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Roberson EDO, Pevsner J. Visualization of shared genomic regions and meiotic recombination in high-density SNP data. PLoS One 2009; 4:e6711. [PMID: 19696932 PMCID: PMC2725774 DOI: 10.1371/journal.pone.0006711] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 07/23/2009] [Indexed: 11/23/2022] Open
Abstract
Background A fundamental goal of single nucleotide polymorphism (SNP) genotyping is to determine the sharing of alleles between individuals across genomic loci. Such analyses have diverse applications in defining the relatedness of individuals (including unexpected relationships in nominally unrelated individuals, or consanguinity within pedigrees), analyzing meiotic crossovers, and identifying a broad range of chromosomal anomalies such as hemizygous deletions and uniparental disomy, and analyzing population structure. Principal Findings We present SNPduo, a command-line and web accessible tool for analyzing and visualizing the relatedness of any two individuals using identity by state. Using identity by state does not require prior knowledge of allele frequencies or pedigree information, and is more computationally tractable and is less affected by population stratification than calculating identity by descent probabilities. The web implementation visualizes shared genomic regions, and generates UCSC viewable tracks. The command-line version requires pedigree information for compatibility with existing software and determining specified relationships even though pedigrees are not required for IBS calculation, generates no visual output, is written in portable C++, and is well-suited to analyzing large datasets. We demonstrate how the SNPduo web tool identifies meiotic crossover positions in siblings, and confirm our findings by visualizing meiotic recombination in synthetic three-generation pedigrees. We applied SNPduo to 210 nominally unrelated Phase I / II HapMap samples and, consistent with previous findings, identified six undeclared pairs of related individuals. We further analyzed identity by state in 2,883 individuals from multiplex families with autism and identified a series of anomalies including related parents, an individual with mosaic loss of chromosome 18, an individual with maternal heterodisomy of chromosome 16, and unexplained replicate samples. Conclusions SNPduo provides the ability to explore and visualize SNP data to characterize the relatedness between individuals. It is compatible with, but distinct from, other established analysis software such as PLINK, and performs favorably in benchmarking studies for the analyses of genetic relatedness.
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Affiliation(s)
- Elisha D. O. Roberson
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland, United States of America
| | - Jonathan Pevsner
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland, United States of America
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: JP:
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Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME. Global variation in copy number in the human genome. Nature 2006; 444:444-54. [PMID: 17122850 PMCID: PMC2669898 DOI: 10.1038/nature05329] [Citation(s) in RCA: 2944] [Impact Index Per Article: 163.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 10/10/2006] [Indexed: 01/08/2023]
Abstract
Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.
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Affiliation(s)
- Richard Redon
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Shumpei Ishikawa
- Genome Science, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 Japan
| | | | - Lars Feuk
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, MaRS Centre- East Tower, 101 College Street, Rm. 14-701, Toronto, Ontario, M5G 1L7, Canada
- Department of Molecular and Medical Genetics, University of Toronto
| | - George H. Perry
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA 02115
| | - T. Daniel Andrews
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Heike Fiegler
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Andrew R. Carson
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, MaRS Centre- East Tower, 101 College Street, Rm. 14-701, Toronto, Ontario, M5G 1L7, Canada
- Department of Molecular and Medical Genetics, University of Toronto
| | | | - Eun Kyung Cho
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA 02115
| | - Stephanie Dallaire
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA 02115
| | - Jennifer L. Freeman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA 02115
| | - Juan R. Gonzalez
- Genes and Disease Program, and Barcelona CeGen Unit, Center for Genomic Regulation, Barcelona, Catalonia, Spain
| | - Monica Gratacos
- Genes and Disease Program, and Barcelona CeGen Unit, Center for Genomic Regulation, Barcelona, Catalonia, Spain
| | | | - Dimitrios Kalaitzopoulos
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daisuke Komura
- Dependable and High Performance Computing, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 Japan
| | - Jeffrey R. MacDonald
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, MaRS Centre- East Tower, 101 College Street, Rm. 14-701, Toronto, Ontario, M5G 1L7, Canada
| | - Christian R. Marshall
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, MaRS Centre- East Tower, 101 College Street, Rm. 14-701, Toronto, Ontario, M5G 1L7, Canada
- Department of Molecular and Medical Genetics, University of Toronto
| | - Rui Mei
- Affymetrix, Inc., Santa Clara, CA, USA
| | - Lyndal Montgomery
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kunihiro Nishimura
- Genome Science, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 Japan
| | - Kohji Okamura
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, MaRS Centre- East Tower, 101 College Street, Rm. 14-701, Toronto, Ontario, M5G 1L7, Canada
- Department of Molecular and Medical Genetics, University of Toronto
| | - Fan Shen
- Affymetrix, Inc., Santa Clara, CA, USA
| | - Martin J. Somerville
- Departments of Medical Genetics and Pediatrics, University of Alberta, Edmonton, Canada
| | - Joelle Tchinda
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA 02115
| | - Armand Valsesia
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Cara Woodwark
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Fengtang Yang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Junjun Zhang
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, MaRS Centre- East Tower, 101 College Street, Rm. 14-701, Toronto, Ontario, M5G 1L7, Canada
| | - Tatiana Zerjal
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Lluis Armengol
- Genes and Disease Program, and Barcelona CeGen Unit, Center for Genomic Regulation, Barcelona, Catalonia, Spain
| | - Donald F. Conrad
- Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois, USA
| | - Xavier Estivill
- Genes and Disease Program, and Barcelona CeGen Unit, Center for Genomic Regulation, Barcelona, Catalonia, Spain
- Department of Life and Health Sciences, Pompeu Fabra University, Barcelona, Catalonia, Spain
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Nigel P. Carter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Hiroyuki Aburatani
- Genome Science, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 Japan
- Japan Science and Technology Agency Kawaguchi, Saitama, 332-0012, Japan
| | - Charles Lee
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA 02115
- Harvard Medical School, Boston, MA, USA 02115
| | | | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, MaRS Centre- East Tower, 101 College Street, Rm. 14-701, Toronto, Ontario, M5G 1L7, Canada
- Department of Molecular and Medical Genetics, University of Toronto
| | - Matthew E. Hurles
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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