AUG 21, 2014 12:15 PM PDT

A Next-Gen Sequencing Software Workflow for Gene Panel Validation Control

Speaker
  • Senior Manager, NGS Applications, DNASTAR
    Biography
      Matthew Keyser is Senior Manager, NGS Applications for DNASTAR, where he has helped scientists address their sequence assembly and analysis challenges for the past seven years. Matts sole focus at DNASTAR is supporting customers in next-gen sequencing applications using DNASTARs broad software toolset. Matt helps customers with their templated and de novo assembly projects, transcriptomes, exomes, metagenomic assemblies, RNA-Seq, ChIP-Seq and numerous other unique experiments. Matt has helped hundreds of scientists optimize their workflows using DNASTARs next-gen software solutions. He has also spoken at numerous conferences and workshops regarding the capabilities of DNASTARs next-gen software tools.

    Abstract

    DNASTAR offers an integrated suite of software for assembling and analyzing sequence data from all major next-generation sequencing platforms. DNASTAR software supports a variety of key workflows on a desktop computer. A new Gene Panel Validation Control workflow supports several types of data sets, including Ion Torrent AmpliSeqTM Comprehensive Cancer Panel, Illumina TruSight Cancer Panel, as well as custom gene panels and evaluates the efficacy of gene panel targeting and the accuracy of variant calling. The accuracy of gene panel targeting is determined by multiple factors, including specificity of primers and probes used for gene panel design, efficiency of the sequencing technology, accuracy of assembly, accuracy of SNP calling, and the SNP filters applied. DNASTARs SeqMan NGen and ArrayStar programs provide an accurate alignment algorithm and variant caller. They then utilize a validated SNP set in the form of a VCF file and a BED or Manifest file that specify targeted regions, to calculate SNP-calling sensitivity, specificity, and accuracy. By utilizing this workflow, users can ultimately validate their entire process to verify that their known variants are being identified.

    Learning objectives:

    • Have a better understanding of sequence assembly and analysis software
    • Learn how to validate the entire gene panel process

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