title: Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  CRAN package 'ExomeCNV'.
  
  
  BACKGROUND
  fsathira@fas.harvard.edu; snelson@ucla.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA. fsathira@fas.harvard.edu
authors.forename: Jarupon Fah
authors.initials: JF
authors.lastname: Sathirapongsasuti
authors.forename: Hane
authors.initials: H
authors.lastname: Lee
authors.forename: Basil A J
authors.initials: BA
authors.lastname: Horst
authors.forename: Georg
authors.initials: G
authors.lastname: Brunner
authors.forename: Alistair J
authors.initials: AJ
authors.lastname: Cochran
authors.forename: Scott
authors.initials: S
authors.lastname: Binder
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Stanley F
authors.initials: SF
authors.lastname: Nelson
mesh_terms: D000465:Algorithms; D001483:Base Sequence / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics*; D059472:Exome; D005838:Genotype; D006801:Humans; D019656:Loss of Heterozygosity; D008545:Melanoma / Q000235:genetics*; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D012878:Skin Neoplasms / Q000235:genetics*