VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data.

ABSTRACT:

Purpose

To develop and validate VisCap, a software program targeted to clinical laboratories for inference and visualization of germ-line copy-number variants (CNVs) from targeted next-generation sequencing data.

Methods

VisCap calculates the fraction of overall sequence coverage assigned to genomic intervals and computes log2 ratios of these values to the median of reference samples profiled using the same test configuration. Candidate CNVs are called when log2 ratios exceed user-defined thresholds.

Results

We optimized VisCap using 14 cases with known CNVs, followed by prospective analysis of 1,104 cases referred for diagnostic DNA sequencing. To verify calls in the prospective cohort, we used droplet digital polymerase chain reaction (PCR) to confirm 10/27 candidat

SUBMITTER: Pugh TJ 

PROVIDER: S-EPMC4940431 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature