Dataset Information
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Ontology highlight
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.eduSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Sathirapongsasuti JF
PROVIDER: S-EPMC3179661 | biostudies-literature | 2011 Oct
REPOSITORIES: biostudies-literature
Publications
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Bioinformatics (Oxford, England) 20110809 19
<h4>Motivation</h4>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.<h4>Results</h4>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 appl ...[more]