araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF 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: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Endodrill vs. Conventional Biopsy. Diagnostics and Genetic Analysis

Summary: Endodrill is a new instrument for biopsy sampling in the GI-channel. The purposes of this study are as follows:
  -  Compare the Endodrill instrument with conventional biopsy forceps in terms of ability to establish the correct diagnosis based on collected biopsies of tumors in the upper GI tract.
  -  Based on the quality of the collected tissue samples we want to evaluate which instrument generates the most useful material for genetic studies of the tumor.

Detailed description: Endodrill is a newly constructed biopsy tool for flexible endoscopic use. It uses a drilling motion within a casing to harvest solid biopsies from tissue through the biopsy channel of a conventional flexible endoscope. It was originally designed for sampling of tissue from submucosal lesions. The investigators´ first study of the instrument is now finished. Endodrill is safe to use and generates more submucosal tissue compared to biopsies with a conventional biopsy forceps.
  In this study the investigators want to compare the Endodrill instrument´s ability to obtain representative tissue samples from tumors in the distal esophagus and cardia with a conventional biopsy forceps. In addition the investigators want to compare the tissue samples in terms of weight, quality, artefacts and whether either instrument is more suited for collecting tissue for genetic analysis. Such analysis will be conducted with Next-Generation Sequensing (NGS) of the whole exome, Whole Exome Sequensing (WES). In the event of positive results from these analysis the investigators will also conduct RNA-sequencing of the tumor tissue in order to start pre-operative mapping of genetic abnormalities.
  20 patients will be enrolled for this study. For each patient the investigators will collect 10 biopsies, 5 biopsies each with conventional biopsy and the Endodrill instrument respectively. The order will be randomized for each patient. For each specific biopsy the investigator will choose a particular site on the suspected tumor tissue without knowing which instrument that will be used for the biopsy. This procedure will be repeated for all 10 biopsies.

Eligibility: Inclusion Criteria:
  -  Patients diagnosed with adenocarcinoma of the distal esophagus/cardia or stomach capable of stating a formal consent to participate in the study.
  Exclusion Criteria:
  -  Mental illness
  -  Extreme co-morbidity (ASA >3)

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: IMP321 (Eftilagimod Alpha) as Adjunctive to a Standard Chemotherapy Paclitaxel Metastatic Breast Carcinoma

Summary: The proposed Phase IIb clinical study aims to investigate the safety and efficacy of the active immunotherapy IMP321 in combination (adjunctive) with paclitaxel chemotherapy in patients with hormone receptor-positive metastatic breast cancer.

Detailed description: This is a multicentre, placebo-controlled, double-blind, 1:1 randomised Phase IIb study in female hormone receptor-positive metastatic breast cancer patients. The study comprises of two stages.
  Stage 1 is the open-label, safety run-in stage consisting of cohort 1 and 2 to confirm the (RPTD) of IMP321 in combination with paclitaxel.
  Stage 2 is placebo-controlled, double-blind randomisation stage, paclitaxel + IMP321 at the RPTD will be compared to paclitaxel + placebo.

Eligibility: Inclusion Criteria:
  1. Able to give written informed consent and to comply with the protocol
  2. Metastatic oestrogen receptor positive and/or progesterone receptor positive breast adenocarcinoma, histologically proven by biopsy of the primary tumour and/or metastasis
  3. Female of age 18 years or above
  4. Patients who are indicated to received first line chemotherapy with weekly paclitaxel
  5. Evidence of measurable disease as defined by Response Evaluation Criteria version 1.1
  6 Laboratory criteria: haematology and biochemistry results within the limits normally expected for the patient population.
  Exclusion Criteria:
  1. Prior chemotherapy for metastatic breast adenocarcinoma
  2. Disease-free interval of less than twelve months from the last dose of adjuvant chemotherapy
  3. Inflammatory carcinoma
  4. Candidate for treatment with trastuzumab (or other Her2/neu targeted agents)
  5. Systemic chemotherapy, radiation therapy or any other investigational agent within 4 weeks, endocrine therapy within 1 week prior to first dose of study treatment or CDK4/6 inhibitors within 5 times half-life (acc.to SPC) prior to first dose of study treatment and until completion of study treatment
  6. Symptomatic known cerebral and/or leptomeningeal metastases
  7. Serious intercurrent infection
  8. Evidence of severe or uncontrolled cardiac disease (NYHA III-IV) within 6 months prior to first dose of study treatment
  9. Active acute or chronic infection
  10. Active autoimmune disease requiring immunosuppressive therapy
  11. Previous malignancies within the last three years other than breast carcinoma
  12. Patients with prior organ or stem cell transplantation
  13. Any condition requiring continuous systemic treatment with either corticosteroids or other immunosuppressive medications within 4 weeks prior to first dose of study treatment.

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Study to Analyze Mutations in V600 BRAF Oncogen in Participants With Metastatic Melanoma

Summary: This is a national, multicenter, cross-sectional epidemiological study in adult Spanish participants diagnosed with advanced or metastatic melanoma.


Eligibility: Inclusion Criteria:
  -  Valid tumor samples from participants diagnosed with Stage IIIc or IV melanoma
  -  Written informed consent granted
  Exclusion Criteria:
  - Do not fulfill one or more inclusion criteria

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Study of Efficacy and Safety of Dabrafenib and Trametinib Combination Therapy in Japanese Patients With BRAF V600E Stage IV NSCLC

Summary: This is an open-label, multicenter, non-randomized, single arm, phase II study to assess efficacy and safety of the dabrafenib and trametinib combination in Japanese patients with any line, stage IV NSCLC harboring a confirmed BRAF V600E mutation.
  Patients will receive oral dabrafenib twice daily and oral trametinib once daily combination therapy. Patients may continue study treatment until disease progression, unacceptable adverse events, start of a new anti-cancer therapy, consent withdrawal, death, or end of the study. Patients who have met the criteria for disease progression (PD) according to RECIST v1.1 may continue to receive study treatment if the investigator believes the patient is receiving clinical benefit and the patient is willing to continue on study treatment. After discontinuation of study treatment, all patients will be followed for survival until death, lost to follow-up, withdrawal of consent, or end of study.


Eligibility: Inclusion Criteria:
  -  Histologically- or cytologically-confirmed diagnosis of NSCLC stage IV (according to AJCC Staging 7th Edition)
  -  Presence of a BRAF V600E mutation in lung cancer tissue. BRAF V600E mutation tested by local laboratory (e.g. study center laboratory, local laboratory company) with proper quality control and license to operation by local health authority is allowed.
  -  Measurable disease according to RECIST v1.1.
  Exclusion Criteria:
  -  Previous treatment with a BRAF inhibitor (including but not limited to dabrafenib, vemurafenib, encorafenib, and XL281/BMS-908662) or MEK inhibitor (including but not limited to trametinib, cobimetinib, binimetinib, AZD6244, and RDEA119) prior to start of study treatment
  -  Patients with brain metastases are excluded if their brain metastases are:
  -  Symptomatic OR
  -  Treated (surgery, radiation therapy) but not clinically and radiographically stable 3 weeks after local therapy (as assessed by contrast enhanced magnetic resonance imaging [MRI] or computed tomography [CT]), OR
  -  Asymptomatic and untreated but >1 cm in the longest dimension
  -  History of malignancy with confirmed activating RAS mutation at any time.
  -  History of interstitial lung disease or pneumonitis
  -  A history or current evidence of retinal vein occlusion (RVO)
  -  Current evidence of unstable aneurysm or one that needs treatment
  Other protocol-defined inclusion/exclusion may apply.

Relevance to patient case: possibly relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Pre-procedure Planning for Radiofrequency Ablation Using CT or MR/US Fusion

Summary: The purpose of this study is to determine whether fusion technique of pre-radiofrequency ablation (RFA) cross-sectional imaging (CT or MR) and real-time ultrasonography would improve feasibility of RFA in patients with liver tumor in comparison with ultrasonography guidance alone.

Detailed description: RFA is one of commonly used local therapies for primary or secondary liver tumors. For successful and safe procedure, safe route of electrode and lesion visibility are essential for RFA, and the conditions are usually evaluated on pre-RFA planning ultrasonography (USG). However, RFA is sometimes aborted due to limited sonic window of various cause and challenging identification of small isoechoic tumors or hepatocellular carcinomas among dysplastic nodules . Therefore, precise targeting and assuring safe route would be of clinical importance. In this preliminary study, investigators attempted to determine US and CT/MR fusion technique would be able to improve RFA feasibility in patients with liver tumors in comparison with conventional US alone technique.

Eligibility: Inclusion Criteria: all conditions should be satisfied for inclusion.
  -  referred to Radiology in our institution for liver tumor RFA
  -  available pre-RFA liver CT or liver MR imaging within 6 weeks
  Exclusion Criteria: patients with any of following condition should be excluded.
  -  any contraindication of liver RFA
  -  any patients who received treatment between pre-RFA imaging and planned RFA
  -  patients referred for palliative purpose.

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

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

Summary: This study is a single arm, pilot study of Sorafenib in patient with BRAF mutation Refractory solid tumor and specific sensitivity to Sorafenib 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 Sorafenib 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
  -  BRAF mutation, Refractory solid tumor and/or specific sensitivity to Sorafenib 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>=100x 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 Sorafenib

Relevance to patient case: possibly relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF 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
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Circulating Tumor DNA Detection in Surveillance of Surgical Lung Cancer Patients

Summary: Conduct a prospective study to confirm blood and urine ctDNA detection value in non-small-cell lung cancer patients.

Detailed description: Studies have shown the feasibility of detecting mutation status by blood and urine circulating tumor DNA (ctDNA)in non-small cell lung cancer (NSCLC) patients. However, no prospective has been conducted for usage of ctDNA in postoperative surveillance of NSCLC patients.
  We plan to compare tumor makers and radiographic approaches with blood and urine ctDNA in surveillance to assess the lead time of postoperative tumor relapse in stage ⅢA NSCLC patients. And evaluate the correlation between ctDNA level with tumor relapse or metastasis.

Eligibility: Inclusion Criteria:
  -  Aged 18 to 80 years
  -  Undergo radical surgery（R0 resection）
  -  Histologically confirmed diagnosis of stage ⅢA non-small cell lung cancer
  -  Positive Driver mutation(EGFR、PTEN、PIK3CA、BRAF、K-RAS、Her2) in tumor tissue
  -  Blood or urine circulating tumor detect the driver mutation detected in tumor tissue
  -  Patients must have given written informed consent
  Exclusion Criteria:
  -  Unable to comply with the study procedure
  -  Malignant tumor history within the past 5 years
  -  Patients who received any treatment prior to resection
  -  R1 or R2 resection
  -  Coexisting small cell lung cancer
  -  Received target drug therapy after surgery
  -  Unqualified blood or urine samples

Relevance to patient case: possibly relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Tarceva With or Without Apatinib in the Advanced Lung Adenocarcinoma

Summary: Tarceva now was established first-line therapy for advanced lung adenocarcinoma with mutant EGFR patients.However,the benefit lasted for about 6-8 months.So we consider to add apatinib,a tyrosine kinase inhibitor of VEGF,to the therapy of these patients.

Detailed description: Lung adenocarcinoma is the most common NSCLC,most patient were diagnosed to advanced stage.The first-line therapy include chemotherapy of targeted therapy .Tarceva now was established first-line therapy for advanced lung adenocarcinoma with mutant EGFR patients.However,the benefit lasted for about 6-8 months.So we consider to add apatinib,a tyrosine kinase inhibitor of VEGF,to the therapy of these patients.We designed the study to find out whether the addition of apatinib to the Tarceva would enhance the efficacy of Tarceva.

Eligibility: Inclusion Criteria:
  -  lung adenocarcinoma proved by histology;with mutant EGFR;ECOG PS 0-2;Clinical stage IIIb or IV;without other fatal disease;without hemorrhagic disease;normal liver,renal and bone marrow function,not pregnant.
  Exclusion Criteria:
  -  ECOG PS 3-5;abnormal liver,renal and bone marrow function,pregnant;with severe diseases;wild type EGFR

Relevance to patient case: not relevant
Patient case: 54-year-old female with lung adenocarcinoma; genetic feature: SND1-BRAF fusion

Clinical trial: Using US to Evaluate Aortic Aneurysm Size Based on 3D Co-registration to Previous CT Scan

Summary: Examine a new method based on fusion between ultrasound (US) and previous ultrasound/computerized tomography(US/CT) studies to evaluate the size of abdominal aneurysm and measure the changes over time and following invasive repair procedure.

Detailed description: Selection test for assessing aortic aneurysm is CT angio, it performed after injection of contrast material and allows a complete demonstration of the blood vessels. This test exposes the patient to ionizing radiation and the injection of iodine contrast medium. Repeated tests pose a risk of developing a malignancy in the future due to the use of ionizing radiation and risk of renal impairment and allergic reactions due to the injection of contrast material. Ultrasound is another test that enables the detection and evaluation of aortic aneurysm. Patients with a known diagnosis of aortic aneurysm detected on CT are required to continuous monitoring in light of its growth over time and the risk of rupture.
  Using Co-registration over the US device will enable to conduct a US directed aorta examination, which uses the information produced from the CT as a "roadmap" for detection and localization of the aneurysm. That can theoretically improve detection capabilities and characteristics of the aneurysm and outcomes of the invasive treatment.

Eligibility: Inclusion Criteria:
  •Patients with abdominal aortic aneurysm diagnosis in clinical follow-up or after an invasive procedure to fix it.
  Exclusion Criteria:
  -  Inability to perform Ultrasound
  -  Pace maker
  -  Hemodynamic instability
  -  Inability to cooperate in US examination
  -  Pregnant Women - does not undergo CT

Relevance to patient case: not relevant