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

Clinical trial: Analysis of Plasma Tumor DNA in Lung Cancer Patients

Summary: The presence of genetic alterations in the tyrosine kinase domain of the oncogene (eg. EGFR and ALK) is associated with the clinical response to tyrosine kinase inhibitors (TKIs) in patients with non-small cell lung cancers. Therefore, the detection of altered genetic alterations is useful for predicting the treatment response for TKIs in non-small cell lung cancer patients. However, good quality tumor tissues are available only in <50% of patients with inoperable lung cancer for mutation analysis. In this study, the investigators will detect and quantify the genetic alterations in plasma. the investigators will investigate if the serial measurement of cancer-derived genetic alterations in plasma can provide a means for monitoring disease progression, as well as treatment response. In addition the investigators will analysis the resistant mechanism of TKIs and chemotherapy with plasma tumor DNA.


Eligibility: Inclusion Criteria:
  -  Have a histologically or cytologically confirmed diagnosis of non-small cell lung cancer
  -  Have molecular evidence of genetic alterations in tumor sample (eg. EGFR mutations, ALK fusions)
  -  Patients must have given written informed consent
  Exclusion Criteria:
  -  Patients who refuse the blood samplings

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

Clinical trial: Treatment of Multifocal Lung Adenocarcinoma

Summary: To gather preliminary safety and outcome data for the multimodality treatment of lung adenocarcinoma in the setting of multifocal BAC.

Detailed description: Lung bronchoalveolar carcinoma (BAC) or adenocarcinoma in situ (AIS) continues to represent a poorly understood clinical entity. A frequent clinical dilemma in lung cancer care is the management of a documented or suspected invasive adenocarcinoma in the setting of multifocal ground glass opacity (GGO) consistent with multifocal AIS. These patients are typically classified as stage IV disease, and treated with palliative chemotherapy. No existing pathologic or molecular test is currently capable of making the distinction between independent primary versus metastatic tumors, a distinction for which substantial treatment impact exists. Many treating physicians suspect that outcomes for this specific patient subgroup are better than norms for stage IV disease, as such patients are frequently node-negative and without distant metastases despite multiple lesions present. To address this issue, we will evaluate a multimodality treatment protocol using aggressive local and targeted systemic therapy for multifocal lung adenocarcinoma, incorporating information from tumor genome sequencing for individualized treatment planning. The results will have significant impact in advancing the biologic understanding and treatment approach for lung adenocarcinoma in the setting of multifocal AIS.

Eligibility: -  Patient must be > 18 years of age
  -  Two or more GGO's or solid lesions suspicious for multifocal disease.
  -  Clinical diagnosis of N0
  -  No evidence of distant metastases
  -  No prior intra-thoracic radiation therapy (NOTE: Previous radiotherapy as part of treatment for head and neck, breast, or other non-thoracic cancer is permitted.), previous chemotherapy, or surgical resection for non-small cell lung cancer (NSCLC).
  -  No other cancer in the past 5 years except early stage prostate cancer, or basal cell of skin.
  -  PFT's that show patient is capable of tolerating a lung resection.
  -  Non-pregnant and non-lactating. Women of child-bearing potential must have a negative urine or serum pregnancy test to participate in the study.
  -  Patient must be able to understand and willing to sign an IRB-approved informed consent document.

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

Clinical trial: A Retrospective Pharmacogenomics Research of EGFR-TKIs,Gefitinib and Erlotinib, in NSCLC Patients Treatment

Summary: For patients of advanced NSCLC (non small cell lung cancer) , Individualized cancer therapy has been widely accepted since the success of crizotinib administration based on EML4-ALK fusion gene detection and gefitinib and erlotinib administration based on EGFR-TKIs sensitive mutations.From clinical points of view ,individual differences often occur between different patients, leading diverse effect in ADR and drug effect.Meanwhile ,the drug effect and adverse drug reaction was significantly influenced by the pharmacokinetic factors and pharmacodynamic factors.In this research ,we try to establish a more sensitive method to detect sensitive mutations in plasma and discover the correlation between somatic and germline mutations , trough concentration and EGFR-TKI drug effect, the association between ADME-associated SNP ,trough concentration and EGFR-TKI adverse effect .Furthermore, in vivo and in vitro research is also crucial for rational explanation for these clinical phenomenon.

Detailed description: The ADME-associated SNPs included are CYP3A4,CYP3A4,CYP1A1,CYP2D6, ABCB1,ABCG2 and so on .The somatic mutations included are EGFR ,K-RAS ,ALK and so on

Eligibility: Inclusion Criteria:
  The main patient entry criteria included: age≥ 18 years ; histologically and cytologically proved NSCLC; Eastern cooperative oncology group performance status (ECOG PS)≤2; adequate hematological , renal, and hepatic functions. Exclusion Criteria:
  uncontrolled systemic disease ,any evidence of clinically active interstitial lung diseases, and other chemotherapy at the time of inclusion. The protocol was approved by the Ethical Committee of Cancer Center of Sun Yat-Sen University (CCSU), and written informed consent was obtained form each patient.

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

Clinical trial: Comparison of qPCR to IHC and FISH for Detection of ALK Fusion Mutations in FFPE Tissue From NSCLC Patients

Summary: The anaplastic lymphoma kinase gene(ALK) is mutated approximately 5% of non-small cell lung cancers. Testing for this gene is important because there are drugs known as ALK inhibitors that have been shown to significantly delay the progression of ALK-mutated lung cancers. There are a number of ways to test for the presence of the ALK gene in lung cancer biopsy tissue. One method involves making slides and staining them to detect the ALK protein. This is called immunohistochemistry. Another method called fluorescence in situ hybridization(FISH)is used to detect rearrangements of the ALK gene associated with lung cancer. Although both these tests are widely used to test for ALK gene abnormalities, the techniques may not always find the ALK gene mutation because they are not sensitive enough or not enough cancer cells are present in the lung biopsy.
  This study is being performed to determine if a technique called quantitation polymerase chain reaction (qPCR) is as accurate or better at finding the ALK gene mutation in lung cancer biopsy tissue.


Eligibility: Inclusion Criteria:
  -  You have a confirmed diagnosis of non-squamous, non-endocrine non-small cell lung cancer.
  -  Your cancer biopsy has sufficient cancer cells to be tested for the (Epidermal Growth Factor Receptor (EGFR) mutation, the ALK fusion gene abnormality and the research ALK testing.
  -  Your lung cancer biopsy is determined not to have a mutation in the EGFR gene.
  -  You are 19 years old or older.
  -  You fully understand the study and give informed consent to participate as demonstrated by signing the consent.

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

Clinical trial: Comparison of cVATS Segmentectomy Versus Lobectomy for Lung Adenocarcinoma in Situ and With Microinvasion

Summary: This is a Prospective, open-label, parallel, multi-center, Phase III randomized trial to evaluate the efficacy and safety of video-assisted thoracoscopic segmentectomy versus Lobectomy in treating patients with Lung adenocarcinoma in situ or with microinvasion.

Detailed description: Lobectomy has long been considered the standard procedure for early-stage lung cancer, and minimally invasive techniques have been demonstrated to be associated with superior outcomes compared with lobectomy by thoracotomy. the us of segmentectomy is under investigation for selected patients with small tumors, and the use of minimally invasive strategies is applicable as well.
  This nationwide, multicenter, prospective, randomized open phase III study of cVATS (complete Video-assisted Thoracoscopic Surgery) segmentectomy versus Lobectomy for stage IA non-small cell lung cancer (NSCLC) patients with Lung adenocarcinoma in situ or with microinvasion, is aiming to evaluate the relapse free survival and 5 year overall survival (OS) rate of two types of surgery. Patients are randomized to 1 of 2 treatment arms.
  -  Arm I: Patients undergo cVATS lobectomy.
  -  Arm II: Patients undergo cVATS segmentectomy.
  Patients will be followed up every 3 months within the first year, and annually for 5 years postoperatively.

Eligibility: Inclusion Criteria:
  Preoperative criteria: peripheral non-small cell lung cancer, no larger than 2 cm in maximal diameter, no lymph node metastasis, FEV1%>50% (FEV1: Forced Expiratory Volume in 1 second);
  Preoperative imaging:pure ground-glass or mixed ground-glass nodules (part-solid, solid areas < 0.5cm);
  Follow-up duration last 3 months or more, HRCT (HRCT: high-resolution computed tomography) lesion maximum diameter was measured three times and took the average, meet the criteria of clinical surgical indications;
  Intraoperative criteria: histologically confirmed NSCLC, adenocarcinoma in situ or with microinvasion;
  No prior ipsilateral thoracotomy;
  No prior anti-neoplastic therapy;
  EOCG Performance status 0-2;
  Sufficient organ functions;
  Written informed consent.
  Exclusion Criteria:
  Active bacterial or fungous infection;
  Simultaneous or prior (within the past 5 years) other malignant disease;
  Interstitial pneumonitis, pulmonary fibrosis, or severe COPD (COPD: chronic obstructive pulmonary disease);
  Abnormal Psychosis;
  Uncontrollable diabetes mellitus;
  History of severe cardiovascular disease;
  Any condition which, in the opinion of the investigator might interfere with the evaluation of the objective.

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

Clinical trial: Sequential Icotinib Plus Chemotherapy Versus Icotinib Alone as First-line Treatment in Stage IIIB/IV Lung Adenocarcinoma

Summary: This randomised, controlled, multicentre trial is designed to assess the efficacy and safety of sequential icotinib plus chemotherapy versus single icotinib as first-line treatment in stage IIIB/IV lung adenocarcinoma patients with EGFR mutation.


Eligibility: Inclusion Criteria:
  -  Pathologic confirmation of lung adenocarcinoma with measurable disease, defined as at least one lesion that can be accurately measured in at least one dimension (longest diameter to be recorded on CT)
  -  Patients must have previously untreated locally advanced or metastatic NSCLC
  -  EGFR activating mutation (exon 19 deletion, L858R) is required
  -  Eastern Cooperative Oncology Group performance status (ECOG PS) score of 0 or 1
  Exclusion Criteria:
  -  Prior chemotherapy or treatment with gefitinib, erlotinib, or other drugs that target EGFR
  -  Patients with wild-type EGFR
  -  Any other investigational agents are not permitted
  -  Any evidence of interstitial lung disease

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

Clinical trial: Efficacy and Safety of LGX818 in Patients With Advanced or Metastatic BRAF V600 Mutant NSCLC

Summary: This is an open-label, multi-center, single arm phase II study to evaluate the efficacy and safety of novel BRAF (B-raf murine sarcoma viral oncogene homolog B1) inhibitor encorafenib (LGX818) when used as single agent in patients with advanced or metastatic (stage IIIB or IV) BRAF V600 mutant NSCLC. Patients must have progressed on or after at least one previous systemic, anti-cancer therapy for locally advanced or metastatic NSCLC.


Eligibility: Inclusion Criteria:
  -  Presence of BRAF V600E mutation in tumor tissue
  -  Histologically or cytologically confirmed diagnosis of Stage IIIB or IV NSCLC
  -  At least one measurable lesion as defined by RECIST v1.1
  -  Patients must have progressed during or after at least one previous systemic, anti-cancer treatment for locally advanced or metastatic NSCLC.
  -  Eastern Cooperative Oncology Group (ECOG)/World Health Organization (WHO) performance status 0-2
  Exclusion Criteria:
  -  Patients with symptomatic Central Nervous System (CNS) metastases
  -  History of leptomeningeal metastases
  -  Prior therapy with a BRAF inhibitor
  -  Patients taking prohibited medication listed in the protocol
  -  Presence or history of a malignant disease other than NSCLC that has been diagnosed and/or required therapy within the past 3 years.
  -  Impaired cardiovascular function or clinically significant cardiovascular diseases
  -  Pregnant or lactating women or woman of childbearing potential

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

Clinical trial: Icotinib Versus Placebo as Adjuvant Therapy in EGFR-mutant Lung Adenocarcinoma

Summary: The purpose of this study is to compare 3years of disease-free survival (DFS) of Icotinib and placebo in the treatment of patients who EGFR mutation-positive II-IIIA lung adenocarcinoma.

Detailed description: This study is designed to compare 3 years of disease-free survival (DFS) of Icotinib and placebo in the treatment of patients who EGFR mutation-positive II-IIIA lung adenocarcinoma.
  Primary Outcome Measure:
  Disease-free survival between Icotinib group and placebo group.
  Secondary Outcome Measures:
  Overall survival between Icotinib group and placebo group. Lung cancer symptoms and health-related quality of life (HRQoL) . Number of participants with adverse events.

Eligibility: Inclusion Criteria:
  -  Pathologically confirmed lung adenocarcinoma after surgical resection
  -  Stage II-IIIA disease according to 7th edition of TNM staging
  -  Patients must harbor sensitive EGFR gene mutation (19/21)
  -  Received four cycles of platinum-based adjuvant chemotherapy.There are many different kinds of chemotherapy regimens including vinorelbine, gemcitabine, docetaxel, paclitaxel, pemetrexed plus cisplatin or carboplatin.The first cycle of chemotherapy with cisplatin dose of 75 mg / m2 ± 10% or carboplatin AUC = 5 ± 10% to calculate the dose of chemotherapy
  Exclusion Criteria:
  -  Previous systemic anti-tumor therapy, including chemotherapy or targeted therapy(Including but not limited to monoclonal antibodies, small molecule tyrosine kinase inhibitor, etc
  -  Presence of metastatic disease
  -  Other co-existing malignancies or malignancies diagnosed within the last 5 years with the exception of basal cell carcinoma or cervical cancer in situ
  -  Any unresolved chronic toxicity from previous anticancer therapy
  -  Received antitumor radiation therapy (except for the stage IIIA N2 patients who received adjuvant radiotherapy after surgery)

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

Clinical trial: An Observational Study of BRAF Inhibitors Effectiveness in Patients With Newly Diagnosed Metastatic Melanoma

Summary: This observational study will evaluate the effectiveness of BRAF inhibitors and current therapies in patients with newly diagnosed metastatic melanoma with or without BRAF V600 mutation. Patients will be treated per the locally approved therapeutic options in clinical practice. The observation period for each patient will be up to 24 months.


Eligibility: Inclusion Criteria:
  -  Adult patients, >/= 18 years of age at diagnosis
  -  Histologically confirmed new diagnosis of unresectable or metastatic melanoma
  -  Patients with tumor samples available for assessment of BRAF V600 mutation
  Exclusion Criteria:
  -  Prior systemic therapy for metastatic disease
  -  Participation in interventional clinical trials

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

Clinical trial: The Oncopanel Pilot (TOP) Study

Summary: The BCCA Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes.
  The purpose of this pilot study is to assess the feasibility and effect on clinical-decision-making of the Oncopanel test. Eligible patients are those with advanced lung, colorectal, melanoma and GIST cancers and patients with diagnosed malignancies being considered for clinical trials.

Detailed description: Somatic mutations in solid tumors represent an established means of characterizing malignancies for prognostic, diagnostic and therapeutic purposes. Mutations in EGFR, KRAS, BRAF, and KIT and PDGFRA genes direct therapy in patients with advanced lung, colorectal, melanoma, and GIST tumors, respectively. Known or novel mutations in other genes may also be of clinical significance but are not identified by current genotyping offered to BC Cancer Agency (BCCA) patients. Furthermore, numerous candidate genes have been implicated as potential prognostic and predictive biomarkers in patients with solid tumours. As such, the Oncopanel is a clinical assay being developed to determine genotype status of a prospectively defined set of genes. The following clinically relevant set of genes and exons are included in the Oncpanel: KRAS, EGFR, BRAF, NRAS and HRAS, PIK3CA Signal Transduction Pathway Genes, RAS-RAF-MEK-MAPK Pathway, HER2, IDH1 and IDH2, ALK, TP53, c-KIT, STAT1&3 and PDGFRA. Additional testing on the tumour material will also include analysis of specific gene variants associated with adverse events or response to therapy.
  Numerous studies have documented the presence of circulating tumour DNA (ctDNA) among patients with advanced and early stage malignancies (20-22). The ability to diagnose standard cancer mutations with a blood-based assay (a "liquid biopsy") has not yet been established but presents obvious advantages. The emergence of "resistance" mutations arising in the metastatic tumor or throughout the course of therapy is well documented (21, 22). A blood biopsy may represent more accurate determination of the tumor's genetic features than archival DNA specimen. Adequate tissue specimens can be difficult to obtain from some patients with diagnosed malignancies, particularly lung cancer. A blood biopsy may represent a less invasive and timelier means of diagnosing both standard and translational cancer mutations.

Eligibility: Patients with archival tumor tissue and a known history of invasive malignancies are eligible if they meet one or more of the following criteria:
  -  Advanced colorectal cancer and eligible for standard KRAS testing,
  -  Advanced non-small cell lung cancer and eligible for standard EGFR testing,
  -  Advanced melanoma and eligible for standard BRAF testing,
  -  Gastrointestinal stromal tumors (GISTs) eligible for standard c-KIT and PDGFRA testing,
  -  Being considered for potential eligibility in clinical trial.

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

Clinical trial: Detection of Oncogenic Tumor Mutations in the Urine and Blood of Lung and Colorectal Cancer Patients

Summary: The purpose of this study is to see whether gene mutations can be found in the urine or blood of lung cancer patients and urine of colorectal cancer patients. Gene mutations are when DNA in a gene is damaged in a way that changes the genetic message carried by that gene. Gene mutations can sometimes cause lung cancers. These gene mutations are only found in lung and colorectal cancer cells, not the normal cells in your body. All lung cancer tumors and colorectal cancer tumors are now tested for different gene mutations as their presence affects lung cancer treatment. Tumor samples obtained from a biopsy or surgery are typically tested for these gene mutations.


Eligibility: Inclusion Criteria:
  Lung cancer:
  For patients participating in Part A (initial testing) and Part B (serial testing):
  -  Patients must have a diagnosis of stage IV lung adenocarcinoma undergoing systemic therapy.
  -  Patients must have had or intend to have EGFR mutation testing (specifically including exon 19 deletions and L858R) performed on their tumor with results available from a CLIA certified laboratory.
  -  ≥ 18 years of age
  Specific to patients participating in Part B (serial testing):
  -  Patients must be planning to receive cancer care at Memorial-Sloan Kettering.
  -  Patients must have a confirmed EGFR mutant lung cancer (exon 19 deletions and L858R) with molecular testing results available from a CLIA certified laboratory.
  -  Must be within 3 months of their diagnosis of metastatic lung cancer.
  -  Treatment plan should include an EGFR tyrosine kinase inhibitor, but may concurrently be on a therapeutic protocol.
  Colorectal Cancer:
  For patients participating in Part A (initial testing) and Part B (serial testing):
  -  Patients must have a diagnosis of stage IV colorectal adenocarcinoma undergoing systemic therapy or have recently progressed on therapy including anti-EGFR based therapy.
  -  Patients must have had or intend to have RAS/RAF mutation testing on their tumor with results available from a CLIA certified laboratory. For the patients who recently progressed on anti-EGFR must have tumor tissue molecular analyses preformed (prior to enrolling or a plan to test it at the time of enrollment).
  -  >18 years of age
  Specific to patients participating in Part B (serial testing):
  -  Patients must be planning to receive cancer care at Memorial-Sloan Kettering.
  -  Patients must have a confirmed RAS/RAF mutant colorectal cancer with molecular testing results available from a CLIA certified laboratory.
  -  Must be within 3 months of their diagnosis of metastatic colorectal cancer.
  Exclusion Criteria:
  lung cancer and colorectal cancer
  -  Comorbidities that would prohibit or make serial urine collection difficult or impossible

Relevance to patient case: possibly relevant