Abstract 45: Detection of focal somatic copy number variants in whole genome, whole exome, and targeted next-generation sequencing data of tumor/normal pairs

Abstract

Abstract We describe the development and validation of an analysis pipeline for detection of focal somatic copy number aberrations from next-generation sequencing (NGS) data. In the clinical setting, tumor samples may be derived from historical tissue or from recently collected fresh frozen biopsies. DNA extracted from samples preserved as formalin-fixed, paraffin-embedded (FFPE) tissue are often highly degraded. We describe challenges inherent to sequencing different tissue sources and algorithmic approaches for optimizing detection of focal alterations in these samples with a high degree of accuracy. The first area of optimization takes into account clonal or fragment coverage based on user-defined intervals by accounting for coverage between paired-end reads. Normalized log2 fold-changes between tumor and normal samples are then calculated and a smoothing window is applied. In addition, we utilize tumor allele frequencies of known heterozygous germline SNPs identified within the normal to both evaluate potential false positives and correct biases. Lastly, a segmentation algorithm (circular binary segmentation as implemented in DNAcopy package1) is applied to summarize the individual log2 fold-changes into intervals with a constant copy number state. The results from the segmentation algorithm are then annotated and reformatted into the VCF format. We have analytically optimized and validated our algorithm across a series of samples with known alterations for implementation on both clinical and research samples. 1. Seshan VE and Olshen A. DNAcopy: DNA copy number data analysis. R package version 1.40.0. Citation Format: Jessica Aldrich, Jonathan J. Keats, Winnie S. Liang, John D. Carpten, David W. Craig. Detection of focal somatic copy number variants in whole genome, whole exome, and targeted next-generation sequencing data of tumor/normal pairs. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 45.