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

共 34 条

[1] High-resolution mapping of copy-number alterations with massively parallel sequencing [J].

Chiang, Derek Y. ;

Getz, Gad ;

Jaffe, David B. ;

O'Kelly, Michael J. T. ;

Zhao, Xiaojun ;

Carter, Scott L. ;

Russ, Carsten ;

Nusbaum, Chad ;

Meyerson, Matthew ;

Lander, Eric S. .

NATURE METHODS, 2009, 6 (01) :99-103

[2] Hypermethylation and loss of heterozygosity of tumor suppressor genes on chromosome 3p in cervical cancer [J].

Choi, Chel Hun ;

Lee, Kyung-Mee ;

Choi, Jung-Joo ;

Kim, Tae-Joong ;

Kim, Woo Young ;

Lee, Jeong-Won ;

Lee, Sun-Joo ;

Lee, Je-Ho ;

Bae, Duk-Soo ;

Kim, Byoung-Gie .

CANCER LETTERS, 2007, 255 (01) :26-33

[3] Genetic diagnosis by whole exome capture and massively parallel DNA sequencing [J].

Choi, Murim ;

Scholl, Ute I. ;

Ji, Weizhen ;

Liu, Tiewen ;

Tikhonova, Irina R. ;

Zumbo, Paul ;

Nayir, Ahmet ;

Bakkaloglu, Aysin ;

Ozen, Seza ;

Sanjad, Sami ;

Nelson-Williams, Carol ;

Farhi, Anita ;

Mane, Shrikant ;

Lifton, Richard P. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (45) :19096-19101

[4] DNA Sequence Capture and Enrichment by Microarray Followed by Next-Generation Sequencing for Targeted Resequencing: Neurofibromatosis Type 1 Gene as a Model [J].

Chou, Lan-Szu ;

Liu, C. -S. Jonathan ;

Boese, Benjamin ;

Zhang, Xinmin ;

Mao, Rong .

CLINICAL CHEMISTRY, 2010, 56 (01) :62-72

[5] Coevolution of Interacting Fertilization Proteins [J].

Clark, Nathaniel L. ;

Gasper, Joe ;

Sekino, Masashi ;

Springer, Stevan A. ;

Aquadro, Charles F. ;

Swanson, Willie J. .

PLOS GENETICS, 2009, 5 (07)

[6] Mutation spectrum revealed by breakpoint sequencing of human germline CNVs [J].

Conrad, Donald F. ;

Bird, Christine ;

Blackburne, Ben ;

Lindsay, Sarah ;

Mamanova, Lira ;

Lee, Charles ;

Turner, Daniel J. ;

Hurles, Matthew E. .

NATURE GENETICS, 2010, 42 (05) :385-U43

[7] Origins and functional impact of copy number variation in the human genome [J].

Conrad, Donald F. ;

Pinto, Dalila ;

Redon, Richard ;

Feuk, Lars ;

Gokcumen, Omer ;

Zhang, Yujun ;

Aerts, Jan ;

Andrews, T. Daniel ;

Barnes, Chris ;

Campbell, Peter ;

Fitzgerald, Tomas ;

Hu, Min ;

Ihm, Chun Hwa ;

Kristiansson, Kati ;

MacArthur, Daniel G. ;

MacDonald, Jeffrey R. ;

Onyiah, Ifejinelo ;

Pang, Andy Wing Chun ;

Robson, Sam ;

Stirrups, Kathy ;

Valsesia, Armand ;

Walter, Klaudia ;

Wei, John ;

Tyler-Smith, Chris ;

Carter, Nigel P. ;

Lee, Charles ;

Scherer, Stephen W. ;

Hurles, Matthew E. .

NATURE, 2010, 464 (7289) :704-712

[8] Genome-wide copy number variation association study suggested VPS13B gene for osteoporosis in Caucasians [J].

Deng, F. -Y. ;

Zhao, L. -J. ;

Pei, Y. -F. ;

Sha, B. -Y. ;

Liu, X. -G. ;

Yan, H. ;

Wang, L. ;

Yang, T. -L. ;

Recker, R. R. ;

Papasian, C. J. ;

Deng, H. -W. .

OSTEOPOROSIS INTERNATIONAL, 2010, 21 (04) :579-587

[9] LOSS OF HETEROZYGOSITY FOR THE SHORT ARM OF CHROMOSOME-1 IN HUMAN NEUROBLASTOMAS - CORRELATION WITH N-MYC AMPLIFICATION [J].

FONG, CT ;

DRACOPOLI, NC ;

WHITE, PS ;

MERRILL, PT ;

GRIFFITH, RC ;

HOUSMAN, DE ;

BRODEUR, GM .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1989, 86 (10) :3753-3757

[10] The frequency distribution of the quotient of two normal variates [J].

Geary, RC .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY, 1930, 93 :442-446

← 1 2 3 4 →