Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

JF Sathirapongsasuti, H Lee, BAJ Horst… - …, 2011 - academic.oup.com
JF Sathirapongsasuti, H Lee, BAJ Horst, G Brunner, AJ Cochran, S Binder, J Quackenbush
Bioinformatics, 2011academic.oup.com
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 …
Abstract
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’.
Contact:  fsathira@fas.harvard.edu; snelson@ucla.edu
Supplementary information:  Supplementary data are available at Bioinformatics online.
Oxford University Press