Mapping copy number variation by population-scale genome sequencing

Nature - Tập 470 Số 7332 - Trang 59-65 - 2011
Ryan E. Mills1, Klaudia Walter2, Chip Stewart3, Robert E. Handsaker4, Ken Chen5, Can Alkan6, Alexej Abyzov7, Seungtai Yoon8, Kai Ye9, R. Keira Cheetham10, Asif Chinwalla5, Donald F. Conrad2, Yutao Fu11, Fabian Grubert12, Iman Hajirasouliha13, Fereydoun Hormozdiari13, Lilia M. Iakoucheva14, Zamin Iqbal15, Shuli Kang14, Jeffrey M. Kidd6, Miriam K. Konkel16, Joshua M. Korn4, Ekta Khurana7, Deniz Kural3, Hugo Y. K. Lam12, Jing Leng7, Ruiqiang Li17, Yingrui Li17, Chang‐Yun Lin18, Ruibang Luo17, Xinmeng Jasmine Mu7, James Nemesh4, Heather E. Peckham11, Tobias Rausch19, Aylwyn Scally2, Xinghua Shi1, Michael P. Strömberg3, Adrian M. Stütz19, Alexander E. Urban12, Jerilyn A. Walker16, Jiantao Wu3, Goo Jun2, Zhengdong D. Zhang7, Mark A. Batzer16, Li Ding20, Gábor Marth3, Gil McVean21, Jonathan Sebat14, M Snyder12, Jun Wang17, Kenny Ye18, Evan E. Eichler22, Mark Gerstein23, Matthew E. Hurles2, Charles Lee1, Steven A. McCarroll24, Jan O. Korbel19
1Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA.
2The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
3Department of Biology, Boston College, Boston, Massachusetts, USA
4Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
5The Genome Center at Washington University, St. Louis, Missouri, USA
6Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
7Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
8Seaver Autism Center and Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
9Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
10Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden CB10 1XL, UK ,
11Life Technologies, Beverly, Massachusetts, USA
12Department of Genetics, Stanford University, Stanford, California, USA
13School of Computing Science, Simon Fraser University, Burnaby, British Columbia, Canada
14Department of Psychiatry, Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA,
15Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
16Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
17BGI-Shenzhen, Shenzhen 518083, China
18Albert Einstein College of Medicine, Bronx, New York, USA
19Genome Biology Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,
20Department of Genetics, Washington University, St. Louis, Missouri, USA
21Department of Statistics, University of Oxford, OX3 7BN, UK
22Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
23Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut, USA
24Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Conrad, D. F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704–712 (2010)

Pinto, D. et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466, 368–372 (2010)

Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445–449 (2007)

Stefansson, H. et al. Large recurrent microdeletions associated with schizophrenia. Nature 455, 232–236 (2008)

McCarthy, S. E. et al. Microduplications of 16p11.2 are associated with schizophrenia. Nature Genet. 41, 1223–1227 (2009)

Craddock, N. et al. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464, 713–720 (2010)

McCarroll, S. A. et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn’s disease. Nature Genet. 40, 1107–1112 (2008)

Hastings, P. J., Lupski, J. R., Rosenberg, S. M. & Ira, G. Mechanisms of change in gene copy number. Nature Rev. Genet. 10, 551–564 (2009)

Stankiewicz, P. & Lupski, J. R. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61, 437–455 (2010)

Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525–528 (2004)

Iafrate, A. J. et al. Detection of large-scale variation in the human genome. Nature Genet. 36, 949–951 (2004)

Sharp, A. J. et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77, 78–88 (2005)

McCarroll, S. A. et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nature Genet. 40, 1166–1174 (2008)

Tuzun, E. et al. Fine-scale structural variation of the human genome. Nature Genet. 37, 727–732 (2005)

Korbel, J. O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420–426 (2007)

Alkan, C. et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genet. 41, 1061–1067 (2009)

Chen, K. et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature Methods 6, 677–681 (2009)

Hormozdiari, F., Alkan, C., Eichler, E. E. & Sahinalp, S. C. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res. 19, 1270–1278 (2009)

Medvedev, P., Stanciu, M. & Brudno, M. Computational methods for discovering structural variation with next-generation sequencing. Nature Methods 6, S13–S20 (2009)

McKernan, K. J. et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 19, 1527–1541 (2009)

Chiang, D. Y. et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nature Methods 6, 99–103 (2009)

Kidd, J. M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56–64 (2008)

Lee, S., Cheran, E. & Brudno, M. A robust framework for detecting structural variations in a genome. Bioinformatics 24, i59–i67 (2008)

Pang, A. W. et al. Towards a comprehensive structural variation map of an individual human genome. Genome Biol. 11, R52 (2010)

Bailey, J. A. et al. Recent segmental duplications in the human genome. Science 297, 1003–1007 (2002)

Campbell, P. J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genet. 40, 722–729 (2008)

Yoon, S., Xuan, Z., Makarov, V., Ye, K. & Sebat, J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 19, 1586–1592 (2009)

Mills, R. E. et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16, 1182–1190 (2006)

Ye, K., Schulz, M. H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865–2871 (2009)

Simpson, J. T. et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117–1123 (2009)

Hajirasouliha, I. et al. Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics 26, 1277–1283 (2010)

Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311–317 (2010)

The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010)

Sudmant, P. H. et al. Diversity of human copy number variation and multicopy genes. Science 330, 641–646 (2010)

Willer, C. J. et al. Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nature Genet. 41, 25–34 (2008)

Levy, S. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007)

Hasin-Brumshtein, Y., Lancet, D. & Olender, T. Human olfaction: from genomic variation to phenotypic diversity. Trends Genet. 25, 178–184 (2009)

Hinds, D. A., Kloek, A. P., Jen, M., Chen, X. & Frazer, K. A. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nature Genet. 38, 82–85 (2006)

Altshuler, D. M. et al. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52–58 (2010)

Conrad, D. F. et al. Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nature Genet. 42, 385–391 (2010)

Lam, H. Y. et al. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nature Biotechnol. 28, 47–55 (2010)

Lupski, J. R. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 14, 417–422 (1998)

Lee, J. A., Carvalho, C. M. & Lupski, J. R. A. DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131, 1235–1247 (2007)

Harrow, J. et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 7, (suppl. 1)S4 (2006)