Systematic assessment of copy number variant detection via genome-wide SNP genotyping (original) (raw)
Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science305, 525–528 (2004). ArticleCAS Google Scholar
Tuzun, E. et al. Fine-scale structural variation of the human genome. Nat. Genet.37, 727–732 (2005). ArticleCAS Google Scholar
Redon, R. et al. Global variation in copy number in the human genome. Nature444, 444–454 (2006). ArticleCAS Google Scholar
Kidd, J.M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature453, 56–64 (2008). ArticleCAS Google Scholar
Cooper, G.M., Nickerson, D.A. & Eichler, E.E. Mutational and selective effects on copy-number variants in the human genome. Nat. Genet.39, S22–S29 (2007). ArticleCAS Google Scholar
Singleton, A.B. et al. alpha-Synuclein locus triplication causes Parkinson's disease. Science302, 841 (2003). ArticleCAS Google Scholar
Gonzalez, E. et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science307, 1434–1440 (2005). ArticleCAS Google Scholar
Sharp, A.J. et al. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat. Genet.38, 1038–1042 (2006). ArticleCAS Google Scholar
Perry, G.H. et al. Diet and the evolution of human amylase gene copy number variation. Nat. Genet.39, 1256–1260 (2007). ArticleCAS Google Scholar
Walsh, T. et al. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science320, 539–543 (2008). ArticleCAS Google Scholar
Estivill, X. & Armengol, L. Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies. PLoS Genet.3, 1787–1799 (2007). ArticleCAS Google Scholar
Shaffer, L.G. & Lupski, J.R. Molecular mechanisms for constitutional chromosomal rearrangements in humans. Annu. Rev. Genet.34, 297–329 (2000). ArticleCAS Google Scholar
Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature447, 661–678 (2007).
Conrad, D.F., Andrews, T.D., Carter, N.P., Hurles, M.E. & Pritchard, J.K. A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet.38, 75–81 (2006). ArticleCAS Google Scholar
Locke, D.P. et al. Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am. J. Hum. Genet.79, 275–290 (2006). ArticleCAS Google Scholar
McCarroll, S.A. et al. Common deletion polymorphisms in the human genome. Nat. Genet.38, 86–92 (2006). ArticleCAS Google Scholar
Peiffer, D.A. et al. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res.16, 1136–1148 (2006). ArticleCAS Google Scholar
Komura, D. et al. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res.16, 1575–1584 (2006). ArticleCAS Google Scholar
Colella, S. et al. QuantiSNP: an objective Bayes hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res.35, 2013–2025 (2007). ArticleCAS Google Scholar
Wang, K. et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res.17, 1665–1674 (2007). ArticleCAS Google Scholar
Day, N., Hemmaplardh, A., Thurman, R.E., Stamatoyannopoulos, J.A. & Noble, W.S. Unsupervised segmentation of continuous genomic data. Bioinformatics23, 1424–1426 (2007). ArticleCAS Google Scholar
Sharp, A.J. et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet.77, 78–88 (2005). ArticleCAS Google Scholar
She, X. et al. Shotgun sequence assembly and recent segmental duplications within the human genome. Nature431, 927–930 (2004). ArticleCAS Google Scholar
Dempster, A.P., Laird, N.M. & Rubin, D.B. Maximum likelihood from incomplete data via the EM algorithm. J. Roy. Statist. Soc. Ser. B. Methodological39, 1–38 (1977). Google Scholar
Newman, T.L. et al. High-throughput genotyping of intermediate-size structural variation. Hum. Mol. Genet.15, 1159–1167 (2006). ArticleCAS Google Scholar
International HapMap Consortium. A haplotype map of the human genome. Nature437, 1299–1320 (2005).
Eichler, E.E. et al. Completing the map of human genetic variation. Nature447, 161–165 (2007). ArticleCAS Google Scholar
Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science318, 420–426 (2007). ArticleCAS Google Scholar
de Smith, A.J. et al. Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males: implications for association studies of complex diseases. Hum. Mol. Genet.16, 2783–2794 (2007). ArticleCAS Google Scholar
Schwarz, G. Estimating the dimension of a model. Annals of Statistics6, 461–464 (1978). Article Google Scholar