Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient Derived Tumors Clinical Application of Whole-Genome Sequencing for Reporting Targetable Variants in Cancer

Publication date: Available online 21 August 2018Source: The Journal of Molecular DiagnosticsAuthor(s): Kazimierz O. Wrzeszczynski, Vanessa Felice, Avinash Abhyankar, Lukasz Kozon, Heather Geiger, Dina Manaa, Ferrah London, Dino Robinson, Xiaolan Fang, David Lin, Michelle F. Lamendola-Essel, Depinder Khaira, Esra Dikoglu, Anne-Katrin Emde, Nicolas Robine, Minita Shah, Kanika Arora, Olca Basturk, Umesh Bhanot, Alex KentsisWe have developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay which provides a comprehensive genomic profile of a patient’s tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, Indels, copy number variants, structural variants, and RNA gene fusions, was analyzed. New York State’s Department of Health NGS guidelines were expanded on for establishing performance validation applicable to whole-genome sequencing. Whole-genome sequencing laboratory protocols were validated for the Illumina HiSeq X Ten platform and RNA sequencing for Illumina HiSeq2500 platform for fresh frozen and formalin-fixed, paraffin-embedded tumor samples. Various bioinformatics tools were also tested, and confidence intervals for sensitivity and specificity thresholds in calling clinically significant somatic aberrations were determined. The validation was performed on a set of 125 tumor normal pairs. RNA sequencing is performed to call fusion and to confi...
Source: The Journal of Molecular Diagnostics - Category: Pathology Source Type: research