Complex SNP-related sequence variation in segmental genome duplications

Nature Genetics

Volumn 36, Issue 8, 2004, Pages 861-866

  Fredman, David ^a   White, Stefan J ^b   Potter, Susanna ^a   Eichler, Evan E ^c   Den Dunnen, Johan T ^b   Brookes, Anthony J ^a,d  

^a KAROLINSKA INSTITUTE   (Sweden)

^b LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^c CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF LEICESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE CONVERSION; GENE DUPLICATION; GENOTYPE; HAPLOIDY; HUMAN; HYDATIDIFORM MOLE; PARALOGY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EVOLUTION, MOLECULAR; FEMALE; GENE DOSAGE; GENETIC MARKERS; GENOME, HUMAN; GENOTYPE; HUMANS; HYDATIDIFORM MOLE; POLYMORPHISM, SINGLE NUCLEOTIDE; PREGNANCY; REPETITIVE SEQUENCES, NUCLEIC ACID; VARIATION (GENETICS);

EID: 3543040014     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1401     Document Type: Article

References (29)

1. Venter, J.C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001).
2. Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409 860-921 (2001).
3. Bailey, J.A. et al. Recent segmental duplications in the human genome. Science 297, 1003-1007 (2002).
4. 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).
5. Istrail, S. et al. Whole-genome shotgun assembly and comparison of human genome assemblies, Proc. Natl. Acad. Sci. USA 101, 1916-1921 (2004).
6. 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).
7. 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).
8. Cheung, J. et al. Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 4, R25 (2003).
9. Sachidanandam, R. et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928-933 (2001).
10. Tsui, C. et al. Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map. Nucleic Acids Res, 31, 4910-4916 (2003).
11. Hurles, M.E. Gene conversion homogenizes the CMTIA paralogous repeats. BMC Genomics 2, 11 (2001).
12. Hurles, M. Are 100,000 "SNPs" useless? Science 298, 1509 (2002).
13. Conant, G.C. & Wagner, A. Asymmetric sequence divergence of duplicate genes. Genome Res. 13, 2052-2058 (2003).
14. 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).
15. 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).
16. Kruglyak, L. & Nickerson, D.A. Variation is the spice of life. Nat. Genet. 27, 234-236 (2001).
17. Smit, A.F. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr. Opin. Genet. Dev. 9, 657-663 (1999).
18. 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).
19. Rozen, S. et al. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423, 873-876 (2003).
20. 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).
21. 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).
22. White, S.J. et al. Two-colour MLPA: detecting genomic rearrangements in hereditary multiple exostoses. Hum. Mutat. 24, 86-92 (2004).
23. Schouten, J.P. et al. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 30, e57 (2002).
24. Lucito, R. et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 13, 2291-2305 (2003).
25. Sherry, S.T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311 (2001).
26. Birney, E. et al. Ensembl 2004. Nucleic Acids Res. 32, D468-D470 (2004).
27. 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).
28. 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).
29. 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).