Complex SNP-related sequence variation in segmental genome duplications (original) (raw)

• Venter, J.C. et al. The sequence of the human genome. Science 291, 1304–1351 (2001).
  Article CAS Google Scholar
• Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
  Article CAS Google Scholar
• Bailey, J.A. et al. Recent segmental duplications in the human genome. Science 297, 1003–1007 (2002).
  Article CAS Google Scholar
• Bailey, J.A., Yavor, A.M., Massa, H.F., Trask, B.J. & Eichler, E.E. Segmental duplications: organization and impact within the current human genome project assembly. Genome Res. 11, 1005–1017 (2001).
  Article CAS Google Scholar
• Istrail, S. et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proc. Natl. Acad. Sci. USA 101, 1916–1921 (2004).
  Article CAS Google Scholar
• Shaw, C.J. & Lupski, J.R. Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum. Mol. Genet. 13, R57–R64 (2004).
  Article CAS Google Scholar
• Estivill, X. et al. Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome. Hum. Mol. Genet. 11, 1987–1995 (2002).
  Article CAS Google Scholar
• Cheung, J. et al. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 4, R25 (2003).
  Article Google Scholar
• Sachidanandam, R. et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933 (2001).
  Article CAS Google Scholar
• Tsui, C. et al. Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map. Nucleic Acids Res. 31, 4910–4916 (2003).
  Article CAS Google Scholar
• Hurles, M.E. Gene conversion homogenizes the CMT1A paralogous repeats. BMC Genomics 2, 11 (2001).
  Article CAS Google Scholar
• Hurles, M. Are 100,000 “SNPs” useless? Science 298, 1509 (2002).
  Article Google Scholar
• Conant, G.C. & Wagner, A. Asymmetric sequence divergence of duplicate genes. Genome Res. 13, 2052–2058 (2003).
  Article CAS Google Scholar
• Prince, J.A. et al. Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation. Genome Res. 11, 152–162. (2001).
  Article CAS Google Scholar
• Sebire, N.J., Fisher, R.A. & Rees, H.C. Histopathological diagnosis of partial and complete hydatidiform mole in the first trimester of pregnancy. Pediatr. Dev. Pathol. 6, 69–77 (2003).
  Article Google Scholar
• Kruglyak, L. & Nickerson, D.A. Variation is the spice of life. Nat. Genet. 27, 234–236 (2001).
  Article CAS Google Scholar
• Smit, A.F. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9, 657–663 (1999).
  Article CAS Google Scholar
• Jeffreys, A.J. & May, C.A. Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nat. Genet. 36, 151–156 (2004).
  Article CAS Google Scholar
• Rozen, S. et al. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423, 873–876 (2003).
  Article CAS Google Scholar
• Hollox, E.J., Armour, J.A. & Barber, J.C. Extensive normal copy number variation of a beta-defensin antimicrobial-gene cluster. Am. J. Hum. Genet. 73, 591–600 (2003).
  Article CAS Google Scholar
• Locke, D.P. et al. BAC microarray analysis of 15q11-q13 rearrangements and the impact of segmental duplications. J. Med. Genet. 41, 175–182 (2004).
  Article CAS Google Scholar
• White, S.J. et al. Two-colour MLPA; detecting genomic rearrangements in hereditary multiple exostoses. Hum. Mutat. 24, 86–92 (2004).
  Article CAS Google Scholar
• Schouten, J.P. et al. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 30, e57 (2002).
  Article Google Scholar
• Lucito, R. et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 13, 2291–2305 (2003).
  Article CAS Google Scholar
• Sherry, S.T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).
  Article CAS Google Scholar
• Birney, E. et al. Ensembl 2004. Nucleic Acids Res. 32, D468–D470 (2004).
  Article CAS Google Scholar
• Fredman, D., Jobs, M., Stromqvist, L. & Brookes, A.J. DFold: PCR design that minimizes secondary structure and optimizes downstream genotyping applications. Hum. Mutat. 24, 1–8 (2004).
  Article CAS Google Scholar
• Carlson, C.S. et al. Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat. Genet. 33, 518–521 (2003).
  Article CAS Google Scholar
• White, S. et al. Comprehensive detection of genomic duplications and deletions in the DMD gene, by use of multiplex amplifiable probe hybridization. Am. J. Hum. Genet. 71, 365–374 (2002).
  Article CAS Google Scholar