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

被引：295

作者：

Sathirapongsasuti, Jarupon Fah ^{[1
,2
,3
]}

Lee, Hane ^{[3
,4
]}

Horst, Basil A. J. ^{[4
,5
,6
]}

Brunner, Georg ^{[7
]}

Cochran, Alistair J. ^{[4
]}

Binder, Scott ^{[4
]}

Quackenbush, John ^{[1
,2
]}

Nelson, Stanley F. ^{[3
,4
]}

机构：

[1] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA

[2] Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA

[3] Univ Calif Los Angeles, David Geffen Sch Med, Dept Human Genet, Los Angeles, CA 90095 USA

[4] Univ Calif Los Angeles, David Geffen Sch Med, Dept Pathol & Lab Med, Los Angeles, CA 90095 USA

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

[6] Columbia Univ, Med Ctr, Dept Pathol & Cell Biol, New York, NY 10032 USA

[7] Skin Canc Ctr Hornheide, Dept Canc Res, Munster, Germany

来源：

BIOINFORMATICS | 2011年 / 27卷 / 19期

基金：

美国国家卫生研究院;

关键词：

CIRCULAR BINARY SEGMENTATION; GENOME-WIDE ASSOCIATION; FREQUENCY-DISTRIBUTION; CAPTURE; GENE; MUTATIONS; QUOTIENT;

D O I：

10.1093/bioinformatics/btr462

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2648 / 2654

页数：7

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