Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease

The American Journal of Human Genetics - Tập 84 - Trang 148-161 - 2009
Andy Itsara1, Gregory M. Cooper1, Carl Baker1, Santhosh Girirajan1, Jun Li2, Devin Absher3, Ronald M. Krauss4, Richard M. Myers3, Paul M. Ridker5, Daniel I. Chasman5, Heather Mefford1, Phyllis Ying1, Deborah A. Nickerson1, Evan E. Eichler1,6
1Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
2Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
3HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
4Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
5Center for Cardiovascular Disease Prevention, Donald W. Reynolds Center for Cardiovascular Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
6Howard Hughes Medical Institute

Tài liệu tham khảo

Iafrate, 2004, Detection of large-scale variation in the human genome, Nat. Genet., 36, 949, 10.1038/ng1416 Redon, 2006, Global variation in copy number in the human genome, Nature, 444, 444, 10.1038/nature05329 Sebat, 2004, Large-scale copy number polymorphism in the human genome, Science, 305, 525, 10.1126/science.1098918 Sharp, 2005, Segmental duplications and copy-number variation in the human genome, Am. J. Hum. Genet., 77, 78, 10.1086/431652 Tuzun, 2005, Fine-scale structural variation of the human genome, Nat. Genet., 37, 727, 10.1038/ng1562 Feuk, 2006, Structural variation in the human genome, Nat. Rev. Genet., 7, 85, 10.1038/nrg1767 Cooper, 2007, Mutational and selective effects on copy-number variants in the human genome, Nat. Genet., 39, S22, 10.1038/ng2054 Trask, 1998, Large multi-chromosomal duplications encompass many members of the olfactory receptor gene family in the human genome, Hum. Mol. Genet., 7, 2007, 10.1093/hmg/7.13.2007 Nguyen, 2006, Bias of selection on human copy-number variants, PLoS Genet, 2, e20, 10.1371/journal.pgen.0020020 Gonzalez, 2005, The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility, Science, 307, 1434, 10.1126/science.1101160 Fellermann, 2006, A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon, Am. J. Hum. Genet., 79, 439, 10.1086/505915 Aitman, 2006, Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans, Nature, 439, 851, 10.1038/nature04489 Stankiewicz, 2002, Genome architecture, rearrangements and genomic disorders, Trends Genet., 18, 74, 10.1016/S0168-9525(02)02592-1 Christian, 1999, Large genomic duplicons map to sites of instability in the Prader-Willi/Angelman syndrome chromosome region (15q11-q13), Hum. Mol. Genet., 8, 1025, 10.1093/hmg/8.6.1025 Ballif, 2007, Discovery of a previously unrecognized microdeletion syndrome of 16p11.2-p12.2, Nat. Genet., 39, 1071, 10.1038/ng2107 Slavotinek, 2008, Novel microdeletion syndromes detected by chromosome microarrays, Hum. Genet., 124, 1, 10.1007/s00439-008-0513-9 Sharp, 2007, Characterization of a recurrent 15q24 microdeletion syndrome, Hum. Mol. Genet., 16, 567, 10.1093/hmg/ddm016 Mefford, 2007, Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy, Am. J. Hum. Genet., 81, 1057, 10.1086/522591 Weiss, 2008, Association between microdeletion and microduplication at 16p11.2 and autism, N. Engl. J. Med., 358, 667, 10.1056/NEJMoa075974 Sharp, 2008, A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures, Nat. Genet., 40, 322, 10.1038/ng.93 Mefford, 2008, Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes, N. Engl. J. Med., 359, 1685, 10.1056/NEJMoa0805384 Sebat, 2007, Strong association of de novo copy number mutations with autism, Science, 316, 445, 10.1126/science.1138659 2008, Rare chromosomal deletions and duplications increase risk of schizophrenia, Nature, 455, 237, 10.1038/nature07239 Walsh, 2008, Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia, Science, 320, 539, 10.1126/science.1155174 Stefansson, 2008, Large recurrent microdeletions associated with schizophrenia, Nature, 455, 232, 10.1038/nature07229 McCarroll, 2008, Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat. Genet., 40, 1166, 10.1038/ng.238 Albert, 2001, Effect of statin therapy on C-reactive protein levels: the pravastatin inflammation/CRP evaluation (PRINCE): a randomized trial and cohort study, JAMA, 286, 64, 10.1001/jama.286.1.64 Simon, 2006, Phenotypic predictors of response to simvastatin therapy among African-Americans and Caucasians: the Cholesterol and Pharmacogenetics (CAP) Study, Am. J. Cardiol., 97, 843, 10.1016/j.amjcard.2005.09.134 Cann, 2002, A human genome diversity cell line panel, Science, 296, 261, 10.1126/science.296.5566.261b Li, 2008, Worldwide human relationships inferred from genome-wide patterns of variation, Science, 319, 1100, 10.1126/science.1153717 Jakobsson, 2008, Genotype, haplotype and copy-number variation in worldwide human populations, Nature, 451, 998, 10.1038/nature06742 Rosenberg, 2006, Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives, Ann. Hum. Genet., 70, 841, 10.1111/j.1469-1809.2006.00285.x Cooper, 2008, Systematic assessment of copy number variant detection via genome-wide SNP genotyping, Nat. Genet., 40, 1199, 10.1038/ng.236 Day, 2007, Unsupervised segmentation of continuous genomic data, Bioinformatics, 23, 1424, 10.1093/bioinformatics/btm096 Bailey, 2002, Recent segmental duplications in the human genome, Science, 297, 1003, 10.1126/science.1072047 Willatt, 2005, 3q29 microdeletion syndrome: clinical and molecular characterization of a new syndrome, Am. J. Hum. Genet., 77, 154, 10.1086/431653 Korn, 2008, Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs, Nat. Genet., 40, 1253, 10.1038/ng.237 Simon-Sanchez, 2007, Genome-wide SNP assay reveals structural genomic variation, extended homozygosity and cell-line induced alterations in normal individuals, Hum. Mol. Genet., 16, 1, 10.1093/hmg/ddl436 McCarroll, 2006, Common deletion polymorphisms in the human genome, Nat. Genet., 38, 86, 10.1038/ng1696 Wang, 2007, PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data, Genome Res., 17, 1665, 10.1101/gr.6861907 Turner, 2008, Germline rates of de novo meiotic deletions and duplications causing several genomic disorders, Nat. Genet., 40, 90, 10.1038/ng.2007.40 Kidd, 2008, Mapping and sequencing of structural variation from eight human genomes, Nature, 453, 56, 10.1038/nature06862 Conrad, 2006, A high-resolution survey of deletion polymorphism in the human genome, Nat. Genet., 38, 75, 10.1038/ng1697 de Vries, 2005, Diagnostic genome profiling in mental retardation, Am. J. Hum. Genet., 77, 606, 10.1086/491719 Szatmari, 2007, Mapping autism risk loci using genetic linkage and chromosomal rearrangements, Nat. Genet., 39, 319, 10.1038/ng1985 Christian, 2008, Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder, Biol. Psychiatry, 63, 1111, 10.1016/j.biopsych.2008.01.009 Marshall, 2008, Structural variation of chromosomes in autism spectrum disorder, Am. J. Hum. Genet., 82, 477, 10.1016/j.ajhg.2007.12.009 Xu, 2008, Strong association of de novo copy number mutations with sporadic schizophrenia, Nat. Genet., 40, 880, 10.1038/ng.162 Kumar, 2008, Recurrent 16p11.2 microdeletions in autism, Hum. Mol. Genet., 17, 628, 10.1093/hmg/ddm376 McDermid, 2002, Genomic disorders on 22q11, Am. J. Hum. Genet., 70, 1077, 10.1086/340363 Lupski, 2005, Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes, PLoS Genet, 1, e49, 10.1371/journal.pgen.0010049 Wagenstaller, 2007, Copy-number variations measured by single-nucleotide-polymorphism oligonucleotide arrays in patients with mental retardation, Am. J. Hum. Genet., 81, 768, 10.1086/521274 Zody, 2008, Evolutionary toggling of the MAPT 17q21.31 inversion region, Nat. Genet., 10.1038/ng.193 Antshel, 2007, Autistic spectrum disorders in velo-cardio facial syndrome (22q11.2 deletion), J. Autism Dev. Disord., 37, 1776, 10.1007/s10803-006-0308-6 Ben-Shachar, 2008, 22q11.2 distal deletion: a recurrent genomic disorder distinct from DiGeorge syndrome and velocardiofacial syndrome, Am. J. Hum. Genet., 82, 214, 10.1016/j.ajhg.2007.09.014 Hannes, 2008, Recurrent reciprocal deletions and duplications of 16p13.11: the deletion is a risk factor for MR/MCA while the duplication may be a rare benign variant, J. Med. Genet.