Wednesday, August 10, 2011

Exome Sequencing-Based Copy-Number Variation and Loss of Heterozygosity Detection: ExomeCNV

Exome Sequencing-Based Copy-Number Variation and Loss of Heterozygosity Detection: ExomeCNV:

Motivation: The ability to detect copy-number variation (CNV) and loss of heterozygosity (LOH) from exome sequencing data extends the utility of this powerful approach that has mainly been used for point or small insertion/deletion detection.

Results: We present ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads, and we assess both the method’s power and the effects of confounding variables. We apply our method to a cancer exome resequencing dataset. As expected, accuracy and resolution are dependent on depth-of-coverage and capture probe design.

Availability: CRAN package "ExomeCNV"

Supplementary information: Supplementary data are available at Bioinformatics online.


(Via Bioinformatics - Advance Access.)