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  • Gene br and bioinformatics tools for

    2020-08-12

     Gene 712 (2019) 143961
    and bioinformatics tools for identification of RNA based theranostic markers thus can be useful for clinical as well as computational cost minimization in future and can be exploited in any other disease models. Supplementary data to this article can be found online at https:// doi.org/10.1016/j.gene.2019.143961.
    Declaration of Competing Interest
    The authors declare no competing interests.
    Acknowledgments
    B acknowledges funding from Indian Institute of Technology Madras as Institute Postdoctoral Fellow.
    Authors' contribution
    SB and DK both conceptualized the work and wrote the manuscript together while SB performed the analyses.
    References
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    TANRIC: an interactive open platform to explore the function of lncRNAs in cancer.
    Wanichwatanadecha, P., Sirisrimangkorn, S., Kaewprag, J., Ponglikitmongkol, M., 2012.
    S. Banerjee and D. Karunagaran
    medicine : official publication, Society of Nuclear Medicine 45, 22–29.
    www.transonc.com
    An Integrated Next-Generation Sequencing System for Analyzing DNA Mutations, Gene Fusions, and RNA Expression in Lung Cancer1
    Brian C. Haynes*, Richard A. Blidner*, Robyn D. Cardwell*, Robert Zeigler*, Shobha Gokul*, Julie R. Thibert*, Liangjing Chen*, Junya Fujimoto†, Vassiliki A. Papadimitrakopoulou‡, Ignacio I. Wistuba† and Gary J. Latham*
    * Asuragen, Inc., Austin, TX, USA; †Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;
    ‡Department of Thoracic/Head and Neck Medical Oncology, Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
    Abstract
    We developed and characterized a next-generation sequencing (NGS) technology for streamlined analysis of DNA and RNA using low-input, low-quality cancer specimens. A single-workflow, targeted NGS panel for non–small cell lung cancer (NSCLC) was designed covering 135 RNA and 55 DNA disease-relevant targets. This multiomic panel was used to assess 219 formalin-fixed paraffin-embedded NSCLC surgical resections and core needle biopsies. Mutations and expression phenotypes were identified consistent with previous large-scale genomic studies, including mutually exclusive DNA and RNA oncogenic driver events. Evaluation of a second cohort of low cell count fine-needle aspirate smears from the BATTLE-2 trial yielded 97% agreement with an independent, validated NGS panel that was used with matched surgical specimens. Collectively, our data indicate that broad, clinically actionable insights that previously required independent assays, workflows, and analyses to assess both DNA and RNA can be conjoined in a first-tier, highly multiplexed NGS test, thereby providing faster, simpler, and more economical results.
    Introduction
    In the last decade, next-generation sequencing (NGS) has precipitated a paradigm shift in clinical molecular pathology from single-gene tests to multigene panels. As a technology, it has doubled as a basic research workhorse as well as a platform for routine clinical diagnostics. Research consortia such as The Cancer Genome Atlas (TCGA) have applied broad NGS profiling to catalog molecular variation in cancer, and these discoveries have been translated to clinically facing assays of prognostic and theranostic value. Routine NGS-based testing is enabling a model in which many therapeutically relevant molecular indications are simultaneously profiled and matched against an array of treatment options, thus overcoming the “one-gene/one-drug” serial testing model [1].
    Clinical sequencing of tumor DNA has received the greatest attention with an emphasis on detection of hotspot single nucleotide variants (SNVs), small insertions and deletions (INDELs), and copy number variants (CNVs) that confer sensitivity to targeted therapies. For example somatic variation in exons 18-21 of EGFR occur in 
    approximately 10%-15% of non–small cell lung cancer (NSCLC) tumors and are sensitizing to first-generation tyrosine kinase inhibitors (TKIs) erlotinib and gefitinib [2,3]. Tumors with innate or acquired resistance mutations are responsive to second- or third-generation inhibitors afatinib and osimertinib [4,5]. Routine profiling