inferior vena cava (IVC)
  -  Eastern Cooperative Oncology Group performance status of 0
  -  Patients who signed informed consent
  Exclusion Criteria: Patients with any of followings are excluded.
  -  Patients with uncontrolled coagulopathy
  -  Patients with Child-Pugh classification C
  -  Patients with tumor invasion in major portal vein or hepatic vein branch
  -  Extrahepatic metastasis

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

Clinical trial: Changes of Macrophage Migration Inhibitory Factor During Orthotopic Liver Transplantation

Summary: Collecting blood, graft liver effluent and urine samples from patients undergoing orthotopic liver transplantation.

Detailed description: Aims are to measure Macrophage Migration Inhibitory Factor in serum, liver graft effluent and urine in and evaluate MIF's role in hepatic ischemia/reperfusion injury, postoperative graft function and kidney function.

Eligibility: Inclusion Criteria:
  -  End stage liver disease, chronic liver failure, orthotopic liver transplantation
  Exclusion Criteria:
  -  Combined transplantations (liver plus kidney or lung), age under 18 y, acute liver failure

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

Clinical trial: Photodynamic Therapy in Locally Advanced Hilar Cholangiocarcinoma

Summary: To determine the safety and efficacy of photodynamic therapy with a novel photosensitizer and a flexible laser probe in locally advanced hilar cholangiocarcinoma.

Detailed description: Photodynamic therapy (PDT) is a way of producing tissue necrosis with light after prior administration of a photosensitizing agent. The most important advantages include the possibility of combining PDT with other target therapies and repeat the process as needed with a favorable outcomes. The combination of diverse therapeutic modalities is one of the new strategies to enhance oncologic treatments for pancreatic cancer. In order to overcome the limitations of each treatment modalities and to prevent the development of resistance, the application of PDT combined with target therapies, without increasing the toxicity for the patient, is being widely investigated.
  PDT has been only extensively studied for the treatment of various superficial skin cancers in the Europe but not available in the United States and Japan due to the overlapping treatment fields. In Korea, the use of first-generation and second-generation photosensitizers are part of the study of Gastroenterology, Dermatology, Otolaryngology, and Gynecology.
  Recently, although the investigators have introduced PDT using novel photosensitizers has not yet been used for the treatment of pancreatic cancers. This study aim to determine the safety and efficacy of photodynamic therapy with a novel photosensitizer in locally advanced hilar cholangiocarcinoma.

Eligibility: Inclusion Criteria:
  1. Locally advanced cholangiocarcinoma confirmed to be unsuitable for surgical resection
  2. Exhibiting disease progression without distant metastasis after conventional chemoradiation therapy at multidisciplinary team discussion in Asan Medical Center
  3. Pathologically proven cholangiocarcinoma
  4. have a negative pregnancy test if appropriate
  5. ECOG(Eastern Cooperative Oncology Group) Score 0-2
  6. patients to give informed consent and age more than >19 years
  Exclusion Criteria:
  1. age less than 18 years
  2. previous history of PDT
  3. uncorrectable coagulopathy
  4. refuse to participate
  5. pregnancy
  6. recent participation in another clinical research trial within 30 days
  7. presence of porphyria or hypersensitivity to photosensitizer
  8. Creatinine clearance < 45ml

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

Clinical trial: Analysis of Oncogenes in Intrahepatic Cholangiocarcinoma or Mixed Hepatocellular-Cholangiocarcinoma in Tumor Tissue Samples

Summary: The primary objective of this study is to estimate the frequency of FGFR2 fusions in archived intrahepatic cholangiocarcinoma (iCCA) or mixed hepatocellular-cholangiocarcinoma (HCC-CCA) tumor samples

Detailed description: This is a non-interventional, observational study of archived human tissue samples; no surgical procedures will be required and no treatment will be provided as part of this study. Approximately 150 archived tissue samples obtained from patients with iCCA or mixed HCC-CCA will be analyzed for somatic alteration status and will include cholangiocarcinoma-specific FGFR2 fusion isoforms.

Eligibility: Inclusion Criteria:
  -  If required by law or local regulations (i.e., the sample is from an identifiable subject), signed written informed consent should be granted prior to use of the sample in the study
  -  ≥ 18 years of age
  -  Histologically or cytologically confirmed iCCA or mixed HCC-CCA, who are/were eligible for systemic therapy (samples collected prior to initiation of the systemic therapy may be submitted for testing)
  -  Have one or more formalin fixed and paraffin embedded blocks available. If blocks are not evaluable, 7-10 unstained, non-baked slides with 5-micron thick sections with at least 20% tumor tissue should be available. (Potential participants who are scheduled to undergo surgical treatment may agree to provide surplus of tissues not required for diagnosis and have to provide informed consent prior to the surgery.)
  Exclusion Criteria:
  -  Not applicable: Patients must meet all of the inclusion criteria.

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

Clinical trial: Utilizing a Multi-gene Testing Approach to Identify Hereditary Pancreatic Cancer

Summary: The primary objective of the study will be to estimate the prevalence of germline mutations in patients who present consecutively within 12 weeks of a confirmed diagnosis of pancreatic ductal adenocarcinoma.

Detailed description: The proposed research is a multi-site prospective and observational plan to investigate the prevalence of germline mutations in patients diagnosed with pancreatic cancer. Thirty two genes will be analyzed, all of which have been associated with an increased risk for cancer. The genes are included on CancerNextTM a multi-gene next generation sequencing and array CGH test. The 32 genes include: APC, ATM, BARD1, BRCA1, BRCA2, BRIP1, BMPR1A, CDH1, CDK4, CDKN2A, CHEK2, EPCAM, GREM1, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, POLD1, POLE, PTEN, RAD50, RAD51C, RAD51D, SMAD4, SMARCA4, STK11, and TP53 .

Eligibility: Inclusion Criteria:
  -  Male and female patients between the ages of 18 and 89 years of age.
  -  Diagnosed within the previous 12 weeks with histologically or cytologically confirmed PDAC Stage I to IV.
  -  Ability of participant to understand and the willingness to sign a written informed consent document.
  -  Participant must agree to sample collection and genetic testing using the 32 gene test, CancerNextTM and allow the test result to be part of their medical record.
  Exclusion Criteria:
  -  Diagnosed with intraductal papillary mucinous neoplasms, mucinous cystic neoplasms, pancreatic neuroendocrine tumors or dysplasia without PDAC.
  -  Diagnosed with PDAC more than 12 weeks before presenting to the clinical site.
  -  Patients meeting the above enrollment criteria who have had CancerNext performed previously.

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

Clinical trial: Rural Interventions for Screening Effectiveness

Summary: This randomized clinical trial studies how well a tailored interactive digital versatile disc (DVD) with or without patient navigation works in improving screening rates in rural women for breast cancer, cervical cancer or colorectal cancer. A tailored interactive DVD and patient navigation may help rural women to learn more about cancer screening and to better understand the results.

Detailed description: PRIMARY OBJECTIVES:
  I. Compare the effectiveness of a tailored and interactive DVD (TIDVD) versus (vs.) TIDVD + telephone-based patient navigation (PN) intervention (TIDVD + PN) vs. usual care (UC), to increase guideline-based cancer screening rates at 12 months post randomization for breast cancer (BC), cervical cancer (CC), and colorectal cancer (CRC) among 1058 women age 50 to 74 living in rural northwest Ohio and northeast Indiana.
  II. Compare the cost effectiveness of the TIDVD and the TIDVD + PN intervention vs. UC, for adherence to each screening outcome or combination of screening tests.
  OUTLINE: Patients are randomized to 1 of 3 arms.
  ARM I: Patients watch a tailored interactive DVD program and answer questions posed by the DVD program.
  ARM II: Patients engage in TIDVD and PN.
  ARM III: Patients receive brochures that explain and provide encouragement for cancer screening.
  After completion of the study, patients are followed up at 2 and 12 months.

Eligibility: Inclusion Criteria:
  -  Be non-adherent to one or more recommended screenings for BC, CC, or CRC by Medical Record Review (MRR)
  -  Reside in one of 32 rural counties in Indiana (IN) or Ohio (OH)
  -  Provide informed consent
  -  Able to speak/read English
  -  Have access to a DVD player or computer that can play DVDs
  Exclusion Criteria:
  -  Have a personal or family history of any hereditary/genetic cancer syndrome such as BRCA1 and BRCA2 polymorphisms, hereditary nonpolyposis colon cancer, or familial adenomatous polyposis
  -  Have a personal history of inflammatory bowel disease (Crohn's disease or colitis), colon polyps, or a history of cancer except non-melanoma skin cancer
  -  Have a first degree relative with a history of breast or colorectal cancer
  -  Plan to move outside of the country within the next year
  -  Reside in a nursing home or other institution
  -  Are pregnant or intend to become pregnant during the study period

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

Clinical trial: Clinical Trial of Adjuvant Chemotherapy Followed by Concurrent Chemoradiotherapy Compared With Adjuvant Chemotherapy Alone in Patients With Gallbladder Carcinoma and Extrahepatic Cholangiocarcinoma

Summary: The present study is designed to determine whether adjuvant concurrent chemoradiotherapy improves overall survivals.

Detailed description: The role of adjuvant radiotherapy in gallbladder carcinoma (GBCA) or extrahepatic cholangiocarcinoma (EHCC) is unknown. A retrospective study suggested that chemoradiotherapy provides greater benefit than chemotherapy alone in GBCA patients. SWOG S0809, a phase II study showed that adjuvant chemoradiotherapy has promising efficacy in GBCA or EHCC. The present phase III clinical trial is designed to compare adjuvant concurrent chemoradiotherapy with chemotherapy alone.

Eligibility: Inclusion Criteria:
  -  The patients with pathologic diagnosis of gallbladder carcinoma (GBCA) or extrahepatic cholangiocarcinoma (EHCC) after radical resection.
  -  The patients with pathologic stage T2-4 or N1 in R0 resection or positive resection margins (R1).
  -  Aged 18 to 70 years old, male or female, body condition score generally ECOG 0～2, expected survival ≥ 6 months.
  -  Subjects were no major organ dysfunction, blood, liver, kidney and heart function was normal, the specific requirements of laboratory indicators:
  -  Blood: Absolute neutrophil count > 1.5 × 109 / L, Platelet count > 100 × 109 / L, Hb > 8.0g/dl.
  -  Liver function: serum bilirubin less than 1.5 times the upper limit of normal; ALT and AST less than 2.5 times the upper limit of normal.
  -  Renal function: creatinine less than 1.5 times the upper limit of normal.
  -  Patients who can understand the circumstances of this study and signed informed consent.
  Exclusion Criteria:
  -  Pregnancy, breast-feeding patients；
  -  Patients received prior anticancer therapy for the current malignancy or upper abdominal radiotherapy or chemotherapy at any time.
  -  Patients with malignant ascites.
  -  Patients with purulent and chronic infected wounds which delayed healing.
  -  Patients with liver, kidney and heart failure and coronary heart disease, angina, myocardial infarction, arrhythmia, cerebral thrombosis, stroke and other serious cardiovascular and cerebrovascular disease;
  -  Patients has a history of mental illness and difficult to control;
  -  Patients who was considered inappropriate to participate in the trials by the researchers.

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

Clinical trial: Genotyping 2 SNPs in Chinese Breast Cancers

Summary: The purpose of this study is to determine the frequency of two Single Nucleotide Polymorphisms (SNPs) by sanger-sequencing in Breast Cancers and healthy controls .

Detailed description: Since the 1990s breast cancers incidence of china has increased more than twice as fast as global rates. Chinese patients are responsible for 12.2% of all newly diagnosed breast cancers and 9.6% of all deaths to world breast cancers. Breast cancer is now the second frequently diagnosed cancer and is the leading cause of cancer-related death in Chinese women.
  Two of the most prevalent breast cancer susceptibility genes are BRCA1and BRCA2. However，because of population based Genetic heterogeneity, the frequency of BRCA1/BRCA2 mutation is not as high in Caucasian population as in China. Anyway, the mean age at diagnosis of breast cancer in China is almost 10 years younger and more cases are diagnosed before 40 than those in Caucasians. Therefore, it is believed that there are certain specific susceptibility loci in Chinese breast cancers.
  In preliminary experiments, investigators found two germline mutations may associate with Chinese breast cancers.
  The purpose of the study is to determine the frequency of two germline mutations by sanger-sequencing in a larger sample of Chinese breast cancers

Eligibility: Inclusion Criteria:
  -  Woman aged superior to 18 years old Inform consent signed Woman without breast cancer and family history of cancer
  Exclusion Criteria:
  -  No inform consent signed Patient under guardianship, curatorship Psychosocial disorder

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

Clinical trial: Efficacy and Safety of INCB054828 in Subjects With Advanced/Metastatic or Surgically Unresectable Cholangiocarcinoma Who Failed Previous Therapy

Summary: The purpose of this study is evaluate the efficacy of INCB054828 in subjects with advanced/metastatic or surgically unresectable cholangiocarcinoma with FGFR2 translocation who have failed at least 1 previous treatment.


Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed cholangiocarcinoma.
  -  Radiographically measurable or evaluable disease per RECIST v1.1.
  -  Tumor assessment for FGF/FGFR gene alteration status completed through the central laboratory.
  -  Documented disease progression after at least 1 line of prior systemic therapy.
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 to 2.
  -  Life expectancy ≥ 12 weeks.
  Exclusion Criteria:
  -  Prior receipt of a selective FGFR inhibitor.
  -  History of and/or current evidence of ectopic mineralization/calcification, including but not limited to soft tissue, kidneys, intestine, myocardia, or lung, excepting calcified lymph nodes and asymptomatic arterial or cartilage/tendon calcifications.
  -  Current evidence of corneal disorder/keratopathy, including but not limited to bullous/band keratopathy, corneal abrasion, inflammation/ulceration, keratoconjunctivitis, etc, confirmed by ophthalmologic examination.
  -  Use of any potent CYP3A4 inhibitors or inducers within 14 days or 5 half-lives, whichever is shorter, before the first dose of study drug. Topical ketoconazole will be allowed.

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

Clinical trial: Inherited Susceptible Genes Among Epithelial Ovarian Cancer

Summary: Purpose: To investigate the prevalence of the germline mutations in the BRCA 1/2 and mismatch repair genes in patients with epithelial ovarian cancer (EOC) and their relatives, and related somatic mutations in tumor tissues in the northern part of china.
  Patients and methods: A multicenter prospective study will be hold in the northern part of china form 2017. About 1000 female patients with epithelial ovarian cancer and their ralatives will be tested for germline mutations in the BRCA 1/2 and mismatch repair genes and related somatic mutations in tumor tissues, regardless of the family history.
  Study type: Observational Official title: Prevalence study of germline mutations in susceptibility ovarian cancer genes in patients with epithelial ovarian cancer and somatic mutations in their tumor tissures in the northern part of china.
  Enrollment: 1000


Eligibility: Inclusion Criteria:
  1. epithelial ovarian cancer and their relatves
  2. living in the north of Huaihe River in China
  3. being Han Chinese
  Exclusion Criteria:
  1. non-epithelial ovarian cancer
  2. without specific pathological diagnosis
  3. non-Han Chinese

Relevance to patient case: not relevant