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

被引：110

作者：

Backenroth, Daniel ^{[1
,2
,3
]}

Homsy, Jason ^{[4
]}

Murillo, Laura R. ^{[5
,6
,7
]}

Glessner, Joe ^{[8
]}

Lin, Edwin ^{[1
,2
,9
,10
]}

Brueckner, Martina ^{[11
]}

Lifton, Richard ^{[11
,12
]}

Goldmuntz, Elizabeth ^{[13
]}

Chung, Wendy K. ^{[9
,10
]}

Shen, Yufeng ^{[1
,2
,3
]}

机构：

[1] Columbia Univ, Med Ctr, Dept Syst Biol, New York, NY 10032 USA

[2] Columbia Univ, Med Ctr, Dept Biomed Informat, New York, NY 10032 USA

[3] Columbia Univ, Med Ctr, JP Sulzberger Columbia Genome Ctr, New York, NY 10032 USA

[4] Massachusetts Gen Hosp, Cardiovascular Res Ctr, Boston, MA 02114 USA

[5] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

[6] Icahn Sch Med Mt Sinai, Dept Pediat & Genet, Boston, MA 02115 USA

[7] Icahn Sch Med Mt Sinai, Dept Gen Sci, Boston, MA 02115 USA

[8] Childrens Hosp Philadelphia, Ctr Appl Gen, Philadelphia, PA 19104 USA

[9] Columbia Univ, Med Ctr, Dept Pediat, New York, NY 10032 USA

[10] Columbia Univ, Med Ctr, Dept Med, New York, NY 10032 USA

[11] Yale Univ, Sch Med, Dept Genet, New Haven, CT 06510 USA

[12] Yale Univ, Howard Hughes Med Inst, New Haven, CT 06510 USA

[13] Univ Penn, Perelman Sch Med, Dept Pediat, Philadelphia, PA 19104 USA

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / 12期

基金：

美国国家卫生研究院;

关键词：

GENOME-WIDE; MODEL; DISCOVERY; SNP;

D O I：

10.1093/nar/gku345

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

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.

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