Bina Bloggers

Detecting Copy Number Aberrations in Targeted Sequencing

Posted by Li Tai Fang on Aug 11, 2015 9:00:00 AM

A copy number gain or loss in a gene can be a critical driver event in carcinogenesis or cancer progression [1]. 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.

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Topics: Bina Tools & Workflows, Secondary Analysis, Copy Number Aberration

Detecting CNAs for High-Coverage WGS Data (>60X) - New Tool in Bina RAVE 2.5

Posted by Li Tai Fang on Jun 2, 2015 8:30:00 AM

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.

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Topics: Somatic Mutation Detection, Secondary Analysis, Tumor-Normal, RAVE, Copy Number Aberration

Detecting CNA Events in WGS With or Without a Normal Control - New in Bina RAVE 2.5

Posted by Li Tai Fang on May 15, 2015 9:00:00 AM

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.  

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Topics: Bina Tools & Workflows, RAVE, Copy Number Aberration

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