araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: Microarray Analysis of microRNA Expression Profiles in Cutaneous Squamous Cell Carcinoma

Summary: MicroRNAs (miRNAs) are a novel class of short RNAs which have shown to be dysregulated in a variety of cancers. Data of miRNA expression in cutaneous squamous cell carcinoma (cSCC) is very limited and microarray based genome wide miRNA expression profiles of cSCC have not been investigated so far.

Detailed description: Patients with cutaneous SCC were enrolled in the present study. Tumor biopsies were taken from the center of the tumor. Adjacent healthy skin was biopsied as a control (intraindividual control). miRNA expression profiles of specimen were detected by microarray miRNA expression profiling. Microarray results were confirmed by TaqMan real-time quantitative polymerase chain reaction (RT-PCR).

Eligibility: Inclusion Criteria:
  -  cutaneous squamous cell carcinoma
  Exclusion Criteria:
  -  other skin cancer than cutaneous squamous cell carcinoma

Relevance to patient case: not relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: Managing Cancer and Living Meaningfully (CALM): A Study to Evaluate the Effectiveness of a Psychological Intervention for Cancer Patients

Summary: The purpose of this study is to test the effectiveness of a brief manualized individual psychotherapy, called Managing Cancer and Living Meaningfully (CALM), to reduce distress and promote psychological well-being in patients with various types of cancer, including metastatic disease.

Detailed description: We have developed and pilot-tested a brief manualized individual psychotherapy, called Managing Cancer and Living Meaningfully (CALM), to reduce distress in patients with various types of cancer, including metastatic disease. We propose to conduct a two-arm randomized controlled trial (RCT) to test the effectiveness of CALM against usual care (UC) for the reduction of distress in patients with various types of cancer, including metastatic disease. Usual care at our center includes routine screening for depression and other distress in oncology outpatient clinics, communication of screening information to the medical treatment team, and referral as needed for non-standardized, and primarily instrumental, psychosocial care and psychiatric assessment and treatment.
  The design will be an unblinded RCT consisting of two conditions (CALM and UC), with a baseline assessment and follow-ups at three and six months. The trial will take place in Princess Margaret Cancer Centre, University Health Network, a comprehensive cancer center in Toronto, Canada. Participants will be outpatients with various types of cancer, including metastatic disease.

Eligibility: Inclusion Criteria:
  -  ≥18 years of age
  -  Fluency in English
  -  Confirmed diagnosis of stage III or IV lung cancer; any stage of pancreatic cancer, unresectable cholangiocarcinoma, unresectable liver cancer, unresectable ampullary/peri-ampullary cancer, or other stage IV (metastatic) gastrointestinal cancer; stage III or IV ovarian and fallopian tube cancers, or other stage IV gynecological cancers; and stage IV breast, genitourinary, sarcoma, melanoma or endocrine cancers (all with expected survival of 12-18 months)
  Exclusion Criteria:
  -  Major communication difficulties (including language barriers)
  -  Inability to commit to the required 3-6 psychotherapy sessions
  -  Cognitive impairment indicated in the medical record, or by the attending oncologist, or as indicated by a score < 20 on the Short Orientation-Memory-Concentration test, unless deemed suitable at the recruiter's discretion
  -  Actively seeing a psychiatrist or psychologist in the Department of Supportive Care (formerly the Department of Psychosocial Oncology and Palliative Care) at Princess Margaret Cancer Centre at the time of study approach

Relevance to patient case: not relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: Nexavar as First Targeted Therapy in Patients With Advanced Renal Cell Carcinoma

Summary: This is an observational study which will investigate the use of Nexavar as first targeted therapy in patients with advanced renal cell carcinoma.


Eligibility: Inclusion Criteria:
  -  Patients with a diagnosis of advanced Renal cell carcinoma (RCC) for whom the decision has been taken by the investigator to prescribe Nexavar.
  -  Patients who failed cytokine therapy or who are not suitable for cytokines for whom Nexavar is the first targeted drug treatment.
  Exclusion Criteria:
  -  Prior targeted therapy for RCC
  -  Contraindications of Nexavar described in the Summary of Product Characteristics (SPC).

Relevance to patient case: not relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: Study of Cetuximab to Treat KRAS Wild Type Metastatic Colorectal Cancer

Summary: The primary purpose of this study is to evaluate the clinical response and safety of cetuximab plus irinotecan synchronously/subsequently in patients with KRAS wild-type metastatic colorectal cancer

Detailed description: CMAB009 is a recombinant, human/mouse chimeric monoclonal antibody (mAb) that binds specifically to the extracellular domain of EGFR. It is composed of the Fv regions of a murine anti-EGFR antibody with human IgG1 heavy and k light chain constant regions and it is expressed by Chinese hamster ovary cells. It is a biosimilar of cetuximab (C225, Erbitux®) and it is developed by Shanghai Zhangjiang Biotechnology Limited Company and produced by Biomabs. Phase I study results suggest that CMAB009 showed well-tolerated safety profile and primary efficacy. This multicenter, open-label study was to determine whether adding cetuximab (CMAB009) to irinotecan increased the response rate and prolongs survival in patients with KRAS wild-type metastatic colorectal cancer (mCRC) previously treated with fluoropyrimidine and oxaliplatin.

Eligibility: Inclusion Criteria:
  -  histologically confirmed metastatic colorectal adenocarcinoma
  -  KRAS wild-type tumors, EGFR-expressing or EGFR-nonexpressing by immunohistochemistry;
  -  has measurable lesion, at least 1cm in diametre by CT or MRI, at least 2cm diametre by physical examination or other iconography
  -  ECOG performance status 0 to 1
  -  Failure (disease progression/discontinuation due to toxicity) of fluoropyrimidine and oxaliplatin treatment,stop at least one month thereafter, irinotecan-naïve
  Exclusion Criteria:
  -  Previous irinotecan or anti-EGFR therapies
  -  hematologic function: hemoglobin, less than 90g per liter; neutrophil count, less than 1500 per cubic millimeter; and platelet count, less than 100,000 per cubic millimeter
  -  liver function: bilirubin, more than 1.0 times the upper limit of normal; aspartate aminotransferase and alanine aminotransferase, more than 5.0 times and 2.5 times the upper limit of normal with hepatic metastasis or not
  -  Renal function: serum creatinine, more than 1.5 times the upper limit of normal
  -  Patients with symptomatic central nervous system metastases

Relevance to patient case: not relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: Endoscopic Characteristics of Duodenal and Ampullary Lesions

Summary: The purpose is to investigate whether polyps that look different at endoscopy, have formed via different mutations and have different risks of turning into cancer.

Detailed description: Laterally spreading tumours (LSTs), are polyps that have a lateral extension along the duodenal wall with minimal vertical growth. It has become evident over the last few years that rather than being a single entity requiring an accumulation of mutations, Duodenal and ampullary cancer is in fact a heterogenous disease forming via multiple distinct genetic pathways. It is therefore hypothesised that different polyp types have different genetic abnormalities, and potentially form via distinct genetic pathways, although this theory has not been widely examined.
  This knowledge would be important in furthering our understanding of the development of cancer. There is accumulating evidence that genetic abnormalities may be a better predictor of cancer behaviour than histological grade. Additionally, guidelines for endoscopy surveillance are currently a one size fits all approach that do not reflect the genetic heterogeneity of the disease and the knowledge that only 5% of polyps progress to cancer. Genetic studies may assess future cancer risk to a person in polyps once removed and plan surveillance endoscopy frequency.

Eligibility: Inclusion Criteria:
  -  Intention to perform Endoscopic Mucosal Resection
  -  Adenoma equal to or greater than 20mm
  -  over 18 years of age
  -  Able to give informed consent to involvement in trial
  Exclusion Criteria:
  -  Pregnancy
  -  Lactation: currently breastfeeding
  -  Taken clopidogrel within 7 days
  -  Taken warfarin within 5 days
  -  Had full therapeutic dose unfractionated heparin within 6 hours
  -  Had full therapeutic dose low molecular weight heparin (LMWH) within 12 hours
  -  Known clotting disorder

Relevance to patient case: not relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: A Study of MEK162 and AMG 479 in Patients With Selected Solid Tumors

Summary: This is a multi-center, open-label, phase Ib/II study. First, the aim of the phase Ib part is to estimate the MTD(s) and/or to identify the recommended phase II dose(s) (RP2D) for the combination of MEK162 and AMG 479 (ganitumab), followed by the phase II part to assess the clinical efficacy and to further assess the safety of the combination in selected patient populations. The dose escalation part of the study will be guided by a Bayesian Logistic Regression Model (BLRM). At least 18 patients are expected to be enrolled in the dose escalation part.
  Following MTD/ RP2D declaration, patients will be enrolled in three phase II arms to assess efficacy of the combination as well as to better understand the safety, tolerability, PK, antibody concentrations and PD of the combination at MTD/RP2D. Phase II arm 1 will consist of approximately 25 patients with KRAS-mutant colorectal adenocarcinoma. Phase II arm 2 will consist of approximately 20 patients with metastatic pancreatic adenocarcinoma. Phase II arm 3 will consist of approximately 28 patients with mutant BRAFV600 melanoma.
  Patients will be treated until progression of disease, unacceptable toxicity develops, or withdrawal of informed consent, whichever occurs first. All patients will be followed up - at minimum patients must complete the safety follow-up assessments 30 days after the last dose of the study treatment.


Eligibility: Inclusion Criteria:
  -  Patients aged ≥ 18 years
  -  Patients with advanced solid tumors (CRC, melanoma) with documented somatic KRAS or BRAFV600 mutations in tumor tissue. Patients with metastatic pancreatic adenocarcinoma may be enrolled irrespectively of KRAS or BRAFV600 mutational status.
  -  Patients must have relapsed or progressed following standard therapy or patients for whom no standard anticancer therapy exists.
  -  Measurable disease as determined by RECIST v1.1. World Health Organization (WHO) Performance Status (PS) ≤ 2.
  -  Adequate organ function
  -  Negative serum pregnancy test
  Exclusion Criteria:
  -  Prior therapy with MEK- or IGF-1R- inhibitor
  -  History or current evidence of central serous retinopathy (CSR), retinal vein occlusion (RVO) or retinal degenerative disease
  -  Patients with known history of severe infusion reactions to monoclonal antibodies
  -  Patients with primary CNS tumor or CNS tumor involvement
  -  History of thromboembolic event requiring full-dose anticoagulation therapy
  -  Clinically significant cardiac disease
  -  History of another malignancy within 2 years
  -  Pregnant or nursing (lactating) women
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: not relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: Pharmacokinetics and Metabolic Activation of Capecitabine

Summary: The objective of this pharmacokinetic study is to exclude a possible influence of CETUX on the plasma disposition and metabolic activation of Capecitabine (CCB) and when this regimen is given combined with Oxaliplatin (OxPt).


Eligibility: Inclusion Criteria selected:
  -  signed written informed consent
  -  male or female > 18 years
  -  K-ras wild type adenocarcinoma of the colon or rectum
  -  metastatic colorectal carcinoma
  -  ECOG <= 2
  Exclusion Criteria selected:
  -  brain metastasis
  -  previous chemotherapy
  -  stage 3 or 4 heart failure
  -  uncontrolled angina
  -  pregnancy or lactation

Relevance to patient case: not relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: Mutation Analysis and Copy Number Changes of KRAS and BRAF Gene in Taiwanese Cases of Biliary Tact Adenocarcinoma

Summary: Cholangiocarcinoma is a fatal malignant neoplasm originating from biliary tracts and constitutes about 5-10% of primary liver cancers, characterized by a poor prognosis. High prevalence in southeast and eastern Asia has been observed. At present, the cellular and molecular mechanisms leading to oncogenesis of cholangiocarcinoma remain unclear.
  The RAS gene product has a key role in controlling cell growth and differentiation through its intrinsic GTPase activity. Point mutations that activate the RAS protein and its downstream cascade have been observed in human tumors. Both KRAS and BRAF are members of the RAS-RAF-MEK-ERK-MAP kinase pathway which mediates cellular response to growth signals. Somatic KRAS mutations are found at high rates in leukemia, colon cancer, pancreatic cancer and lung cancer. Studies from European and Japanese groups have recently described that activating KRAS/ BRAF mutations may play a role in the carcinogenesis of cholangiocarcinoma of the biliary tracts, but our preliminary data demonstrated low frequency of KRAS and BRAF mutation in the same tumor as well as the results from Thailand. In this study, the investigators hypothesize copy number changes rather than genetic mutation of either KRAS or BRAF genes may be the key findings of Taiwanese cases of the adenocarcinoma from the biliary tracts.


Eligibility: Inclusion Criteria:
  -  The patients diagnosed as biliary tact adenocarcinoma.

Relevance to patient case: definitely relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: An Observational Study of Avastin (Bevacizumab) in Patients With Metastatic Colorectal Cancer in Italy (BEWARE)

Summary: This observational, multicenter, retrospective/prospective study will evaluate the use of Avastin (bevacizumab) in clinical practice in patients with metastatic colorectal cancer. Patients having initiated first-line treatment with a fluoropyrimidine-based chemotherapy and Avastin will be followed for up to 15 months.


Eligibility: Inclusion Criteria:
  -  Adult patients, >/= 18 years of age
  -  Metastatic colorectal cancer
  -  Having initiated first-line treatment with fluoropyrimidine-based chemotherapy plus Avastin between 1. September 2011 and 29. February 2012
  -  Availability of test fro K-RAS genotyping
  Exclusion Criteria:
  -  Participation in a clinical trial during treatment with Avastin

Relevance to patient case: not relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: Observational Study on Treatment of Metastatic Colorectal Cancer and the Role of K-Ras

Summary: The purpose of this study is to describe the treatments received and outcomes of patients with metastatic colorectal cancer, what percentage of these patients have K-Ras mutation of the tumor, and to describe the costs of treatments. Information will also be collected regarding risk factors, variables among treatment centers and patients, and explorative analyses will be done to try to identify factors that impact prognosis and factors that predict tolerability and response to treatment.


Eligibility: Inclusion Criteria:
  -  Histologic diagnosis colorectal carcinoma
  -  Metastatic disease
  -  Signed informed consent
  Exclusion Criteria:
  -  Prior treatment of metastatic colorectal cancer
  -  Refusal or incapability of providing informed consent

Relevance to patient case: not relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: Palliative Stereotactic Radiation for Pancreatic or Periampullary Adenocarcinoma

Summary: The investigators are looking to see if a certain dose of stereotactic body radiation therapy (SBRT) may be a viable treatment option for recurrent or residual pancreatic or periampullary adenocarcinoma.

Detailed description: No standard treatment option has yet been established for patients with recurrent or residual disease after definitive treatment of pancreatic or periampullary cancers (duodenal, ampullary, bile duct). Linac based stereotactic body radiation therapy (SBRT) administered in 1-3 fractions has been shown to be an effective treatment option for patients with unresectable, locally advanced pancreatic adenocarcinoma, achieving local control rates of 84-92% at one year. Associated late gastrointestinal toxicity rates have been reported to be 22-25% at 1 year. We hypothesize that similarly excellent local control rates (80-90% at one year) with a reasonable rate of toxicity (≤20%) can be achieved using Linac based SBRT delivered as 5 Gy x 5 for patients with local failure (remaining disease) after previous treatment with conventional chemoradiation therapy (CRT) with or without surgery and as 6.6 Gy x 5 for radiation-naïve patients with local failure (remaining disease) after previous treatment with surgery and/or chemotherapy. The toxicities of note for this trial are grade 2 and greater gastritis, fistula, enteritis, ulcer, or any other grade 3 or greater gastrointestinal toxicity.

Eligibility: Inclusion Criteria:
  -  18 years of age or older
  -  Karnofsky Performance Status greater than or equal to 70%
  -  confirmed pancreatic or periampullary adenocarcinoma
  -  pancreatic or periampullary tumor less than 8.0 cm in greatest axial dimension
  -  Either:
  -  standard of care treatment for pancreatic cancer that included radiation therapy
  * patients may be receiving continued chemotherapy post initial CRT. or
  -  standard of care treatment for pancreatic cancer that did not include radiation therapy * patients must have attempted chemotherapy upon initial diagnosis
  -  acceptable organ and marrow function as determined by blood tests
  -  ability to understand and give consent
  -  must be a patient to be treated with SBRT only at Johns Hopkins Hospital
  -  life expectancy of greater than 3 months
  Exclusion Criteria:
  -  extensive metastatic disease
  -  performance status of less than 70
  -  children are excluded form the study
  -  no uncontrolled intercurrent illness
  -  no concurrent malignancy other than melanoma
  -  pregnant or breast feeding women are excluded
  -  women who are not post-menopausal and have a positive pregnancy test
  -  life expectancy of less than 3 months

Relevance to patient case: not relevant
Patient case: 61-year-old male with Ampullary carcinoma. Genetic variant: KRAS. Other conditions: None.

Clinical trial: Comparison Between Fully Covered Metal Stents and Plastic Stents in Preoperative Biliary Drainage

Summary: This study is a prospective, randomized study to compare of outcome of fully covered metal stents with that of plastic stents for preoperative biliary drainage in distal common bile duct cancer, pancreas head cancer or ampullary cancer with respect to the incidence of stent-related adverse events, the re-intervention rate, the effectiveness of biliary drainage, surgical outcomes and hospital stays.

Detailed description: Pancreaticoduodenectomy is curative option in periampullary tumor. Preoperative endoscopic retrograde cholangiopancreatog-raphy (ERCP) is usually undertaken in patients with resectable disease to relieve biliary obstruction, which is thought to impair immune response, clotting, and other functions that impact intraoperative and postoperative outcomes. Despite conflicting data pertaining to preoperative biliary drainage, ERCP with biliary stenting has become standard practice in patients with periampullary malignancies. In a recent multicenter randomized trial, patients who underwent preoperative biliary drainage had a 74% rate of complications compared with 39% for those who directly underwent surgery without preoperative biliary drainage. In this trial, however, all patients underwent placement of plastic stents. In ERCP, self-expandable metal stent are being increasingly placed for palliation of malignant biliary obstruction. Compared with plastic stents, self-expandable metal stents have large caliber and have demonstrated longer patency duration. Even in patients with resectable malignant disease, self-expandable metal stents which are placed below the level of transection may not impair technical outcomes at surgery and can be safely removed along with the surgical specimen.
  This prospective study is designed to compare the incidence of stent-related adverse events, the re-intervention rate, the effectiveness of biliary drainage, surgical outcomes and hospital stays in patients with periamupllary tumors who are undergone with self-expandable metal stents or plastic stents placement for preoperative biliary drainage

Eligibility: Inclusion Criteria:
  -  Older than 20 years old of age
  -  Obstructive jaundice due to common bile duct cancer and pancreas head cancer, or ampullary cancer
  -  No evidence of distant metastases or locally advanced tumor
  Exclusion Criteria:
  -  Unresectable stage of cancer
  -  Preoperative gastric operation that preclude ERCP (total gastrectomy and subtotal gastrectomy with B-II anastomosis)
  -  Severe gastric outlet obstruction or duodenal obstruction
  -  Severe comorbidity (Karnofsky<50%)

Relevance to patient case: not relevant