Copy-number variation and association studies of human disease (original) (raw)

• Inoue, K. & Lupski, J.R. Molecular mechanisms for genomic disorders. Annu. Rev. Genomics Hum. Genet. 3, 199–242 (2002).
  Article CAS Google Scholar
• Lupski, J. R. Genomic rearrangements and sporadic disease. Nat. Genet. 39, S43–S47 (2007).
  Article CAS Google Scholar
• Padiath, Q.S. et al. Lamin B1 duplications cause autosomal dominant leukodystrophy. Nat. Genet. 38, 1114–1123 (2006).
  Article CAS Google Scholar
• Le Marechal, C. et al. Hereditary pancreatitis caused by triplication of the trypsinogen locus. Nat. Genet. 38, 1372–1374 (2006).
  Article CAS Google Scholar
• Lee, J.A. & Lupski, J.R. Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders. Neuron 52, 103–121 (2006).
  Article CAS Google Scholar
• Gonzalez, E. et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307, 1434–1440 (2005).
  Article CAS Google Scholar
• Aitman, T.J. et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439, 851–855 (2006).
  Article CAS Google Scholar
• Yang, Y. et al. Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am. J. Hum. Genet. 80, 1037–1054 (2007).
  Article CAS Google Scholar
• Fanciulli, M. et al. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat. Genet. 39, 721–723 (2007).
  Article CAS Google Scholar
• Stranger, B.E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848–853 (2007).
  Article CAS Google Scholar
• de Bakker, P.I. et al. Efficiency and power in genetic association studies. Nat. Genet. 37, 1217–1223 (2005).
  Article CAS Google Scholar
• Pe'er, I. et al. Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat. Genet. 38, 663–667 (2006).
  Article CAS Google Scholar
• Altshuler, D. et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513–516 (2000).
  Article CAS Google Scholar
• Reich, D.E., Gabriel, S.B. & Altshuler, D. Quality and completeness of SNP databases. Nat. Genet. 33, 457–458 (2003).
  Article CAS Google Scholar
• Hinds, D.A. et al. Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072–1079 (2005).
  Article CAS Google Scholar
• International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299–1320 (2005).
• Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525–528 (2004).
  Article CAS Google Scholar
• Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949–951 (2004).
  Article CAS 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).
  Article CAS Google Scholar
• Tuzun, E. et al. Fine-scale structural variation of the human genome. Nat. Genet. 37, 727–732 (2005).
  Article CAS Google Scholar
• 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).
  Article CAS Google Scholar
• 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. Nat. Genet. 38, 82–85 (2006).
  Article CAS Google Scholar
• McCarroll, S.A. et al. Common deletion polymorphisms in the human genome. Nat. Genet. 38, 86–92 (2006).
  Article CAS 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).
  Article CAS Google Scholar
• Khaja, R. et al. Genome assembly comparison identifies structural variants in the human genome. Nat. Genet. 38, 1413–1418 (2006).
  Article CAS Google Scholar
• Redon, R. et al. Global variation in copy number in the human genome. Nature 444, 444–454 (2006).
  Article CAS Google Scholar
• Zhang, J., Feuk, L., Duggan, G.E., Khaja, R. & Scherer, S.W. Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet. Genome Res. 115, 205–214 (2006).
  Article CAS Google Scholar
• Eichler, E.E. et al. Completing the map of human genetic variation. Nature 447, 161–165 (2007).
  Article CAS Google Scholar
• Fiegler, H. et al. Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res. 16, 1566–1574 (2006).
  Article CAS Google Scholar
• McVean, G.A. et al. The fine-scale structure of recombination rate variation in the human genome. Science 304, 581–584 (2004).
  Article CAS Google Scholar
• Gabriel, S.B. et al. The structure of haplotype blocks in the human genome. Science 296, 2225–2229 (2002).
  Article CAS Google Scholar
• Lieberfarb, M.E. et al. Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP. Cancer Res. 63, 4781–4785 (2003).
  CAS PubMed Google Scholar
• Zhao, X. et al. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res. 64, 3060–3071 (2004).
  Article CAS Google Scholar
• Garraway, L.A. et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436, 117–122 (2005).
  Article CAS Google Scholar
• Zhao, X. et al. Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res. 65, 5561–5570 (2005).
  Article CAS Google Scholar
• Cohen, J.C. et al. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 305, 869–872 (2004).
  Article CAS Google Scholar
• Cohen, J.C., Boerwinkle, E., Mosley, T.H., Jr. & Hobbs, H.H. Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. N. Engl. J. Med. 354, 1264–1272 (2006).
  Article CAS Google Scholar
• Campbell, C.D. et al. Demonstrating stratification in a European American population. Nat. Genet. 37, 868–872 (2005).
  Article CAS Google Scholar
• Pritchard, J.K., Stephens, M., Rosenberg, N.A. & Donnelly, P. Association mapping in structured populations. Am. J. Hum. Genet. 67, 170–181 (2000).
  Article CAS Google Scholar
• Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006).
  Article CAS Google Scholar
• Clayton, D.G. et al. Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat. Genet. 37, 1243–1246 (2005).
  Article CAS Google Scholar
• Lohmueller, K.E., Pearce, C.L., Pike, M., Lander, E.S. & Hirschhorn, J.N. Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat. Genet. 33, 177–182 (2003).
  Article CAS Google Scholar