Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls.

ABSTRACT:

Background

Next-generation sequencing (NGS) is rapidly becoming common practice in clinical diagnostics and cancer research. In addition to the detection of single nucleotide variants (SNVs), information on copy number variants (CNVs) is of great interest. Several algorithms exist to detect CNVs by analyzing whole genome sequencing data or data from samples enriched by hybridization-capture. PCR-enriched amplicon-sequencing data have special characteristics that have been taken into account by only one publicly available algorithm so far.

Results

We describe a new algorithm named quandico to detect copy number differences based on NGS data generated following PCR-enrichment. A weighted t-test statistic was applied to calculate probabilities (p-values) of copy number changes.

SUBMITTER: Reinecke F 

PROVIDER: S-EPMC4384318 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature