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

Clinical trial: CAP7.1 for the Treatment of Advanced Stage, Therapy Refractory Lung and Biliary Tract Tumors

Summary: To assess the anti-tumor activity of CAP7.1 based on the observed objective response rate and rate of disease stabilization, as defined by the below primary and secondary endpoints, in patients with NSCLC, SCLC or biliary cancer who have progressed despite one or more previous chemotherapy line.

Detailed description: A phase II evaluation will be performed in adult patients in parallel studies in 3 tumor types: NSCLC, SCLC and Biliary Tract Cancer. All patients will have advanced or metastatic disease with primary or secondary resistance to standard therapy. In each tumor type the patients will be randomized to receive either therapy with CAP7.1 or best supportive care according to institution standards. Patient in the Control group who progress may cross over to CAP7.1, however these patients will be analyzed separately from the patients randomized to CAP7.1.

Eligibility: Inclusion Criteria:
  -  Histologically- or cytologically-confirmed, advanced disease with documented progression (RECIST1.1.) after one or several chemotherapy line
  -  Patients may also have received molecular targeted therapy and progressed while on therapy or after completion
  -  Must have recovered from the acute reversible effects of previous anti-cancer chemotherapy, usually 3-4 weeks after myelosuppressive chemotherapy
  Exclusion Criteria:
  -  Serious concurrent medical condition, which could affect compliance with the protocol or interpretation of results.
  -  Patients with uncontrolled infection and patients known to be infected with the human immunodeficiency virus (HIV) or hepatitis infection are not eligible for the study
  -  Pregnancy or breast-feeding

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

Clinical trial: Erlotinib Combined With Chemotherapy in TKI Resistant Non-Small Cell Lung Cancers

Summary: Numerous evidences verified that erlotinib could dramatically improve the PFS and OS of non-small cell lung cancers who harbor EGFR sensitive mutations, however, primary or secondary resistance will be developed after TKI treatment, doctors do plenty of researches to overcome TKI resistance. FAST ACT-2 study present that, first line erlotinib combined with chemotherapy could improved mOS to more than 30 months in NSCLCs who harbor EGFR sensitive mutations, several study shows that sensitive mutations still exist after TKI resistance, because of the next generation TKIs(such as BIBW2992) are not avaliable at present, agents for met amplification(such as Crizotinib) are so expensive that many Chinese patients could not support. Thus, the investigators hypothesis that, after first line TKI treatment, the patients who developed TKI resistance could still benefit from second line TKI combined with chemotherapy.

Detailed description: The investigators will enroll patients diagnosed with advanced non-squamous,non-small cell lung cancer, patients with EGFR TKI sensitive mutations and developed TKI resistance in first line treatment. After enrollment, the investigators will do biopsy again before second line treatment to find out the potential mechanism of TKI resistance, do EGFR mutation test for both sensitive and resistant mutation in exon 18, 19, 20 and 21; do KRAS, BRAF and PI3K mutation test, do FISH for MET and HER-2, the investigators do all these test to evaluated both primary and secondary resistance, the investigators do all these tests to get an overview for EGFR mutation status of each patient who develop TKI resistance. For second line treatment, patients will received a 28 days gemcitabine platinum combined with erlotinib scheme, after 4 cycle of combined chemotherapy, patients will receive erlotinib for further treatment until progression disease. For the patients who have stable brain metastases, combined chemotherapy should begin after local treatment, such as whole brain radiotherapy or sterotactic radiosurgery.
  the main endpoint of this study is mean PFS, second endpoints of this study consist of mean OS, 8 week ORR.

Eligibility: Inclusion Criteria:
  -  advanced non-small cell lung cancer, stage IIIB/IV
  -  non-squamous
  -  EGFR sensitive mutations, such as exon 19 del, or exon 21 L858R
  -  received first line TKIs treatment and developed TKI resistance
  -  ECOG 0-2
  Exclusion Criteria:
  -  squamous non-small cell lung cancer
  -  patients have unstable brain metastasis, predict survival less than 8 weeks
  -  spinal-cord compression without evidence of stabilisation or treatment
  -  women who were pregnant or lactating; women with a positive or no available pregnancy test result at baseline
  -  patients have any unstable illness that could not receive further treatment

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

Clinical trial: EUS-guided Biliary Drainage Versus Percutanenous Transhepatic Biliary Darinage for Malignant Biliary Obstruction After Failed ERCP

Summary: Although ERCP is almost always successful in patients with malignant biliary obstruction, selective biliary cannulation fails in some cases and conventional ERCP may not be possible in patients with tumor invasion of the duodenum or major papilla, surgically altered anatomy (e.g., Roux-en-Y anastomosis), or complex hilar biliary strictures. In such cases, percutaneous transhepatic biliary drainage (PTBD) is an useful alternative. However, PTBD had various complications and the presence of an external drainage catheter would also have a cosmetic problem related to the external drainage and an adverse impact on quality of life (QOL) of terminally ill patients.
  Since endoscopic ultrasound-guided bile duct puncture was described in 1996, sporadic case reports of EUS-guided biliary drainage (EUS-BD) suggested that it was a feasible and effective alternative in patients with failed conventional ERCP stenting. The potential benefits of EUS-BD include one-stage procedure in ERCP unit, and internal drainage for avoiding long-term external drainage in cases where external PTBD drainage catheters cannot be internalized, thus significantly improving the QOL of terminally ill patients, and possibly lower morbidity than PTBD or surgery.
  Up to date, only a few case series of EUS-BD with small numbers of patients have been published, and known the feasibility and safety in terms of the incidence of procedure-related clinical outcomes.10-21 There has been no comparative study between the outcomes of PTBD and EUS-BD focusing on the QOL, cost-effectiveness, and complications.
  The researchers investigated the technical success of EUS-BD and PTBD in patients with malignant biliary obstruction after failed conventional ERCP as a prospective randomized comparative study in multicenters. Secondary endpoints were the cost-effectiveness and complications rates between EUS-BD and PTBD.


Eligibility: Inclusion Criteria:
  -  Presence of unresectable malignant distal biliary obstruction (greater 2cm than distal to hilum, i.e., pancreatic cancer, common bile duct cancer, ampulla of Vater cancer, gallbladder cancer, duodenal cancer, and metastatic biliary obstruction)
  -  Failed conventional ERCP and inaccessible papilla because of accompanying duodenal obstruction, periampullary tumor infiltration, ampulla stenosis, or surgically altered anatomy (Billroth II operation, Roux-an-Y operation.)
  -  Histologic or cytologic diagnosis of malignancy, d) A Karnofsky index of ≧30%, e) No serious or uncontrolled medical illness
  -  Provided informed consent.
  Exclusion Criteria:
  -  patient age of less than 18 years
  -  uncorrectable coagulopathy
  -  history of allergy to radiocontrast agents
  -  refusal to participate in this study.

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

Clinical trial: Results of Bile and Blood Culture in Patients With Acute Cholangitis

Summary: Cholangitis is a complication of biliary statsis. Bile juice is sterile when there is no obstruction, however, it can be infected with bacteria when there is a stasis or obstruction. After infection, cholangitis can be developed because of systematic endotoxemia or bacteremia. Though identification of bacteria is very important for selection of adequate antibiotics, treatment with empirical antibiotics is commonly performed when identification of bacteria is not possible.
  Identification of bacteria is usually done with blood or bile culture. In the previous studies, the same results from blood and bile were common in patients with cholangitis. However, the data of these studies were based on the bile juice which was aspirated by surgery. Considering that bile duct obstruction is usually treated with endoscopy or radiological intervention without surgery, it is necessary to collect data with endoscopic or radiologic intervention. In addition, the concordant rate of these two tests has not been reported according to severity of cholangitis. As a result, the necessities of bile and blood culture are not agreed among experts in this fields.
  Our hypothesis is that concordant rates of bile and blood culture are same in patients with each moderate or severe cholangitis. However, the concordant rates of bile and blood culture are different between patients with moderate and severe cholangitis. This study will assess the positive rates of blood and bile culture in patients with moderate or severe cholangitis, respectively and compare the results according to the different severity.


Eligibility: Inclusion Criteria:
  -  Patients with moderate or severe cholangitis which fullfilled the criteria by the Tokyo Guidelines (Tanaka A, Takada T, Kawarada Y, et al. Antimicrobial therapy for acute cholangitis: Tokyo Guidelines. J Hepatobiliary Pancreat Surg 2007;14:59-67.)
  -  Patients who are successfully treated with endoscopic or radiologic biliary drainage
  -  Patients who undergo both blood and bile culture tests
  Exclusion Criteria:
  -  Patients with other infections except cholangitis or cholecystitis
  -  Patients who received surgical biliary drainage treatment
  -  Patients who are treated with endoscopic or radiologic biliary drainage more than 24 hours after using initial antibiotics
  -  Patients who does not agree with informed consent or who are vulnerable subjects

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

Clinical trial: Ovarian Clear Cell Adenocarcinoma Review

Summary: Clear cell carcinoma comprises 5-10% of surface epithelial ovarian cancers, and about 30-40% of the patients with clear cell carcinoma are diagnosed in the advanced stage. The investigators studied the response to chemotherapy and survival for either paclitaxel-platinum based chemotherapy or conventional platinum-based chemotherapy among all stages clear cell ovarian carcinoma. Prognostic factors for survival among the patients with pure, advanced, clear cell ovarian carcinoma were also evaluated.

Detailed description: 1. Several authors have reported frequent admixtures of clear cell ovarian carcinoma with serous, mucinous, and endometrioid tumors. However, few papers addressed the difference in response to chemotherapy and survival between patients with pure and mixed-type advanced clear cell carcinoma.
  2. Recent trends in the clinical management of advanced ovarian cancer include increased attention to maximal cytoreduction and general acceptance of paclitaxel-platinum-based adjuvant chemotherapy.
  3. The introduction of paclitaxel markedly changed the postoperative management of ovarian cancer patients, but the results and value of these newer efforts and therapies applied to clear cell carcinoma are as yet undetermined.
  4. Today, paclitaxel-platinum-based chemotherapy is becoming the standard regimen for ovarian cancer worldwide. Previous research suggests a potential benefit of paclitaxel plus carboplatin regimens for stage I clear cell carcinoma. However, few papers specifically addressed the efficacy of paclitaxel-platinum-based chemotherapy for advanced clear cell carcinoma because clear cell carcinoma occurs only rarely in Western countries.

Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of Ovarian clear cell carcinoma
  Exclusion Criteria:
  -  not undergo operation

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 Different Dosing Schedules of Selumetinib With Cisplatin/Gemcitabine (CIS/GEM) Versus CIS/GEM Alone in Biliary Cancer

Summary: This is a phase II study (the second stage of testing a new drug or new drug combinations) to see how useful two different schedules of study drug selumetinib with cisplatin and gemcitabine are compared to cisplatin and gemticabine alone in patients with biliary cancer.
  Selumetinib, an oral drug which plays an important role in the regulation of cell growth (MEK 1/2 inhibitor) has been shown to shrink tumours in patients with biliary cancer and other types of human cancers. Selumetinib has also been shown to shrink tumours when given in combination with cisplatin and gemcitabine in research studies done in animals and in some patients with biliary tract cancer. Cisplatin and gemcitabine are intravenous drugs that work by damaging DNA in tumor cells so that they are unable to grow and divide.


Eligibility: Inclusion Criteria:
  -  Unresectable, recurrent or metastatic, measurable biliary tract cancer or gall bladder cancer
  -  No prior systemic therapy
  -  Performance status 0, 1, or 2
  -  Age 18 years or older
  -  Estimated life expectancy > 3 months
  -  Adequate hematological, liver, renal function
  -  No evidence of active uncontrolled infection
  -  Capable of giving written consent
  -  Acceptable recovery of previous side effects
  Exclusion Criteria:
  -  Progressing within 3 or 6 months of receiving certain treatments
  -  Prior chemotherapy for non-resectable or metastatic disease or a MEK inhibitor
  -  Progressing within 6 months of adjuvant treatment.
  -  May not have received prior chemotherapy for non-resectable/metastatic disease.
  -  Prior MEK, RAS, or RAF inhibitors or history of hypersensitivity to study drugs.
  -  Ampullary carcinoma
  -  Incomplete recovery from previous surgery
  -  Undergoing treatment with curative intent
  -  Prior malignancy that could interfere with the response evaluation
  -  Severe or uncontrolled systemic diseases or lab finding that makes it undesirable for patient to participate
  -  Any psychiatric or other disorder likely to impact consent
  -  Pregnant or breastfeeding
  -  Patients with significant cardiac-related issues
  -  History of eye-related issues.
  -  Systemic disease, active infection, bleeding diatheses or renal transplant, including hep B, hep C or HIV
  -  Receiving potent inhibitors or inducers of CYP3A4/5, CYP2C19 and CYP1A2 can continue with caution

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 Abemaciclib (LY2835219) in Participants With Previously Treated KRAS Mutated Lung Cancer

Summary: The main purpose of this study is to evaluate how safe and effective the study drug known as abemaciclib is in participants with lung cancer.


Eligibility: Inclusion Criteria:
  -  Have confirmed diagnosis of stage IV non-small cell lung cancer (NSCLC) according to the American Joint Committee on Cancer Staging Handbook.
  -  Determined to have detectable mutations in codons 12 or 13 of the kirsten rat sarcoma (KRAS) oncogene by an investigational assay at the study JPBK central laboratory. A KRAS positive mutation result in codons 12 or 13 of the KRAS oncogene from tumor tissue per local laboratory will be permitted in no more than 10% of randomized participants.
  -  Have progressed after platinum-based chemotherapy (with or without maintenance therapy) AND have received one additional therapy which may include an immune checkpoint inhibitor or other anti-cancer therapy for advanced and/or metastatic disease OR is judged by the physician as ineligible for further standard second-line chemotherapy. Participants who have progressed after platinum-based chemotherapy and an immune checkpoint inhibitor (immunotherapy) e.g. pembrolizumab or nivolumab alone or in combination with other agents are eligible.
  -  Have measureable disease as defined by the Response Evaluation Criteria in Solid Tumors (RECIST 1.1).
  -  Have a performance status (PS) of 0 to 1 on the Eastern Cooperative Oncology Group (ECOG) scale.
  -  Have discontinued all previous therapies for cancer (including chemotherapy, radiotherapy, immunotherapy, and investigational therapy) for at least 21 days for myelosuppressive agents or 14 days for nonmyelosuppressive agents prior to receiving study drug.
  Exclusion Criteria:
  -  Have received treatment with a drug that has not received regulatory approval for any indication within 14 or 21 days of the initial dose of study drug for a nonmyelosuppressive or myelosuppressive agent, respectively.
  -  Have a personal history of any of the following conditions: presyncope or syncope of either unexplained or cardiovascular etiology, ventricular arrhythmia (including but not limited to ventricular tachycardia and ventricular fibrillation), or sudden cardiac arrest.
  -  Have the presence of unstable central nervous system (CNS) metastasis. History of CNS metastasis or stable CNS metastases is allowed (no longer requiring active therapy such as steroid medications). Participants with a history of CNS metastases must have a brain scan (for example, magnetic resonance imaging [MRI]) within 28 days of randomization to document stability, even if there have been no changes in symptoms.

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

Clinical trial: Comparison on the Efficacy of Endoscopic Snare Papillectomy With or Without Submucosal Injection

Summary: Because the ampulla of Vater is strategically located at the confluence of the pancreatic and common bile ducts, endoscopic resection of papillary neoplasms may be technically different from endoscopic mucosal resection in other parts of the gastrointestinal tract. The best method of endoscopic ablation and the optimal period for surveillance have not been established.

Detailed description: While some endoscopists advocate the use of submucosal injection of either physiologic saline solution or dilute epinephrine, some do not. Whether physiologic saline solution or dilute epinephrine should be used is also not established. Submucosal injection of either dilute epinephrine or saline solution may be useful for avoiding inappropriate resection because failure to lift the tumor from the proper muscle layer of the duodenum may indicate deeper invasion18 and is the strongest predictor of malignancy.
  In adenomas of the major duodenal papilla, however, some investigators do not recommend submucosal injection. Not only the surrounding mucosa at the region of the duodenal papilla but also the tumor is lifted by submucosal injection, so capturing the lesion with a snare becomes difficult.

Eligibility: Inclusion Criteria:
  -  ampulla of Vater adenoma
  -  no uncontrolled coagulopathy
  Exclusion Criteria:
  -  adenocarcinoma of ampulla of Vater
  -  uncontrolled coagulopathy
  -  refusal to this study

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

Clinical trial: The Oncopanel Pilot (TOP) Study

Summary: The BCCA Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes.
  The purpose of this pilot study is to assess the feasibility and effect on clinical-decision-making of the Oncopanel test. Eligible patients are those with advanced lung, colorectal, melanoma and GIST cancers and patients with diagnosed malignancies being considered for clinical trials.

Detailed description: Somatic mutations in solid tumors represent an established means of characterizing malignancies for prognostic, diagnostic and therapeutic purposes. Mutations in EGFR, KRAS, BRAF, and KIT and PDGFRA genes direct therapy in patients with advanced lung, colorectal, melanoma, and GIST tumors, respectively. Known or novel mutations in other genes may also be of clinical significance but are not identified by current genotyping offered to BC Cancer Agency (BCCA) patients. Furthermore, numerous candidate genes have been implicated as potential prognostic and predictive biomarkers in patients with solid tumours. As such, the Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes. The following clinically relevant set of genes and exons are included in the Oncpanel: KRAS, EGFR, BRAF, NRAS and HRAS, PIK3CA Signal Transduction Pathway Genes, RAS-RAF-MEK-MAPK Pathway, HER2, IDH1 and IDH2, ALK, TP53, c-KIT, STAT1&3 and PDGFRA. Additional testing on the tumour material will also include analysis of specific gene variants associated with adverse events or response to therapy.
  Numerous studies have documented the presence of circulating tumour DNA (ctDNA) among patients with advanced and early stage malignancies (20-22). The ability to diagnose standard cancer mutations with a blood-based assay (a "liquid biopsy") has not yet been established but presents obvious advantages. The emergence of "resistance" mutations arising in the metastatic tumor or throughout the course of therapy is well documented (21, 22). A blood biopsy may represent more accurate determination of the tumor's genetic features than archival DNA specimen. Adequate tissue specimens can be difficult to obtain from some patients with diagnosed malignancies, particularly lung cancer. A blood biopsy may represent a less invasive and timelier means of diagnosing both standard and translational cancer mutations.

Eligibility: Patients with archival tumor tissue and a known history of invasive malignancies are eligible if they meet one or more of the following criteria:
  -  Advanced colorectal cancer and eligible for standard KRAS testing,
  -  Advanced non-small cell lung cancer and eligible for standard EGFR testing,
  -  Advanced melanoma and eligible for standard BRAF testing,
  -  Gastrointestinal stromal tumors (GISTs) eligible for standard c-KIT and PDGFRA testing,
  -  Being considered for potential eligibility in clinical trial.

Relevance to patient case: not relevant