Abstract 4707: Comprehensive integrated genomic analysis
Authors: Foo Catherine K. , John John St. , Hahner Nicholas , Westesson Oscar , Skinner Mitchell E. , Parikh Urvish , Lung Kimberly , Cauhlin Aleah F. , Catalano Jeffrey P. , Wellde Anne S. , Barry Jonathan K. , Wellde George W. , Ma Patrick , Rosell Rafael , Zorilla Andres Felipe Cardona , Polkinghorn William R. , Bivona Trever G. , Weissman Jonathan S. , Giannikopoulos Petros 
Published: May 2015

Abstract
Despite recent advances in the understanding of the biology and genetics of lung cancer, and despite the introduction of multiplex somatic mutation testing in the clinic, the long-term survival for all lung cancer patients, particularly for those with advanced disease, remains low. Lung cancer is the leading cause of cancer death globally, resulting in 1.4 million deaths annually, including 165,000 patients in the United States per year. In order to address the critical need for comprehensive profiling of these patients, we developed a novel, CLIA-certified, whole exome and low-coverage whole genome sequencing assay that applies a disease-focused, integrated approach to identify therapeutically actionable drivers of disease. A panel (12) of surgically resected NSCLC specimens along with corresponding adjacent normal tissue underwent DNA extraction in a clinical (CLIA) environment. Tumor and normal genomic DNA was prepared for whole exome sequencing using the using the Agilent SureSelectXT Human All Exon V5 kit according to the manufacturer's instructions, and libraries were sequenced on the Illumina HiSeq2500 at an average depth of 500X. Genomic DNA was then prepared for whole genome sequencing using Illumina's Nextera system and run on the Illumina HiSeq2500 platform at an average depth of 1-2X. Somatic variants were detected using Strelka and somatic copy number alterations (SCNAs) were identified using a novel algorithm comparing normalized read counts within genomic segments as well as genes in the tumor to a panel of normal tissues. In parallel, the same tumor/normal specimens were analyzed by two separate CLIA laboratories via 1) a clinically validated Ion Torrent AmpliSeq Cancer Panel assay, and 2) a clinically validated cancer-focused, high-resolution comparative genome hybridization (CGH) array. In addition, a well-characterized panel of 10 germline samples obtained from the 1000 Genomes Project were pooled to simulate a broad spectrum of somatic single nucleotide variant and indel allele frequencies. Sequencing, data analysis and clinical reporting were completed for all 12 cases with an average turnaround time of less than 3 weeks. Single nucleotide variants and indels were identified with an accuracy of greater than 99%, with a limit of detection of 5-10% mutant allele frequency. Somatic copy number alterations were observed with an overall accuracy of greater than 95%. Actionable variants were identified by cross-referencing individual results with our internally developed, lung-cancer focused therapeutic association database.
Citation Format: Catherine K. Foo, John St. John, Nicholas Hahner, Oscar Westesson, Mitchell E. Skinner, Urvish Parikh, Kimberly Lung, Aleah F. Cauhlin, Jeffrey P. Catalano, Anne S. Wellde, Jonathan K. Barry, George W. Wellde, Patrick Ma, Rafael Rosell, Andres Felipe Cardona Zorilla, William R. Polkinghorn, Trever G. Bivona, Jonathan S. Weissman, Petros Giannikopoulos. Comprehensive integrated genomic analysis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4707. doi:10.1158/1538-7445.AM2014-4707