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

Bioinformatics. 2011 Oct 1;27(19):2648-54. doi: 10.1093/bioinformatics/btr462. Epub 2011 Aug 9.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Base Sequence / genetics
  • DNA Copy Number Variations / genetics*
  • Exome*
  • Genotype
  • Humans
  • Loss of Heterozygosity*
  • Melanoma / genetics*
  • Models, Genetic
  • Polymorphism, Single Nucleotide
  • Sequence Analysis, DNA / methods*
  • Skin Neoplasms / genetics*