A copy number gain or loss in a gene can be a critical driver event in carcinogenesis or cancer progression . For instance, a copy number gain in HER2 gene is a driver event in many breast, lung, and colorectal cancers, and has important clinical implications that may be predictive of drug response [2,3,4]. As we have described previously, a copy number aberration (CNA) event leaves behind a variety of signatures in whole genome sequencing (WGS) data, such as read depth, B-allele frequency, soft-clipped reads and discordant reads. These signatures can be used as evidence by detection algorithms for calling CNAs.
In addition to Control-FREEC that was incorporated into Bina RAVE™ for improving copy number aberrations (CNA) detection, we'd like to share with you another tool added to version 2.5 of the software in this post.
Previously we've shared our top contenders for evidence indicative of a Copy Number Aberration (CNA) occurrence in whole genome sequencing. In this post, we'll examine one of the tools added to version 2.5 of the Bina RAVE™ software module to help improve detection sensitivity.