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

Clinical trial: A Study to Assess the Efficacy and Safety of the VEGFR-FGFR Inhibitor, Lucitanib, Given to Patients With Advanced/Metastatic Lung Cancer and FGF, VEGF, or PDGF Related Genetic Alterations

Summary: The purpose of this study is to determine whether lucitanib is safe and effective in the treatment of patients with advanced/metastatic lung cancer and fibroblast growth factor (FGF), vascular endothelial growth factor receptor (VEGF), or platelet derived growth factor (PDGF) related genetic alterations.

Detailed description: Lucitanib is an oral inhibitor of the tyrosine kinase activity of FGFR 1-3, VEGFR 1-3, and PDGFR α/β. Lucitanib has demonstrated potent anti-tumor and anti-angiogenic activity in vitro proliferation assays and in vivo using human tumor xenograft models, with a trend for stronger efficacy in those with genomic aberrancies of FGF or PDGF. Abnormalities in the FGF, VEGF, and PDGF-related genes are observed across lung cancer histologies.
  The first in human trial of lucitanib demonstrated that daily lucitanib is clinically active in patients with advanced solid tumors. Specifically, patients with FGFR1-amplification appeared to derive particular benefit from lucitanib.
  Based on these results, this study is designed to explore the safety and anti-tumor activity of daily lucitanib in lung cancer patients with FGF, VEGF, and PDGF genetic alterations.

Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed advanced/metastatic SCLC or NSCLC
  -  Any of the following tumor tissue based genetic alterations: FGFR1, FGFR2, FGFR3, VEGFA, or PDGFRα amplification; Any FGFR1, FGFR2, or FGFR3 gene fusion; FGFR1, FGFR2, or FGFR3 activating mutation
  -  Availability of tumor tissue sample suitable for the central confirmation of the genetic alteration and exploratory analyses
  -  Eastern Cooperative Oncology Group (ECOG) of 0 or 1
  -  Measurable disease per RECIST 1.1
  -  Documented radiographic disease progression following at least one line of therapy in the advanced/metastatic setting
  Exclusion Criteria:
  -  Tumors that are invading a major vessel; NSCLC tumors abutting to a major vessel
  -  Uncontrolled hypertension, defined as SBP ≥ 140 mmHg and/or DBP ≥ 90 mmHg with optimized anti-hypertensive therapy
  -  Uncontrolled hypothyroidism defined as serum thyroid stimulating hormone (TSH) higher than 5 mIU/mL while receiving appropriate thyroid hormone therapy
  -  Symptomatic and/or untreated central nervous system metastases
  -  Presence of another active cancer
  -  Ongoing adverse events from surgery or prior anti-cancer therapies, including radiation, targeted, or cytotoxic therapies
  -  Pregnant or breastfeeding women

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

Clinical trial: A Phase II, Single Arm Study of BGJ398 in Patients With Advanced Cholangiocarcinoma

Summary: This is a multi-center, open label, single arm phase II study evaluating BGJ398 anti-tumor activity in advanced or metastatic cholangiocarcinoma patients with Fibroblast Growth Factor receptor (FGFR) genetic alterations.

Detailed description: Adult patients with histologically or cytologically confirmed advanced or metastatic cholangiocarcinoma with FGFR genetic alterations who have evidence of radiologic progression following a cisplatin-and gemcitabine-containing regimen for advanced disease or a gemcitabine-containing regimen for those who are considered intolerant to cisplatin will be enrolled. Approximately 55 adult patients over age 18, both male and female will be enrolled. Of these 55 patients, 40 patients will have cholangiocarcinoma with identified FGFR2 gene fusions and up to 15 patients may have other FGFR genetic alterations. All patients will receive oral BGJ398, once daily, on a three weeks on (21 days), one week off (7 days) schedule. One treatment cycle will consists of 28 days.

Eligibility: Inclusion criteria:
  - Adult patients with histologically or cytologically confirmed cholangiocarcinoma at the time of diagnosis.
  Patients with cancers of the gallbladder or ampulla of Vater are not eligible.
  - Patients must have received at least one prior regimen containing gemcitabine with or without cisplatin for advanced/ metastatic disease. Patient should have evidence of progressive disease following prior regimen, or if prior treatment discontinued due to toxicity must have continued evidence of measurable or evaluable disease.
  Exclusion criteria:
  -  Prior or current treatment with a MEK or selective FGFR inhibitor
  -  insufficient organ function
  -  Absolutely Neutrophil Count (ANC) < 1,000/mm3 [1.0 x 109/L]
  -  Platelets < 75,000/mm3 [75 x 109/L]
  -  Hemoglobin < 109.0 g/dL
  -  Total bilirubin > 1.5x ULN
  -  Aspartate aminotransferase/glutamic oxaloacetic transaminase/GOT (AST/SGOT) and Alanine aminotransferase/glutamic pyruvic transaminase/GPT (ALT/SGPT) > 2.5x ULN (AST and ALT) > 5x upper limit of normal (ULN) in the presence of liver metastases)
  -  Serum creatinine > 1.5x ULN and a calculated or measured creatinine clearance < 45 mL/min
  -  Inorganic phosphorus outside of normal limits
  -  Total and ionized serum calcium outside of normal limits
  Other protocol-defined inclusion/exclusion criteria may apply.

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

Clinical trial: One Step Nucleic Acid Amplification in Endobronchial Ultrasound-guided Needle Aspiration Samples

Summary: The aim of our study is to investigate if CK19 mRNA-detection via OSNA can accurately detect lymph node metastases in lung cancer patients using EBUS-TBNA samples.

Detailed description: Regional lymph nodes are assessed before tumor resection and before initiation of chemo- or radiotherapy. Endobronchial ultrasound-guided needle aspiration (EBUS-TBNA) is a well-established method for mediastinal and hilar lymph node staging [2, 3]. Samples obtained via this route are much smaller than surgical lymph node biopsies, yet they are able to provide complete and thorough evaluation, this includes current molecular testing.
  One Step Nucleic Acid Amplification (OSNA), a molecular test that utilizes CK 19 mRNA-concentration as a target marker is becoming a rapidly dynamic method in quick detection of sentinel lymph node (SLN) metastases in breast cancer, colon cancer and other cancers.
  In lung cancer, the role of SLN is not well established. However, recent publications suggest an accurate and rapid detection of lymph node metastases in NSCLC. However this requires complete lymph node dissection either with mediastinoscopy or by other surgical means such as thoracotomy.
  The aim of our study is to investigate if CK19 mRNA-detection via OSNA can accurately detect lymph node metastases in lung cancer patients using EBUS-TBNA samples.

Eligibility: Inclusion Criteria:
  -  CT-scan suspicious for lung cancer,
  -  enlarged mediastinal lymph nodes (>10 mm),
  -  EBUS-TBNA to be performed,
  -  age: 18-99 years
  Exclusion Criteria:
  -  age: <18 years

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 to Assess the Safety and Efficacy of the VEGFR-FGFR-PDGFR Inhibitor, Lucitanib, Given to Patients With Metastatic Breast Cancer

Summary: The purpose of this study is to determine whether lucitanib is safe and effective in the treatment of patients with FGF aberrant metastatic breast cancer, as well as in the treatment of patients with biomarker negative (FGF non-aberrant) metastatic breast cancer.

Detailed description: Lucitanib is a selective, orally available tyrosine kinase inhibitor targeting FGFR1-3, VEGFR1-3, and PDGFRα and β, with activity in relevant cell lines and animal models.
  The first in human trial of lucitanib demonstrated that daily dosing with lucitanib can provide durable clinical responses in patients with FGFR1- or 11q (FGF3, FGF4, Cyclin D1, or FGF19)-amplified breast cancer. RECIST partial responses (PRs) were also observed in patients not known to have FGF abnormalities.
  Based on these results, is study is designed to explore the safety and anti-tumor activity of daily lucitanib in breast cancer patients with and without alterations of the FGF pathway.

Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed metastatic breast cancer relapsed or refractory to approved standard available treatment
  -  Prior treatment with standard first line therapy in the metastatic setting
  -  Availability of tumor tissue sufficient for confirmatory testing of FGFR1 and 11q amplification status
  -  Demonstrated progression of disease by radiological or clinical assessment (Measurable disease according to RECIST Version 1.1 is NOT required for enrollment)
  -  Estimated life expectancy >6 months
  Exclusion Criteria:
  -  Current or recent treatment with biologic anticancer therapies
  -  Ongoing AEs from prior anticancer therapies
  -  Active central nervous system (CNS) metastases
  -  Clinically significant or uncontrolled hypertension or cardiac disease
  -  Females who are pregnant or breastfeeding

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

Clinical trial: BIBF1120 in Patients With Advanced FGFR3 Mutated,Overexpressed,or Wild Type Urothelial Carcinoma

Summary: BIBF1120 in patients with advanced FGFR3 mutated, FGFR3 overexpressed, or FGFR3 wild type urothelial carcinoma of urinary bladder, urethra, ureter, and renal pelvis and who have failed platinum-based chemotherapy.


Eligibility: Inclusion Criteria:
  -  KPS 60%
  -  Histological confirmation of urothelial carcinoma , with metastatic disease
  -  Measurable disease
  -  Previously treated with platinum-based chemotherapy administered
  Exclusion Criteria:
  -  Radiographic evidence of cavitary or necrotic tumours
  -  Active brain metastasis.Leptomeningeal metastasis
  -  Chemotherapy, radiotherapy, targeted therapy with monoclonal antibodies or small tyrosine kinase inhibitors
  -  Grade 1 treatment-related toxicity from previous chemotherapy, radiotherapy, or targeted therapy
  -  Prior treatment with BIBF 1120 or other VEGFR inhibitors
  -  Significant cardiovascular diseases:
  -  Pericardial effusion
  -  Significant bleeding or thrombosis
  -  Gastrointestinal disorders or abnormalities that would interfere with absorption of the study drug
  -  Major injuries within the past 10 days with incomplete wound healing and/or planned surgery during the on-treatment study period

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

Clinical trial: Detection of Tumor DNA in Blood Samples From Cancer Patients

Summary: The aim of this study is to employ genomic detection methodologies to measure the relative amount of tumor nucleic acids in the blood of a cancer patient with diagnosed metastatic disease that is either commencing, currently undergoing or completed cytotoxic chemotherapy treatment. More generally, this approach will allow us to develop a quantitative measure of therapy efficacy via the counting of the relative changes in tumor molecules over the course of treatment.


Eligibility: Inclusion Criteria:
  -  Age 18 years or older
  -  Have metastatic disease with from a solid tumor (e.g. breast, lung, colon, pancreas, ovary, prostate...) or stage II or III solid tumors undergoing curative surgery or neoadjuvant therapy followed by surgery
  -  Starting treatment or a new line of treatment
  -  Able to understand and grant informed consent
  -  Able to have their blood drawn
  Exclusion Criteria:
  -  Unable to grant informed consent or comply with all study procedures.
  -  Has a hematological malignancy, i.e. myeloma, lymphoma, MDS, leukemia

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

Clinical trial: Phase I, Dose-escalation Trial of BAY1187982 in Subjects With Advanced Solid Tumors Known to Express Fibroblast Growth Factor Receptor 2 (FGFR2)

Summary: To evaluate the safety, tolerability, maximum tolerated dose, pharmacokinetics, and pharmacodynamics of the anti-FGFR2 antibody drug conjugate BAY1187982 in subjects with advanced solid tumors known to express fibroblast growth factor receptor 2 (FGFR2)


Eligibility: Inclusion Criteria:
  -  All subjects must be >/= 18 years at the first screening examination / visit
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 to 1
  -  Subjects with advanced, histologically or cytologically confirmed solid tumors described to express fibroblast growth factor receptor 2 (FGFR2) that are refractory to any standard therapy
  -  For maximum tolerated dose (MTD) Dose Expansion: Subjects with advanced, histologically or cytologically confirmed triple-negative breast cancer who had undergone within 4 lines of systemic anti-cancer treatment and not eligible for standard therapy anymore.
  -  Subjects need to have evaluable disease (measurable or not measurable).
  -  Women of childbearing potential must have a negative pregnancy test performed within 7 days prior to the start of treatment
  Exclusion Criteria:
  -  History of allergic reactions to monoclonal antibody therapy (or excipients in the formulation)
  -  Anti-cancer chemotherapy, experimental cancer therapy including clinical trial, or cancer immunotherapy within 4 weeks prior to the first dose of the investigational drug.
  -  Toxic effects of previous anti-cancer chemotherapy, experimental cancer therapy, or cancer immunotherapy have not normalized.
  -  History of symptomatic metastatic brain or meningeal tumors unless the subject is longer than 3 months from the end of definitive therapy before the first dose of the investigational drug and has clinically or radiologically no evidence of tumor growth.
  -  History of clinically significant cardiac disease
  -  Congenital coagulation abnormalities
  -  Subjects who are pregnant or are breast-feeding

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

Clinical trial: Multimodal Monitoring of Radiotherapy Response in Squamous Cell Cancer

Summary: The study's aim is to define imaging and molecular bio-markers for prediction of radiotherapy response of squamous cell carcinomas, in an early treatment phase.

Detailed description: Patients with squamous cell carcinoma of the head & neck, anal canal, cervix, esophagus or lung will be assessed before start of radiotherapy and 1-2 weeks after start. Multi-parametric MRI and 18F-2-fluoro-2-deoxy-D-glucose fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) will be performed in parallel to metabolomic analyses of tumour tissue. The investigators will correlate changes in imaging bio-markers to corresponding changes in tissue or blood bio-markers by repeated imaging and biopsies for better understanding of the image parameters.
  The data from the two assessments will be used for identifying imaging bio-markers, predictive for outcome. The patient data will be divided into one set of data for hypothesis generation and another set for validation.

Eligibility: Inclusion Criteria:
  1. Morphologically (pathology or cytology) verified, previously untreated squamous cell carcinoma (SCC) of the oral cavity, oropharynx, uterine cervix, oesophagus or lung.
  2. The patient should be planned for treatment with radiotherapy alone or in combination with concomitant medical therapy
  3. The tumour shall be radiologically and/or visually identifiable and accessible for biopsy without the need for general anaesthesia or other major interventions
  4. The patient must be at least 18 years of age, able to understand the given information and, leave a written informed consent to participate
  Exclusion Criteria:
  1. The patient is unwilling to participate in the study
  2. Patients with adjuvant post-operative radiotherapy (i.e. no visible remaining tumour)
  3. Pregnancy or lactation
  4. Contraindications to investigations with MRI, gadolinium contrast or PET-tracers
  5. Patients with an estimated glomerular filtration rate (GFR) <60 ml/min/1.73m2.
  6. Severe co-morbidities that are judged to significantly compromise survival in a two-years perspective.

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 Potential Biomarkers Associated With Clinical Phenotype of EGFR-TKIs in No-small Cell Lung Cancer in China

Summary: To understand 295 gene mutation mutation status (include EGFR, HER2, KRAS, BRAF, PIK3CA,ect) by deep sequencing in Chinese patients with pulmonary adenocarcinoma and their relationships with the patients' clinical features (including sex, age, smoking history and adenocarcinoma subtype), specify the predictive significance of the genes mutations for new targeted therapies in NSCLC patients, and better understand the molecular mechanism drug resistance to EGFR-TKIs.

Detailed description: This study is prospective to identify biomarkers to resistant to afatinib，gefitinib and erlotinib in non-small cell lung cancer patients. Mutations of whole exon of 295 gene are analysed by deep sequencing in Chinese patients with non-small cell lung cancer and their relationships with the patients' clinical features (including sex, age, smoking history and adenocarcinoma subtype), specify the predictive significance of the genes mutations for new targeted therapies in NSCLC patients, and better understand the molecular mechanism drug resistance to EGFR-TKIs.

Eligibility: Inclusion Criteria:
  -  Age>18 years,both male and female
  -  Histologically confirmed patients with pulmonary adenocarcinoma (Stage I-IV)
  -  ECOG 0-2
  -  Patients with enough paraffin tissue specimens or fresh tissue for detection
  -  Quality of the DNA extracted from the tissue samples ensures that the DNA can be used in DNA sequencing
  -  Subjects who provide detailed clinical and follow-up information
  Exclusion Criteria:
  -  Patients with other tumors
  -  Patients suffering from other serious diseases like infectious diseases (viral hepatitis, HIV,etc)
  -  Pregnant women shall be excluded

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

Clinical trial: A Trial of Trametinib and Panitumumab in RAS/RAF Wild Type Advanced Colorectal Cancer

Summary: This is a phase 2 study (the second phase in testing a new drug or drug combination) to see how useful the combination of two drugs, panitumumab and trametinib, are in patients with advanced colorectal cancer with KRAS, NRAS, or BRAF wild type (genes that are not mutated).
  Panitumumab is a drug that is approved by Health Canada for the treatment of advanced colorectal cancer with KRAS wild type. Panitumumab works by binding to and blocking the protein, epidermal growth factor receptor (EGFR) from working.
  Trametinib is a drug that is approved by Health Canada for the treatment of melanoma with a mutation in the BRAF gene. Trametinib works by binding to and blocking mitogen-activated protein kinase kinase (MEK) 1 and MEK2 from working.
  Previous studies have shown that the combination of panitumumab and trametinib may be more useful in KRAS, NRAS, or BRAF wild type colorectal cancer.


Eligibility: Inclusion Criteria:
  -  18 years of age or older
  -  KRAS/NRAS/BRAF wild type colorectal cancer, not responsive to standard therapies, no approved or curative therapy, refuse standard therapy
  -  Prior 5-FU, oxaliplatin and irinotecan
  -  ECOG Performance Status of 0 or 1
  -  Able to swallow/retain oral drugs
  -  Able and agree to have provide tumor tissue/have biopsies
  -  Agree to use contraception
  -  Not pregnant
  -  Adequate organ system function
  Exclusion Criteria:
  -  Chemotherapy, radiotherapy, immunotherapy, or other anti-cancer therapies <28 days or 5 half lives
  -  Prior EGFR, MEK, or RAF inhibitor or regorafenib
  -  Current use of prohibited medications
  -  Unresolved side effects
  -  GI disease or other condition affecting GI absorption
  -  Mucosal or internal bleeding
  -  Any major surgery <four weeks
  -  HIV, HBV, or HCV positive
  -  Active infection
  -  Leptomeningeal disease
  -  Brain metastases
  -  Unacceptable QTcF interval
  -  Significant uncontrolled arrhythmias
  -  Acute coronary syndromes, myocardial infarction, coronary angioplasty, or stenting or bypass grafting < 6 mos.
  -  Class II, III, or IV heart failure
  -  Other clinically significant ECGs
  -  Intra - cardiac defibrillators
  -  Cardiac metastases
  -  Condition that may interfere with patient safety
  -  Hypersensitivity to study drugs
  -  Severe or uncontrolled systemic diseases
  -  Pregnant or lactating
  -  Retinal vein occlusion
  -  Interstitial lung disease or pneumonitis
  -  Active liver or biliary disease

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

Clinical trial: T790M Mutation on ctDNA in Patients With NSCLC After EGFR-TKI Failure

Summary: The purpose of this study is to compare the frequency and abundance of T790M mutation among the different Clinical modes of EGFR-TKI failure.

Detailed description: An observational, non-interventional, multi-central study of comparison of the frequency and abundance of T790M mutation using both amplification refractory mutation system (ARMS) and digital droplet PCR (ddPCR) methods among the different Clinical modes of non-small cell lung cancer (NSCLC) patients with epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) failure

Eligibility: Inclusion Criteria:
  -  Histologically confirmed stage IIIB/IV NSCLC.
  -  Investigator confirmed progression according RECIST 1.1 during EGFR-TKI treatment within 28 days of the enrollment
  -  Activating mutation (G719A/C/S; Exon 19 insertion/deletion; L858R; L861Q) in the EGFR gene or have had at least partial response with EGFR TKI lasting ≥ 6 months
  -  Patient must be able to comply with the protocol
  Exclusion Criteria:
  -  Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 defined disease progression for more than 28 days while on previous EGFR-TKI treatment.
  -  Patient has been treated with any investigational agent for any indication within 4 weeks of study treatment.
  -  Histologically confirmed small cell lung cancer or other metastatic tumors
  -  Patient with no histologic or cytological diagnosis.

Relevance to patient case: not relevant