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

Clinical trial: A Study to Detect V-Raf Murine Sarcoma Viral Oncogene Homolog B1 (BRAF) V600 Mutation on Cell-Free Deoxyribonucleic Acid (cfDNA) From Plasma in Participants With Advanced Melanoma

Summary: This is a single arm, multicenter, open label, and non-randomized clinical study on adult participants with unresectable or metastatic melanoma. The study will be conducted in two phases. Pre-screening phase will assess the BRAF V600 mutation in a new mutation analysis triggered by a mutant plasma cfDNA test result. Treatment phase will assess the clinical outcome for the participants treated with vemurafenib plus cobimetinib. The length of the study will be approximately 38 months.


Eligibility: Inclusion Criteria:
  Pre-screening phase:
  -  Participants with histologically confirmed cutaneous melanoma, either unresectable Stage IIIc or Stage IV metastatic melanoma, as defined by American Joint Committee on Cancer 7th edition
  -  Documentation of BRAF V600 test result mutation-positive status on melanoma tumor tissue using a validated tissue test
  Treatment Phase:
  -  Eastern Cooperative Oncology Group performance status of 0-2
  -  Adequate hematologic and end organ function obtained within 14 days prior to first dose of study drug treatment
  -  Negative serum pregnancy test prior to commencement of dosing in women of childbearing potential
  -  Absence of any psychological, familial, sociological, or geographical condition that potentially hampers compliance with the study protocol and treatment regimen and follow-up after treatment discontinuation schedule
  -  Female participants of childbearing potential and male participants with partners of childbearing potential must agree to always use two effective forms of contraception during the course of this study and for at least 6 months after completion of study therapy
  -  Participants should be able to swallow tablets
  -  Documentation of BRAF mutation positive status in melanoma tissue
  Exclusion Criteria:
  Treatment Phase:
  -  History of prior rapidly accelerated fibrosarcoma or mitogen-activated protein kinase pathway inhibitor treatment
  -  Use of prior chemotherapy or immunotherapy (including treatment with an anti-programmed death 1, or anti- programmed death ligand 1 or anti-cytotoxic T-lymphocyte-associated protein 4 monoclonal antibody) within 4 weeks before first study drug administration
  -  Palliative radiotherapy within 14 days prior to the first dose of study treatment
  -  Evidence of retinal pathology on ophthalmologic examination
  -  Systemic risk factors for retinal vein occlusion
  -  History of clinically significant cardiac dysfunction
  -  Current severe, uncontrolled systemic disease
  -  Pregnancy, lactating or breast feeding
  -  Intake of St. John's wort or hyperforin (a potent cytochrome P450 3A4 [CYP3A4 enzyme inducer] and grapefruit juice (a potent CYP3A4 enzyme inhibitor) at least 7 days prior to initiation of and during the study treatment

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

Clinical trial: An Expanded Access Study of Brigatinib for Patients With ALK-positive Advanced Non-Small Cell Lung Cancer

Summary: The purpose of this study is to provide brigatinib for those patients with locally advanced and/or metastatic patients with ALK+ NSCLC on an expanded access basis due to their inability to meet eligibility criteria for on-going recruiting trials, inability to participate in other clinical trials (e.g., poor performance status, lack of geographic proximity), or because other medical interventions are not considered appropriate or acceptable.


Eligibility: Inclusion Criteria:
  1. Have histologically or cytologically confirmed locally advanced or metastatic NSCLC that is determined to have an ALK-rearrangement detected according to local standard procedure.
  2. Resistant to or intolerant of at least 1 prior ALK TKI.
  3. Recovered from toxicities related to prior anticancer therapy to NCI CTCAE, v4.0) grade ≤2.
  4. Are a male or female patient ≥18 years old.
  5. Have adequate organ and hematologic function, as defined by the study protocol.
  6. Have Eastern Cooperative Oncology Group (ECOG) performance status ≤2.
  7. Have normal QT interval on screening electrocardiogram (ECG) evaluation, defined as QT interval corrected (Fridericia) (QTcF) of ≤450 ms in males or ≤470 ms in females.
  8. For female patients of childbearing potential, a negative pregnancy test must be documented prior to enrollment (<7 days prior to the first dose).
  9. Female and male patients who are fertile must agree to use a highly effective form of contraception as defined by the study protocol.
  10. Must provide a signed and dated informed consent indicating that the patient has been informed of all pertinent aspects of the study, including the potential risks, and is willingly participating.
  Exclusion Criteria:
  1. Received an ALK TKI within 10 days prior to the first dose of brigatinib.
  2. Received cytotoxic chemotherapy, investigational agents, or radiation within 14 days, except stereotactic radiosurgery (SRS) or stereotactic body radiosurgery.
  3. Received prior brigatinib therapy.
  4. Received monoclonal antibodies within 30 days of the first dose of brigatinib.
  5. Had major surgery within 30 days of the first dose of brigatinib.
  6. Have current spinal cord compression.
  7. Have significant, uncontrolled, or active cardiovascular disease within 6 months prior to first dose, as defined by the study protocol.
  8. Have a history or the presence of pulmonary interstitial disease, drug-related pneumonitis, or radiation pneumonitis.
  9. Have a known or suspected hypersensitivity to brigatinib or its excipients.
  10. Have any condition or illness that, in the opinion of the investigator, would compromise patient safety.
  11. Are pregnant or breastfeeding.
  12. Are eligible for and have reasonable access to participate in another ongoing brigatinib clinical study.

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

Clinical trial: Association of Bone and Metabolic Parameters With Overall Survival in Patients With Bone Metastases From Adenocarcinoma Lung Cancer (POUMOS)

Summary: Mortality due to non small cell lung cancers is the first cause of cancer death in men around the world. Lung adenocarcinoma regularly induces bone metastases responsible for high morbidity and impaired life quality. Overall survival of these patients is poor. Thus the investigators aimed to identify if some bone and metabolic parameters were associated with overall survival.
  Patients and Methods POUMOS is a prospective cohort of patients suffering from adenocarcinoma lung cancers with a first bone metastasis (stage IV). All patients have a bone biopsy with molecular status characterization of the tumor for EGFR, KRAS, BRAF and ALK. Bone metastasis localizations are obtained by bone scintigraphy or FDG-PET/CT. Whole body composition is obtained by DEXA scan (Hologic®). The investigators assessed also fasting blood levels of bone and metabolic biomarkers.
  Survival analyses will be performed using a proportional hazard regression model.


Eligibility: Inclusion Criteria:
  -  adults over 18 years
  -  both gender
  -  covered by the French National Insurance
  -  first bone metastases of adenocarcinoma lung cancer (synchronous or metachrone)
  Exclusion Criteria:
  - adenocarcinoma previously treated by systemic oncologic treatment (chemotherapy, targeted therapy, immunotherapy)

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

Clinical trial: Molecular Analysis of 150 Lung Adenocarcinoma

Summary: LUNG-EST is a retrospective study including 152 patients who benefit from lung surgery during the years 2012 to 2013 at Hospices civils de Lyon and with a diagnosis of lung adenocarcinomas. For all patients, clinical data and histopathological data are available. The objective of this study is to characterize these lung adenocarcinomas by the LungCarta Panel using the mass spectrometry array Sequenom. This panel could identify 214 DNA mutations and/or frameshift insert/deletion among 26 oncogenes. Once included in the study, the adenocarcinomas are also included in a Tissue MicroArray (TMA) in order to perform immunohistochemical analysis. Immunohistochemical staining with innovative antibodies are correlated with clinical, histopathological and molecular data.
  Our hypothesis is that this TMA could constitute a good tool to screen interesting protein's expression.


Eligibility: Inclusion Criteria:
  -  Adults
  -  lung adenocarcinoma
  -  Surgical specimen
  Exclusion Criteria:
  -  not adenocarcinoma subtype of lung cancer
  -  Tumour biopsy
  -  insufficient material for DNA extraction

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

Clinical trial: Chemotherapy Plus Gefitinib for Advanced Lung Adenocarcinoma and Sensitive EGFR Mutations: a Randomized Controlled Trial

Summary: The purpose of this study is to compare chemotherapy and gefitinib in combination with gefitinib alone as first-line therapy for adenocarcinoma, in terms of efficacy and safety.

Detailed description: The primary endpoints is to compare the progression-free survival (PFS) of pemetrexed plus carboplatin combined with gefitinib to gefitinib alone as first-line therapy for lung adenocarcinoma.
  In addition, the overall survival and safety index will be collected for analyses.

Eligibility: Inclusion Criteria:
  1. Patients had to voluntarily join the study and give written informed consent for the study;
  2. Histologically documented, unresectable, inoperable, locally advanced, recurrent or metastatic stage IIIB or IV Non-Small Cell Lung Cancer (NSCLC);
  3. A cytologic diagnosis is acceptable (FNA or pleural fluid cytology)
  4. Sensitive EGFR mutations (19del, 21L858R);
  5. At least 1 unidimensionally measurable lesion meeting Response Evaluation Criteria in Solid Tumours (RECIST) criteria;
  6. Patients did not receive systemic anti-cancer therapy previously;
  7. Able to comply with study and follow-up procedures;
  8. Age >= 18 years, ECOG PS: 0-1, estimated survival duration more than 3 months;
  Exclusion Criteria:
  1. Small cell lung cancer (including patients with mixed small cell lung cancer and non-small cell lung cancer);
  2. Evidence of small cell, carcinoid, or mixed small cell/non-small cell histology;
  3. EGFR wild-type patients, or patients with rare EGFR mutations or complex EGFR mutations;
  4. Previously (within 5 years) or presently suffering from other malignancies, except for cured cervical carcinoma in situ, non-melanoma skin cancers and superficial bladder cancer [Ta (noninvasive carcinoma), Tis (carcinoma in situ) and T1 (invasion into lamina propria)];
  5. Symptomatic or untreated brain metastases;
  6. Unstable systemic disease, including active infection, uncontrolled hypertension, unstable angina, congestive heart failure, or myocardial infarction within 6 months prior to Day 1, or serious cardiac arrhythmia requiring medication (patients with chronic atrial arrhythmia, i.e., atrial fibrillation or paroxysmal supraventricular tachycardia, are eligible);
  7. History of other diseases, metabolic dysfunction, physical examination finding, or clinical laboratory finding giving reasonable suspicion of a disease or condition that contraindicates the use of an investigational drug or that might affect the interpretation of the results of the study or render the patient at high risk from treatment complications;
  8. Gastrointestinal tract disease resulting in an inability to take oral medication or a requirement for intravenous (IV) alimentation, or prior surgical procedures affecting absorption;
  9. Pregnancy or lactation.

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

Clinical trial: Pre-procedure Planning for Liver Biopsy or Radiofrequency Ablation Using CT or MR/US Fusing Imaging

Summary: The purpose of this study is to determine whether fusion technique of preradiofrequency ablation (RFA) or percutaneous liver biopsy cross-sectional imaging (CT or MR) and real-time ultrasonography would improve feasibility of RFA or liver biopsy in patients with liver tumor in comparison with ultrasonography guidance alone. And assessment of a new point shear-wave elastography method (pSWE, S-shear wave) and compare its accuracy in assessing liver stiffness (LS) with another pSWE technique (ARFI).

Detailed description: RFA is one of commonly used local therapies for primary or secondary liver tumors. And percutaneous liver biopsy is very important technique to confirm the diagnosis of focal hepatic lesion whether benign or malignancy.
  For successful and safe procedure, safe access route and lesion visibility are essential , and the conditions are usually evaluated on pre-procedure planning ultrasonography (USG). However, these procedure 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 or liver biopsy feasibility in patients with liver tumors in comparison with conventional US alone technique.
  In addition, to assess intra- and inter-observer reproducibility of a new point shear-wave elastography method (pSWE, S-shear wave) and compare its accuracy in assessing liver stiffness (LS) with another pSWE technique (ARFI).

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

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

Clinical trial: A Phase Ib Study of LXH254-centric Combinations in NSCLC or Melanoma

Summary: To characterize safety and tolerability and identify a recommended dose and regimen for the LXH254 in combination with LTT462 or trametinib or ribociclib.


Eligibility: Inclusion Criteria:
  -  Patients must have advanced or metastatic NSCLC or melanoma
  -  Presence of KRAS or BRAF mutation (NSCLC) or NRAS mutation (melanoma) in tumor tissue
  -  All patients participating in this clinical trial must have progressed following standard therapy or, in the opinion of the Investigator, no effective standard therapy exists, is tolerated, appropriate or is considered equivalent to study treatment.
  -  ECOG (Eastern Cooperative Oncology Group) performance status ≤ 2
  Exclusion Criteria:
  -  Dose expansion - KRAS or NRAS mutant patients groups: Prior treatment with a RAFi (including any BRAFi and pan-RAFi), MEKi and/or ERKi. BRAF mutant patients group: Prior treatment with an ERKi and/or a pan-RAFi.
  -  History or current evidence of retinal vein occlusion (RVO) or current risk factors for RVO.
  -  Any medical condition that would, in the investigator's judgment, prevent the patient's participation in the clinical study due to safety concerns or compliance with clinical study procedures.
  -  Patients receiving proton pump inhibitors (PPI) which cannot be discontinued 3 days prior to the start study treatment and for the duration of the study.
  -  Patients with Gilbert's syndrome or other heritable diseases of bile processing.
  Other protocol-defined inclusion/exclusion criteria may apply

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

Clinical trial: Poziotinib in Stage IV Lung Adenocarcinoma With HER2 Mutation (KASTT001)

Summary: In this trial, treatment efficacy and safety of Poziotinib will be assessed in patients with stage IV lung adenocarcinoma harboring HER2 mutation.

Detailed description: This study is designed to be multi-center, open-label, single-arm, prospective, phase II trial of patient with stage IV lung adenocarcinoma with HER2 mutation who have not received prior EGFR-TKI. Approximately 47 patients will be enrolled into the trial, and expected study duration is 36 months from IRB and Korea: MFDS approval date.
  The study drug(poziotinib) will be administered orally as one 12 mg tablet once a day until disease progression or manifestation of unacceptable toxicity. The initial dose of the study drug 12 mg daily can be reduced to 8 mg once daily according to dose reduction criteria in protocol. A cycle of study treatment is defined as 28 days.

Eligibility: Inclusion Criteria:
  1. lung adenocarcinoma, stage IV
  2. Patients with HER2 mutation by sequencing
  - Confirmed triple-negative patients with remnant tumor DNA
  3. Patients who have histories of previous exposure to at least one more systemic chemotherapies (not EGFR-TKI)
  4. ECOG performance status 0~2
  5. Patient with at least one measurable lesions according to RECIST
  6. Patients who have proper organ functions as follows
  -  Neutrophil count: > 1,500/uL
  -  Platelet count: > 100,000/uL
  -  Hb: > 9.0g/dL
  -  AST/ALT : < 2.0 x upper normal limit
  -  Bilirubin: < 1.25 x upper normal limit
  -  Serum creatinine : < upper normal limit
  Exclusion Criteria:
  1. Expected lie expectancy < 3 months
  2. CNS metastasis or spinal cord compression which were not treated with operation and/or radiation therapy(but, Patient with medically stable condition after operation and/or radiation therapy, or without symptomatic metastasis of brain in accordance with the investigator's judgment could participate in the study)
  3. Patients who have severe or unstable systemic disease in accordance with the investigator's judgment(ex, unstable or uncompensated respiratory, cardiac, hepatic or renal disease)
  4. Patients who have histories of previous exposure to EGFR-TKI

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

Clinical trial: Early Rebiopsy to Identify Biomarkers of Tumor Cell Survival Following EGFR, ALK, ROS1 or BRAF TKI Therapy

Summary: A comparison of baseline tumor characteristics in oncogene-driven cancers to tumor characteristics after early response to Tyrosine Kinase Inhibitor (TKI) targeted treatment will allow identification of early adaptive mechanisms of cell survival. This will facilitate targeting and termination of these survival/ resistance pathways before they develop with rational combinations of therapeutic agents to improve outcomes.


Eligibility: Inclusion Criteria:
  -  Carry a diagnosis of stage IV lung adenocarcinoma with an activating mutation determined to respond to an estimated glomerular filtration rate (EGFR) TKI, alkaline phosphatase (ALK) or ROS Proto-Oncogene 1 (ROS1) fusion or BRAF V600E.
  -  Aged 18 - 85 years or older
  -  ECOG 0-2
  -  Have a histologically confirmed diagnosis of lung adenocarcinoma harboring an EGFR sensitizing mutation (including, but not limited to: G719X, del exon 19, or L858R).
  -  No prior therapy for metastatic disease.
  -  Planned treatment with a single agent EGFR TKI including but not limited to:
  1. erlotinib,
  2. gefitinib,
  3. rociletinib (CO-1686),
  4. afatinib, or
  5. osimertinib (AZD-9291).
  -  Patients must have at least one site of measurable disease ≥ least 2cm.
  -  Primary disease site or site of metastatic disease must be amenable to biopsy.
  -  Patients must have the ability to understand and willingness to sign an informed consent document.
  -  Patients must be willing to undergo an initial pre-treatment biopsy of tumor tissue (or have previously collected frozen tissue) and a follow-up biopsy 2 weeks (+/- 1 week) after treatment start
  Exclusion Criteria:
  -  Concurrent health problem which would preclude tissue biopsy (eg hemophilia or other bleeding predisposition).
  -  Patients whose only source of biopsiable disease is:
  1. intracranial,
  2. pleural effusion or any lesion that is deemed unsafe to biopsy by the treating physician or,
  3. interventional radiology.

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

Clinical trial: Therapeutic ResistAnce and Clonal Evolution Assessed With Liquid Biopsy of NSCLC Patients in China

Summary: To evaluate the concordance of sensitizing mutations detected between paired plasma and tissue samples; the correlation between the clonal status of sensitizing mutations and targeted therapy response; and the prognostic impact of the relative abundance of sensitizing / resistance mutations.

Detailed description: In the study, 500 advanced NSCLC patients will be recruited. All the patients will receive biopsy genotype assay and circultating tumor DNA (ctDNA) liquid biopsy. Patients who carry actionable EGFR mutation, ROS1 fusion, ALK fusion or MET exon 14 skipping mutation will receive TKI treatment according to guidelines. During the TKI treatment, every patients will take liquid biopsy assay to monitor the mutation status. The study will be ended when all the patients had a progressive disease (PD) in their targeted lesion.

Eligibility: Inclusion Criteria:
  -  Provision of informed consent
  -  Newly diagnosed and histological or cytological confirmed stage IIIB-IV lung adenocarcinoma or non-smoking squamous cell carcinoma patients according to the AJCC staging system. The stage IV lung cancer and brain metastasis can be diagnosed by imaging and enhanced CT respectively
  -  ECOG performance status 0-2 with expected more than 6 months of survival time
  -  Willingness to comply with required protocols and give permission to use the data for clinical research and products development
  Exclusion Criteria:
  -  Patients have other primary cancers
  -  Patients have symptomatic brain metastasis, complications that are associated with brain metastasis or cognitive disorders
  -  Patients failed in either plasma or tissue sample QC

Relevance to patient case: not relevant