CANOES: detecting rare copy number variants from whole exome sequencing data

Nucleic Acids Res. 2014 Jul;42(12):e97. doi: 10.1093/nar/gku345. Epub 2014 Apr 25.


We present CANOES, an algorithm for the detection of rare copy number variants from exome sequencing data. CANOES models read counts using a negative binomial distribution and estimates variance of the read counts using a regression-based approach based on selected reference samples in a given dataset. We test CANOES on a family-based exome sequencing dataset, and show that its sensitivity and specificity is comparable to that of XHMM. Moreover, the method is complementary to Gaussian approximation-based methods (e.g. XHMM or CoNIFER). When CANOES is used in combination with these methods, it will be possible to produce high accuracy calls, as demonstrated by a much reduced and more realistic de novo rate in results from trio data.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • DNA Copy Number Variations*
  • Exome*
  • Genotyping Techniques
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Oligonucleotide Array Sequence Analysis
  • Sequence Analysis, DNA*