Abstract 2714: 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
Authors: Wrzeszczynski Kazimierz O. , Abhyankar Avinash , Felice Vanessa , Dikoglu Esra , Kozon Lukasz , Robine Nicolas , Emde Anne-Katrin , Basturk Olca , Bhanot Umesh K. , Kentsis Alex , Mansukhani Mahesh , Bhagat Govind , Jobanputra Vaidehi 
Published: July 2017

Next Generation DNA Sequencing (NGS) technologies are currently being applied in the clinical setting for the treatment of disease. The goal is to use high-throughput sequencing to identify specific variants within each tumor and recommend personalized treatment approaches or clinical trials tailored to the individual’s disease and genomic profile. These assays are comprised of either predefined sequencing panels, where a handpicked set of clinically significant genes are examined within each patient, or are cancer type specific targeted sequencing protocols or whole exome platforms covering only the coding region of the patient’s genome. Whole genome sequencing allows hypothesis-free interrogation of both coding and non-coding regions of the genome revealing more potential therapeutic options than examining a small set of genes or genomic loci. The protocol eliminates sequence capture related bias observed in whole exome or panel sequencing. The New York Genome Center therefore has performed analytical validation of whole genome and transcriptome sequencing (WGTS) of patient derived tumors and matched normals for the purposes of clinical testing and have devised a clinical reporting strategy of significant driver and therapeutic associated mutations. Many clinical NGS guidelines are directed toward targeted panel or exome sequencing validation. Here, we expanded on New York State’s Department of Health NGS guidelines developing them into novel standards applicable to WGTS for the purposes of clinical test validation. We first sequenced a virtual tumor at very high coverage (300x) and downsampled to determine the optimum depth of sequencing necessary for high confidence somatic variant calling across the entire genome. We then validated whole genome sequencing laboratory protocols for DNA and RNA sequencing on a total of 50 specimens derived from fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tumor samples. We performed a series of experiments to assess the accuracy and reliability of the results based on our laboratory and bioinformatics protocols. We performed our validation on the 50 tumor normal pairs, a subset of which had known genomic profiles. Comparisons were also made for variant calling concordance and reproducibility between matched FF and FFPE tumors. Here, we present our validation results and clinical WGTS standards for depth of sequencing, reproducibility, sensitivity, and present limit of detection analysis for SNV calling, copy number identification and structural variants. RNA sequencing is performed to call fusion or exon skipping events and to confirm the DNA variants. The New York Genome Center WGTS clinical assay is intended to provide a more comprehensive patient variant discovery approach suitable for directed oncological therapeutic applications.

Citation Format: Kazimierz O. Wrzeszczynski, Avinash Abhyankar, Vanessa Felice, Esra Dikoglu, Lukasz Kozon, Nicolas Robine, Anne-Katrin Emde, Olca Basturk, Umesh K. Bhanot, Alex Kentsis, Mahesh Mansukhani, Govind Bhagat, Vaidehi Jobanputra. 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 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2714. doi:10.1158/1538-7445.AM2017-2714