araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: Fursultiamine in Esophageal Squamous Cell Carcinoma Patients Who Receive Concurrent Chemoradiotherapy

Summary: Esophageal cancer is a common and fatal malignancy. It is the eighth most common incident cancer and the sixth leading cause of cancer death in the world. In Taiwan, esophageal cancer was newly diagnosed in 2199 patients and was the cause of 1507 deaths in 2011. Squamous cell carcinoma is the predominant histological tumor type, accounting for about 90% of the cases. Esophageal squamous cell carcinoma (ESCC) is an aggressive disease, characterized with extensive local growth and frequent metastases. Concurrent chemoradiotherapy (CCRT) with or without surgery is the treatment option for locally advanced ESCC. Further, target therapy is used in conjunction with CCRT and surgery in ESCC since several years ago. However, the therapeutic outcomes are not satisfactory due to the emergence of chemo-radioresistance. It is imperative to investigate new biomarkers and to find novel treatment targets in ESCC.
  A small population of tumor-initiating cells or cancer stem cells (CSCs) possess some biological functions like normal stem cells, including self-renewal, asymmetric cell division, slowly proliferation rate and drug-resistance. CSCs from many primary tumors and cell lines express specific stem cell markers, including Oct4, Sox2, Nanog, CD133 (promimin-1), Nestin, CD44 ,CD24, ALDH (Aldehyde dehydrogenase) and c-Kit. There are many evidences that CSCs are responsible for tumor initiation, progression and metastasis. CSCs are also believed to have important roles in cancer recurrence due to their resistance to anti-cancer drugs and radiation. CSCs express high levels of ATP-binding cassette (ABC) transporters. ABC transporter can pump cytotoxic drugs out of cells and is one important mechanism of multidrug resistance in CSCs. In addition, CSCs have high reactive oxygen species (ROS) scavenger expression to remove ROS produced from irradiation therapy.
  Fursultiamine (also known as thiamine tetrahydrofurfuryl disulfide, TTFD) is a derivative of vitamin B and currently used for nutrition supplement. The investigators have identified that Fursultiamine suppressed OCT-4, SOX-2, NANOG expression and decreased ABCB1 and ABCG2 in tumor sphere of ESCC cell lines. In this project, the investigators will conduct a prospective phase II study to investigate the effect of Fursultiamine combined with CCRT in ESCC patients. Stem cell markers in clinical specimens collected before and after CCRT will be evaluated.


Eligibility: Inclusion Criteria:
  -  newly diagnosed stage II and III esophageal squamous cell carcinoma
  Exclusion Criteria:
  -  ECOG≧2;
  -  impaired function of lung, liver, kidney or bone marrow

Relevance to patient case: not relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: Single-arm Study to Evaluate the Safety and Efficacy of Sunitinib, in Subjects With RET Fusion Positive or FGFR2 Amplification, Refractory Solid Tumors

Summary: This is a pilot study of sunitinib in patients with RET fusion positive or FGFR2 Amplification Refractory solid tumors.
  This study is a single-arm, pilot study of sunitinib in subjects with Refractory solid tumors harboring RET fusion positive or FGFR2 Amplification sunitinib 50mg will be administered orally once a day 42 days.Study treatment will be continued until objective disease progression.
  To investigate the efficacy of sunitinib in subjects with Refractory solid tumors harboring RET fusion positive or FGFR2 Amplification.


Eligibility: Inclusion Criteria:
  1. Provision of fully informed consent prior to any study specific procedures.
  2. Patients must be ≥20 years of age.
  3. RET fusion positive,FGFR amplification, Refractory Solid Tumors that has recurred or progressed following standard therapy, or that has not responded to standard therapy, or for which there is no standard therapy.
  4. ECOG performance status 0-2.
  5. Have measurable or evaluated disease based on RECIST1.1. as determined by investigator.
  6. Adequate Organ Function Laboratory Values
  -  Absolute neutrophil count ≥ 1.5 x 109/L, Hemoglobin ≥ 9g/dL, Platelets ≥ 75 x 109/L
  -  bilirubin ≤ 1.5 x upper limit of normal AST/ALT ≤ 2.5 x upper limit of normal (5.0 X upper limit of normal , for subjects with liver metastases)
  -  creatinine ≤1.5 x UNL
  7. Patients of child-bearing potential should be using adequate contraceptive measures (two forms of highly reliable methods) should not be breast feeding and must have a negative pregnancy test prior to start of dosing.
  8. Adequate heart function.
  Exclusion Criteria:
  1. Patients with second primary cancer, except: adequately treated non-melanoma skin cancer, curatively treated in-situ cancer of the cervix, or other solid tumours curatively treated with no evidence of disease for ≤5 years.
  2. Has known active central nervous system (CNS) metastases.
  3. Has an active infection requiring systemic therapy.
  4. Pregnancy or breast feeding
  5. Patients with cardiac problem.
  6. Any previous treatment with sunitinib

Relevance to patient case: not relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: Crizotinib (Xalkori) Expanded Access Protocol For The Treatment Of Adult Or Pediatric Patients

Summary: This is an open label expanded access protocol for the treatment of up to approximately 40 adult or pediatric (defined as age <18 years) patients with tumors harboring either a chromosomal translocation or activating mutation involving the ALK or ROS1 gene or an activating genetic alteration involving the cMET gene who cannot swallow the crizotinib capsule but may be able to derive benefit from treatment with an alternative oral formulation of crizotinib.

Detailed description: Crizotinib is indicated in the U.S. for the treatment of patients with metastatic non-small cell lung cancer (NSCLC) whose tumors are anaplastic lymphoma kinase (ALK)-positive as detected by an FDA-approved test. Commercially available dosage forms are 250 mg and 200 mg capsules. This expanded access protocol (EAP) is designed to provide access to an alternative oral formulation of crizotinib for those patients who are unable to swallow capsules.

Eligibility: Inclusion Criteria:
  -  Histologically or cytologically proven diagnosis of a primary or metastatic malignancy that is positive for a chromosomal translocation or activating mutation involving the ALK or ROS1 gene or an activating genetic alteration involving the c MET gene, as determined by local clinical testing that is appropriately validated in accordance with applicable regulatory guidelines and/or practice standards (patients with tumors harbouring other genetic alterations that may potentially benefit from treatment with crizotinib eg NTRK3 ETV6 fusion gene may be considered on a case by case basis subject to approval by the sponsor).
  -  Inability to swallow crizotinib capsules, adult patients of whom must either have a feeding tube in place or have completed clinical evaluation of dysphagia without any reversible causes identified.
  -  At least 12 months of age (patients <12 months of age will be evaluated on a case by case basis and discussed with the sponsor).
  Exclusion Criteria:
  -  Currently receiving crizotinib, another ALK inhibitor, or an investigational product.
  -  Adult patients who have been previously treated with crizotinib.

Relevance to patient case: possibly relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: ALK Rearrangements in Lung Adenocarcinoma: Epidemiology in Latin America (CLICaP)

Summary: Evaluation of the frequency and clinical characteristics of ALK rearrangements in Latin-American countries.
  Latin American countries are heterogeneous in terms of lung cancer incidence, ethnicity, and exposure to potential carcinogens. The discovery of the echinoderm microtubule-associated protein like 4-anaplastic lymphoma kinase (EML4-ALK) translocation as an oncogenic driver has led to the development of novel therapies with activity in vitro and in the clinic.

Detailed description: The precise frequency of ALK in Latin American population has not been determined. Studies isolated in some Latin American countries like Brazil report a frequency of 3.2%, Argentina of 4.2% and Mexico of 9.0% of ALK fusion in a small number with lung cancer. Reliable information about ALK frequencies and disparities among ethnic groups is critical. Our study pretends to know the frequency and clinical characteristics of ALK rearrangement of Latin American patients with NSCLC. Discusses the difficulty of having a single diagnostic test for this chromosome abnormality.
  The development of efficient and reliable laboratory test is critical in the selection of patients likely to respond to these targeted agents. Currently, the current gold standard for testing for EML4-ALK translocation is fluorescent in situ hybridization (FISH) for selecting patients for ALK-tyrosine kinase inhibitors (TKI) therapy according to the United States Food and Drug Administration (FDA). But, an important aspect is the amount of available tumor present in a determined sample, given the labor-intensive nature and cost of the test, there has been interest in validating other screening and diagnostic tools. Recent evidence suggests that ALK Immunohistochemistry (IHC) instruments globally protocols, can be very effective in the detection of ALK rearrangement in NSCLC (ALK+) tumors expressing the fusion ALK protein.

Eligibility: Inclusion Criteria:
  -  Histologically confirmed lung cancer and tissue availability for ALK analysis.
  Exclusion Criteria:
  -  Not lung cancer

Relevance to patient case: not relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: Study of Apatinib in RET Fusion Positive Advanced Non-small Cell Lung Cancer

Summary: RET fusions are present in 1% to 2% of unselected population of non-small cell lung cancer (NSCLC). Existing US Food and Drug Administration-approved inhibitors of RET tyrosine kinase show promising therapeutic effects in a non-small cell lung cancer patients. Apatinib is an oral multi-kinase inhibitors including RET fusions. This study is designed to evaluate the safety and tolerability of Apatinib in patients with RET fusion positive advanced NSCLC.

Detailed description: To observe objective response rate (ORR) of apatinib in RET fusion positive pre-treated advanced NSCLC.
  To observe Progression free survival （PFS）. To assess the overall survival (OS). To assess safety and tolerability. To evaluate quality of life. To explore the relationship between biomarkers and the toxicity/efficacy of apatinib.

Eligibility: Inclusion Criteria:
  -  Aged ≥18 and ≤80 years.
  -  ECOG performance status of 0 to 1.
  -  Life expectancy of more than 12 weeks.
  -  At least one measurable lesion exists.(RECIST 1.1)
  -  Histologically or cytologic confirmed RET fusion positive advanced Non-small cell lung cancer who failed to prior therapies.
  -  Required laboratory values including following parameters: ANC: ≥ 1.5 x 10^9/L, Platelet count: ≥ 80 x 10^9/L, Hemoglobin: ≥ 90 g/L, Total bilirubin: ≤ 1.5 x upper limit of normal, ULN, ALT and AST: ≤ 1.5 x ULN, BUN and creatine clearance rate: ≥ 50 mL/min LVEF: ≥ 50% QTcF: < 470 ms
  -  Signed informed consent
  -  Females of child-bearing potential must have negative serum pregnancy test. Sexually active male and those having childbearing potential must practice contraception during the study.
  Exclusion Criteria:
  -  Squamous carcinoma (including adeno-squamous carcinoma), small cell lung cancer
  -  Subjects with third space fluid that can not be controled by drainage or other methods.
  -  Obvious cavity or necrosis formed in the tumor
  -  Uncontrolled hypertension
  -  Hymoptysis, more than 2.5ml daily
  -  Thrombosis in 12 months, including pulmonary thrombosis, stroke, or deep venous thrombosis
  -  Received big surgery, had bone fracture or ulcer in 4 weeks
  -  Urine protein >++, or urine protein in 24 hours> 1.0g
  -  pregnant or lactating woman
  -  Receiving any other antitumor therapy.
  -  Known history of hypersensitivity to apatinib or any of it components.

Relevance to patient case: not relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: Genomic Landscape of Ceritinib

Summary: The investigators propose to conduct a retrospective study of single agent ceritinib in patients with previously untreated anaplastic lymphoma kinase (ALK) rearranged adenocarcinoma of the lung with the sole purpose of characterizing the genomic landscape before ceritinib and at the time of disease progression.

Detailed description: Further improvements in therapy can only be achieved with a better understanding of the genomic landscape of ALK rearranged non-small cell lung cancer (NSCLC), specifically at the time of disease progression following treatment with ALK inhibitors. Recently, secondary ALK mutations, L1196M and G1269A have been described in patients with acquired resistance to crizotinib. A small subset of ALK positive lung cancer patients who progressed after treatment with ceritinib had tumors available for molecular analysis. Secondary mutations found included G1202R, F1174C, and F1174V. While this is interesting, an unbiased genomic study (exome or whole genome sequencing) using massively parallel sequencing at the time of disease progression is critical to fully understand the clonal evolution and the molecular mechanisms underpinning treatment resistance. To the best of the investigators' knowledge, such a study has not yet been reported.
  The investigators believe the time is ripe now to comprehensively characterize genomic alterations using massively parallel sequencing technology of ALK driven adenocarcinoma of the lung to fully understand the clonal heterogeneity before therapy and fully understand the clonal evolution and the molecular mechanisms underpinning treatment resistance. A better understanding of genomic alterations through an unbiased comprehensive approach likely would lead to rationally designed therapy to augment response to ALK inhibitors.

Eligibility: Inclusion Criteria
  -  Diagnosis of metastatic stage IIIB/IV lung adenocarcinoma.
  -  Presence of known ALK gene rearrangement.
  -  Consented to HRPO# 201305031 ("Tissue and Blood Acquisition for Genomic Analysis and Collection of Health Information from Patients with Thoracic Malignancies, Suspected Thoracic Malignancies, or Mesothelioma") with an existing specimen prior to initiation of treatment with ceritinib.
  -  At least 18 years of age.
  -  Received treatment with standard of care ceritinib

Relevance to patient case: not relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: PPI And Food Effect Study For PF-06463922 In Healthy Volunteers

Summary: The current study will be conducted in healthy adult subjects to evaluate the effect of proton pump inhibitor and food on pharmacokinetics of PF-06463922, to evaluate the bioavailability of the oral solution relative to the tablet formulation of PF-06463922.

Detailed description: PF-06463922 is a selective, ATP competitive small molecule tyrosine kinase inhibitor (TKI) of the Anaplastic Lymphoma Kinase (ALK) positive (ALK+) or ROS oncogene 1 (ROS1) positive (ROS1+) receptor tyrosine kinases (RTK) that also potently inhibits ALK kinase domain mutations responsible for resistance to crizotinib. PF-06463922 is being developed as a novel anticancer agent for the treatment of patients with advanced ALK+ NSCLC or ROS1+ NSCLC.
  The current study is a Phase 1, randomized, open label, 4 period, 4 treatment, 4 sequence, crossover study conducted in healthy adult subjects. Each subject will receive four single oral doses of 100 mg PF-06463922 as tablets alone, tablets with food, tablets with rabeprazole, and oral solution after overnight fasting with at least a 10 day washout period between each PF-06463922 dose.
  Twenty four (24) subjects will be enrolled to obtain at least 20 evaluable subjects who complete all treatments. Subjects who withdraw will not be replaced unless the total number of completed subjects falls below 20.

Eligibility: Inclusion Criteria:
  -  Healthy female subjects of non-childbearing potential and/or male subjects
  -  Body Mass Index (BMI) of 17.5 to 30.5 kg/m2; and a total body weight >50 kg (110 lbs).
  -  Evidence of a personally signed and dated informed consent document.
  -  Subject must be willing to avoid direct sunlight exposure or any high intensity ultraviolet light exposure
  Exclusion Criteria:
  -  Evidence or history of clinically significant hematological, renal, endocrine, pulmonary, gastrointestinal, cardiovascular
  -  Any condition possibly affecting drug absorption
  -  A positive urine drug screen.
  -  Use of tobacco- or nicotine containing products within 90 days of screening or a positive urine cotinine test and history of regular alcohol consumption exceeding 14 drinks/week for females or 21 drinks/week for males within 6 months of Screening.

Relevance to patient case: not relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: Study of Split-course Chemoradiotherapy For Bulky Local Advanced None-small Cell Lung Cancer

Summary: This Phase II randomized study is to determine the efficacy of split-course irradiation with concurrent chemotherapy in locally advanced none-small cell lung cancer patients with bulky tumor.

Detailed description: This Phase II randomized study is to determine the efficacy of split-course chemoradiotherapy(CCRT) in locally advanced non-small cell lung cancer with bulky tumor.
  Patients received four cycles of weekly docetaxel(25mg/㎡) and nedaplatin(25mg/㎡), each of 1 day's duration, combined with split-course thoracic radiotherapy of 51 Gy/17 fractions and 15 Gy/5 fractions administered in the first and second courses, respectively, with one-month break. The primary end point is progression-free survival, which is the time that passes from the first day of radiotherapy to the date at which disease progresses. Progression-free survival will be calculated using the Kaplan-Meier method.Toxicities will be graded according to CTCAE v. 4.0.

Eligibility: Inclusion Criteria:
  -  Pathologic confirmation of NSCLC.
  -  Patients have measurable or evaluable lesions based on the Response Evaluation Criteria in Solid Tumors (RECIST) criteria.
  -  Unresectable phase IIIA(N2) and IIIB lung cancer confirmed by PET/CT, CT or MRI.
  -  Whole lung V20>=35% when giving 60Gy which is the minimum dose of radical irradiation.
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0-1.
  -  Previously treated with chemotherapy or treatment-naive
  -  No previous chest radiotherapy, immunotherapy or biotherapy
  -  Hemoglobin≥10 mg/dL, platelet≥100000/μL,absolute neutrophil count ≥1500/μL
  -  Serum creatinine ≤1.25 times the upper normal limit(UNL), or creatinine clearance≥60 ml/min
  -  Bilirubin ≤1.5 times UNL, AST（SGOT）≤2.5 times UNL ,ALT（SGPT）≤2.5 times UNL,alkaline phosphatase ≤5 times UNL
  -  FEV1 >0.8 L
  -  CB6 within normal limits
  -  patients and their family signed the informed consents
  Exclusion Criteria:
  -  Previous or recent another malignancy, except nonmelanoma skin cancer or cervical cancer in situ
  -  Contraindication for chemotherapy
  -  Malignant pleural or pericardial effusion.
  -  Women in pregnancy, lactation period, or no pregnancy test 14 days before the first dose
  -  Women who has the probability of pregnancy without contraception
  -  Tendency of hemorrhage
  -  In other clinical trials within 30 days
  -  Addicted in drugs or alcohol, AIDS patients
  -  Uncontrollable seizure or psychotic patients without self-control ability
  -  Severe allergy or idiosyncrasy
  -  Not suitable for this study judged by researchers

Relevance to patient case: not relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: Phase 1 Study of DS-6051b in Japanese Subjects With Advanced Solid Malignant Tumors

Summary: This is a Phase 1 study to evaluate the safety, tolerability, and pharmacokinetics of DS-6051b in Japanese subjects with advanced solid malignant tumors harboring either a ROS1 or NTRK fusion gene.

Detailed description: This study is single arm study with DS-6051b in approximately 9 subjects with advanced solid malignant tumors harboring either a ROS1 or NTRK fusion gene. Safety and tolerability, pharmacokinetics (PK), maximum tolerated dose/recommended phase 2 dose (MTD/RP2D) and preliminary efficacy of DS-6051b will be evaluated.

Eligibility: Inclusion Criteria:
  -  Advanced solid malignant tumors that are refractory to standard therapy or for which no standard therapy is available.
  -  An Eastern Cooperative Oncology Group (ECOG) performance status (PS) 0-1.
  Exclusion Criteria:
  -  Previously had or currently has any of the following diseases:
  Cardiac failure (NYHA Functional Classification ≥ Class III), myocardial infarction, cerebral infarction, unstable angina, arrhythmia requiring treatment, coronary/peripheral artery disease, pulmonary thrombosis, uncontrolled deep vein thrombosis, clinically severe thromboembolic event, or autoimmune disease requiring treatment.
  -  Previously had or currently has clinically severe pulmonary disease (eg, interstitial pneumonia, pneumonitis, pulmonary fibrosis, radiation pneumonia).
  -  Severe or uncontrolled concomitant disease.
  -  Clinically active brain metastases or central nervous system tumor requiring steroid or anticonvulsant treatment.

Relevance to patient case: possibly relevant
Patient case: 72-year-old male with lung adenocarcinoma; genetic feature: EZR-ROS1 fusion

Clinical trial: Study to Evaluate the Safety and Efficacy of Sunitinib, in Subject With Refractory Solid Tumors

Summary: This study is a single arm, pilot study of Sunitinib in patient with RET fusion positive, FGFR2 fusion/FGFR mutation Refractory solid tumor and/or specific sensitivity to Sunitinib by Avatar scan that has progressed following standard therapy or that has not responded to standard therapy or for which there is no standard therapy.
  To investigate the efficacy and safety of Sunitinib in patient with Refractory solid tumor.


Eligibility: Inclusion Criteria:
  -  Provision of fully informed consent prior to study specific procedures.
  -  Patients must be >= 19 years of age
  -  RET fusion positive or FGFR2 fusion/other FGFR mutation Refractory solid tumor and/or specific sensitivity to Sunitinib by Avatar scan that has progressed following standard therapy or that has not responded to standard therapy or for which there is no standard therapy.
  -  ECOG Performance status0-2
  -  Have measurable or evaluated disease based on RECIST 1.1 as determined by investigator.
  -  Adequate Organ Function Laboratory values
  -  Absolute neutrophil count >= 1.5 x 109/L, Hemoglobin >= 9g/dL, Platelets>=100 x 109/L Bilirubin <= 1.5 x upper limit of normal AST/ALT <= 2.5 X upper limit of normal(5.0 x upper limit of normal, for subject with liver metastases) Creatinine<= 1.5 X UNL
  -  Patients of child-bearing potential should be using adequate contraceptive measures should not be breast feeding and must have a negative pregnancy test prior to start of dosing
  -  Adequate heart function
  Exclusion Criteria:
  -  Patients with second primary cancer, except:adequately treated non-melanoma skin cancer, curatively treated in-situ cancer of the cervix, or other solid tumor curatively treated with no evidence of disease for <= 5 years.
  -  Has known active central nervous system(CNS) metastases
  -  Has an active infection requiring systemic therapy
  -  Pregnancy or breast feeding
  -  Patients with cardiac problem
  -  Any previous treatment with sunitinib

Relevance to patient case: not relevant