Copy number variant analysis using genome‐wide mate‐pair sequencing

Abstract

Copy number variation (CNV) is a common form of structural variation detected in human genomes, occurring as both constitutional and somatic events. Cytogenetic techniques like chromosomal microarray (CMA) are widely used in analyzing CNVs. However, CMA techniques cannot resolve the full nature of these structural variations (i.e. the orientation and location of associated breakpoint junctions) and must be combined with other cytogenetic techniques, such as karyotyping or FISH, to do so. This makes the development of a next-generation sequencing (NGS) approach capable of resolving both CNVs and breakpoint junctions desirable. Mate-pair sequencing (MPseq) is a NGS technology designed to find large structural rearrangements across the entire genome. Here we present an algorithm capable of performing copy number analysis from mate-pair sequencing data. The algorithm uses a step-wise procedure involving normalization, segmentation, and classification of the sequencing data. The segmentation technique combines both read depth and discordant mate-pair reads to increase the sensitivity and resolution of CNV calls. The method is particularly suited to MPseq, which is designed to detect breakpoint junctions at high resolution. This allows for the classification step to accurately calculate copy number levels at the relatively low read depth of MPseq. Here we compare results for a series of hematological cancer samples that were tested with CMA and MPseq. We demonstrate comparable sensitivity to the state-of-the-art CMA technology, with the benefit of improved breakpoint resolution. The algorithm provides a powerful analytical tool for the analysis of MPseq results in cancer.

Using Genomics to Differentiate Multiple Primaries From Metastatic Lung Cancer

“…Additionally, as several of these copy changes are considered drivers of tumor growth, many are frequently observed in lung tumors, such as 3q gains in SQ. [37][38][39]46 By negatively scoring discordant copy changes, in addition to positively scoring shared changes, the CNVscore applied in this study minimized the effects of shared changes by chance. Weighting a discordant CNV change from normal diploid (2N) in one sample (score:-1), less than an opposing gain versus loss (score:-3) accounted for potential miss-calling through lower tumor percentage or heterogeneity.…”

RNA sequencing identifies a novel USP9X‐USP6 promoter swap gene fusion in a primary aneurysmal bone cyst

“…Alignment is performed using the BIMAv3 alignment method . The mapped sequences are then analyzed using SVAtools, which consists of a breakpoint junction detection step and a copy number variant detection step …”

Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma

“…19 We recently published (1) how MPseq provides comparable sensitivity to the state-of-the-art chromosomal microarray technology for the detection of copy number variations, with the benefit of improved breakpoint resolution; (2) how use of an internal database of polymorphisms is used to mask germline events; and (3) that display of MPseq results with a U plot which provides enhanced resolution of rearrangements and copy number variations than some other commonly used displays. [20][21][22] Germline events were filtered with this mask.…”