Abstract 1654: Detection of structural variations in a cancer reference sample with multiple NGS platforms

Abstract

Structural Variations (SVs) are genetic variations or rearrangements in the structure of chromosome. SVs study plays an important role in cancer research as cancer genome is commonly altered with thousands of structural rearrangements such as insertions, deletions, translocation, inversions, duplications, copy number variations (CNVs). Next-generation sequencing (NGS) technology has provided a cost-effective approach for the comprehensive detection of SVs in human cancer cells. In this study, we systematically investigated the somatic structural variations in a pair of breast cancer cell lines with multiple NGS platforms including Illumina short-read, 10x genomics linked-read, PacBio long-read, and high-throughput chromosome conformation capture HiC. We systematically evaluated the factors that impact the SVs detection accuracy. We measured the reproductivity of somatic SV detections across platforms and benchmarked the different software tools’ performance. We performed SV integration from different platforms and established a high-confident SV call set for the reference samples. To independently evaluate the accuracy of our SV call set, we used orthogonal methods such as cytogenetic array as well as fusion gene detected from RNA-seq for cross validation. From this study, we identified the unique strengths of each NGS technologies and provide a practical guide to integrate multiple platform data to improve SV detection sensitivity and accuracy in cancer genome. Note: This abstract was not presented at the meeting. Citation Format: Yongmei Zhao, Wenming Xiao, on behalf of Somatic Mutation Working Group of theSEQC2 Consortium. Detection of structural variations in a cancer reference sample with multiple NGS platforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1654.