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

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

Author information

1
Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA JP Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY 10032, USA.
2
Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
3
Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
4
Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
5
Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA.
6
Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
7
Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA Howard Hughes Medical Institute, Yale University, New Haven, CT 06510, USA.
8
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
9
Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA ys2411@columbia.edu.
10
Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA JP Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY 10032, USA ys2411@columbia.edu.

Abstract

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.

PMID:
24771342
PMCID:
PMC4081054
DOI:
10.1093/nar/gku345
[Indexed for MEDLINE]
Free PMC Article

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