araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Single-arm Study to Evaluate the Safety and Efficacy of Pazopanib, in Subjects With FGFR2 Amplification, FGFR2 Mutation Refractory Solid Tumors

Summary: This is a pilot study of Pazopanib in patients with FGFR2 Amplification or FGFR2 mutation Refractory solid tumors.
  This study is a single-arm, pilot study of Pazopanib in subjects with Refractory solid tumors harboring FGFR2 Amplification or FGFR2 mutation Pazopanib 800mg will be administered orally once a day 28 days.Study treatment will be continued until objective disease progression.
  To investigate the efficacy of Pazopanib in subjects with Refractory solid tumors harboring FGFR2 Amplification or FGFR2 mutation.


Eligibility: Inclusion Criteria:
  1. Provision of fully informed consent prior to any study specific procedures.
  2. Patients must be ≥20 years of age.
  3. FGFR2 amplification or FGFR2 mutation 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 ≥ 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 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 Pazopanib.

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Afatinib and Selumetinib in Advanced KRAS Mutant and PIK3CA Wildtype Non-small Cell Lung Cancer

Summary: This is a multi-center open-label proof-of-concept study consisting of two parts: PART A - a phase I dose-finding study (3 + 3 classical design) evaluating the RP2D of afatinib in combination with selumetinib in KRASm NSCLC; and PART B - a randomized phase II study investigating the progression free survival and safety of selumetinib/afatinib combination therapy compared to standard of care chemotherapy in KRASm NSCLC.


Eligibility: Inclusion Criteria:
  -  Histological or cytological proof of advanced NSCLC; for PART B: treated with first line therapy for metastatic disease only.
  -  Written documentation of a known pathogenic KRAS (exon 2, 3 or 4) mutation and PIK3CA wildtype (defined as absence of mutations in exon 9 and 20)
  -  Able and willing to give written informed consent
  -  Able and willing to undergo blood sampling for PK and PD analysis
  -  Life expectancy >=3 months allowing adequate follow up of toxicity evaluation and antitumor activity.
  -  WHO performance status of 0 or 1.
  -  Able and willing to undergo a tumor biopsies prior to start, after two weeks (part A only) and upon progression of disease
  -  Measurable disease according to RECIST 1.1
  -  Adequate organ system function measured by laboratory values
  Exclusion Criteria:
  -  Any treatment with investigational drugs within 30 days prior to receiving the first dose of investigational treatment.
  -  History of another malignancy Exception PART A: Patients who have been disease-free for at least 3 years, or patients with a history of completely resected non-melanoma skin cancer and/or patients with indolent second malignancies are eligible. Exception PART B: Adequately treated carcinoma in situ of the cervix and adequately treated basal cell carcinoma of the skin. 3. Symptomatic or untreated leptomeningeal disease.
  -  Symptomatic brain metastasis.
  -  Patients previously treated with any drug combination known to interfere with EGFR, HER2, HER3, HER4 or MAPK- and PI3K-pathway components, including inhibitors of PTEN, PI3K, AKT, mTOR, BRAF, MEK and ERK.
  -  History of interstitial lung disease or pneumonitis
  -  Radio-, immuno- or chemotherapy within the last 2 weeks prior to receiving the first dose of investigational treatment. Palliative radiation (1x 8Gy) is allowed.
  -  Opthalmological diseases
  -  Patients with left ventricular ejection fraction (LVEF) < 55%
  -  Patients with cardiac comorbidities
  -  Concomitant or recent use (in the past 14 days) of strong inhibitors and inducers of CYP1A2, CYP2C19, CYP3A4, 3A5 and P-glycoprotein (P-gp)

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: A Safety and Efficacy Study of INC280 Alone, and in Combination With Erlotinib, Compared to Chemotherapy, in Advanced/Metastatic Non-small Cell Lung Cancer Patients With EGFR Mutation and cMET Amplification

Summary: The purpose of this study is to determine the maximum tolerated dose (MTD) or recommended phase II dose (RP2D) of INC280 in combination with erlotinib in the Phase Ib of this study, and to assess the anti-tumor activity and safety of INC280 alone, and in combination with erlotinib, versus platinum with pemetrexed in the Phase II of this study, in adult patients with EGFR mutated, cMET amplified, advanced/metastatic non-small cell lung cancer with acquired resistance to prior EGFR TKI.

Detailed description: The decision was taken to halt study enrollment with Cohort #3 in Phase 1b. Therefore, activities for the planned Phase 2 were not initiated.
  This decision to stop further development of this combination was taken due to the challenge for enrollment in this very rare patient population along with the rapidly evolving disease landscape setting.

Eligibility: Inclusion Criteria:
  -  Locally advanced or metastatic NSCLC
  -  EGFR mutation (L858R and /or ex19del)
  -  cMET amplification by FISH (GCN ≥ 6),
  -  Acquired resistance to EGFR TKI (1st or 2nd génération)
  -  ECOG performance status (PS) ≤ 1.
  Exclusion Criteria:
  -  Prior treatment with 3rd generation TKI
  -  PhaseII : Prior treatment with any of the following agents:
  -  Crizotinib, or any other cMET inhibitor or HGF-targeting inhibitor.
  -  Concomitant EGFR TKI and platinum based chemotherapy as first line regimen.
  -  Platinum-based chemotherapy as first line treatment

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: The Effect of Antacids on the Pharmacokinetics (PK) of Raltegravir in Human Immunodeficiency Virus (HIV)-Infected Participants (MK-0518-824)

Summary: In order to define the safe windows for co-dosing of metal-cation antacids with once daily administered raltegravir, this study will evaluate the effect of both calcium carbonate and magnesium/aluminum hydroxide antacids on the pharmacokinetics of raltegravir, due to dosage of 1200 mg raltegravir in HIV-infected participants already taking 400 mg raltegravir twice daily as part of their HIV treatment regimen.


Eligibility: Inclusion Criteria:
  -  Is HIV positive
  -  Is on a stable raltegravir-containing (400 mg every 12hr) antiretroviral (ARV) regimen for at least 1 month prior to study entry, with no changes, including dose adjustments; and agrees to maintain their current ARV therapy throughout the study.
  -  Be male, or a non-pregnant and non-breast feeding female at least 18 years of age at the pre-trial (screening)
  -  Has a Body Mass Index (BMI) =< 32 kg/m^2
  Exclusion Criteria:
  -  Has a history of clinically significant endocrine, gastrointestinal, cardiovascular, hematological, hepatic, immunological, renal, respiratory, genitourinary or major neurological (including stroke and chronic seizures) abnormalities or diseases (excluding HIV)
  -  Has a history of gastric bypass surgery
  -  Has a history of cancer (malignancy)
  -  Has a history of chronic diarrhea within approximately 3 months prior to the pre-trial visit
  -  Has a history of significant multiple and/or severe allergies (e.g. food, drug, latex allergy), or has had an anaphylactic reaction or significant intolerability to prescription or non-prescription drugs or food
  -  Has had major surgery, donated or lost 1 unit of blood (approximately 500 mL) within 4 weeks prior to the pre-trial visit
  -  Has participated in another investigational trial within 4 weeks prior to the pre-trial visit
  -  Is currently taking rifampin or atazanavir or is unable to refrain from the use of 1) any proton pump inhibitor from two weeks prior to the study through the completion of Period 4, and 2) any H2-blockers, over-the-counter antacids, calcium supplements or multivitamins from one week prior to the study through the completion of Period 4
  -  Consumes greater than 3 glasses of alcoholic beverages or distilled spirits per day
  -  Consumes greater than 6 servings of coffee, tea, cola, energy-drinks, or other caffeinated beverages per day
  -  Is currently a regular user (including "recreational use") of any illicit drugs or has a history of drug (including alcohol) abuse within approximately 6 months of screening

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Identification of Prognostic Biomarkers for Progression of Invasive Squamous Cell Carcinoma

Summary: The study will utilize both retrospective and prospective data collection from patients that already had a bronchoscopy and lung resection or will have a bronchoscopy and lung resection for squamous cell carcinoma. The investigators plan to prospectively collect 5 bronchoscopic biopsies, 10ml blood and one tumor and adjacent normal samples from 200 qualified patients who meet the study criteria.

Detailed description: The study will utilize both retrospective and prospective data collection from patients that have already had a bronchoscopy and lung resection or will have a bronchoscopy and lung resection for squamous cell carcinoma. The investigators plan to prospectively collect 5 bronchoscopic biopsies, 10ml blood and one tumor and adjacent normal samples from 200 qualified patients who meet the study criteria. If a patient has already had a bronchoscopy and has consented to have samples stored for research at the Mayo Clinic Rochester we will access them for the research study if available. Otherwise, if the patient has already had surgery and tissue has not been stored for research the investigators will consent patients to use their clinical specimens for the research study. The investigators will then extract DNA from tissue sections and blood and use a custom targeted sequencing panel of 23 cancer driver genes with significant mutations in squamous cell carcinoma that they have developed to find the prognostic biomarkers. The DNA will be used in a PCR reaction to generate amplicons for library preparation using Illumina Nextera XT library preparation protocol and targeted sequencing on the Illumina Hiseq sequencer. The reads will be aligned to the HG19 using BWA aligner and variant detection performed with Agilent SureCall and GATK analytic tools.

Eligibility: Inclusion Criteria:
  -  known or suspected squamous cell carcinoma of the lung
  -  able to provide consent
  -  could have already had a bronchoscopy or surgical resection with tissue saved at the Mayo Clinic Rochester
  -  will be undergoing a bronchoscopy and having a surgical resection at the Mayo Clinic Rochester
  Exclusion Criteria:
  -  unable to provide consent
  -  pregnant

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Nimotuzumab Combined With Chemoradiotherapy for Unresectable Locally Advanced Squamous Cell Lung Cancer

Summary: This Phase II randomized study is to determine the efficacy and toxicity of Nimotuzumab in combined with chemoradiotherapy for unresectable,local advanced squamous cell lung cancer.

Detailed description: This Phase II randomized study is to determine the efficacy and toxicity of Nimotuzumab in combined with chemoradiotherapy for unresectable,local advanced squamous cell lung cancer.
  All patients received five cycles of weekly docetaxel and cisplatin, each of 1 day's duration. Thoracic RT includes the delivery of 65 Gy in 25 fractions on weekdays for a total of five weeks.
  Nimotuzumab group was treated with five doses of weekly nimotuzumab (200mg, IV) combined with chemoradiotherapy, while placebo group was treated with five doses of placebos.
  150 patients are needed to be enrolled for an 80% power to detect an improvement in overall survival from 15 months to 25 months.

Eligibility: Inclusion Criteria:
  -  histologically confirmed squamous cell lung cancer
  -  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 CT or MRI
  -  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:
  -  adenosquamous carcinoma
  -  previous or recent another malignancy, except for nonmelanoma skin cancer or cervical cancer in situ
  -  contraindication for chemotherapy
  -  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: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: A Retrospective Study About Treatment Strategy After First/Second Line EGFR-TKI Failure

Summary: This is a multi-center retrospective study, designing to access the best treatment strategy in non-small cell lung cancer (NSCLC) patients harboring EGFR mutant type after first/second line EGFR-TKI failure. The study end point is Progression Free Survival 2 (PFS2), which is defined as the time period from Progression Disease 1(PD1) to Progression Disease 2(PD2). PD1 is defined as the first tumor progression time from taking EGFR-TKI evaluated by Recist 1.1 criterion, and PD2 as the second tumor progression time after EGFR-TKI failure no matter what second/third line treatment was, PD2 is also evaluated by Recist 1.1 criterion.


Eligibility: Inclusion Criteria:
  -  Patients who was confirmed stage IV (according to International Association for the Study of Lung Cancer（IASLC） TNM staging, 2009) non-small cell lung cancer (NSCLC) by histology or cytology between year 2009 to 2013, harboring EGFR mutant type (19 and/or 21 exon mutation).
  -  Appraisable disease, that is there must be at least one lesion with the longest diameter>10mm according to Recist 1.1 criterion (by contrast CT).
  -  Patients who take EGFR-TKI as first/second line therapy.
  Exclusion Criteria:
  -  Patients who has taken EGFR-TKI before.
  -  Patients who take EGFR-TKI as third or more line.
  -  Patients who take EGFR-TKI concurrent with chemotherapy or other anti-tumor drug.
  -  The evaluated lesions has treated with radiotherapy before or concurrent with EGFR-TKI.
  -  Patients whose EGFR expression is positive by immunochemical and/or EGFR amplification is positive by Fluorescence In Situ Hybridization(FISH), without mutation detection evidence.

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

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

Summary: This study is a single arm, pilot study of pazopanib in patient with FGFR2 amplification Refractory solid tumor and/or specific sensitivity to pazopanib 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 pazopanib 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
  -  FGFR2 amplification ,Refractory solid tumor and/or specific sensitivity to 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, pazopanibPlatelets>=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 pazopanib

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: A Study of Prevalence of EGFR Mutations in Participants With NSCLC

Summary: This is a non-interventional, local, multicenter, cross-sectional study to determine the prevalence of epidermal growth factor receptor (EGFR) mutations in participants diagnosed with non-squamous non-small cell lung cancer (NSCLC).


Eligibility: Inclusion Criteria:
  -  Informed consent form signature
  -  Jordanian male and female participants greater than or equal to (>=) 18 years of age
  -  Histologically confirmed NSCLC
  -  Not participating in a study that involves an investigational agent within 30 days prior to enrollment
  Exclusion Criteria:
  -  Other primary malignancy
  -  Fine needle aspiration samples

Relevance to patient case: not relevant
Patient case: 65-year-old female with squamous cell lung cancer; genetic feature: FGFR1 amplification

Clinical trial: Study on Fluids Associated to Lung Cancer

Summary: The diagnosis of lung cancer is the first cause of cancer deaths for man and woman. It requires invasive procedures (at least endoscopy, transthoracic puncture, or surgery).
  This study is about the set up of an innovative test for lung cancer prognosis, based on biopsies and surgical material : LungCancerTest, with the creation of a start-up in progress.
  The main goal of this study is to approve the diagnostic value of the molecular signature of the 26 genes (LungCancerTest) revealed in blood and respiratory fluids among patients with lung cancer.


Eligibility: Inclusion Criterias :
  -  Patients with lung cancer in stage 1-2, lung cancer of all histology kind eligible for surgery (Group 1).
  -  Patients with lung cancer in stage 3-4 (no adenocarcinoma or squamous) receiving classical or targeted chemotherapy on genetic anomalies (Group 2).
  -  Control patients : carriers of non-cancerous radiological anomalies : benign nodules, cicatricial lesions, infectious or inflammatory, paired with the two other groups by age, sex or tobacco (Group 3).
  -  Adults patients : over 18 years.
  -  Persons affiliated to national social security.
  -  Free signed consent.
  Exclusion Criterias :
  -  Persons referred to in articles L1121-5 to L1121-8 of CSP ( protected people) : pregnants, parturients or breastfeeding women, person deprived of liberty by judicial or administrative decision, person under legal protection.

Relevance to patient case: not relevant