The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data.

ABSTRACT: Recent advances in high-throughout sequencing technologies have made it possible to accurately assign copy number (CN) at CN variable loci. However, current analytic methods often perform poorly in regions in which complex CN variation is observed. Here we report the development of a read depth-based approach, CNVrd2, for investigation of CN variation using high-throughput sequencing data. This methodology was developed using data from the 1000 Genomes Project from the CCL3L1 locus, and tested using data from the DEFB103A locus. In both cases, samples were selected for which paralog ratio test data were also available for comparison. The CNVrd2 method first uses observed read-count ratios to refine segmentation results in one population. Then a linear regression model is applied to adjust

SUBMITTER: Nguyen HT 

PROVIDER: S-EPMC4117933 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature