Fine-scale structural variation of the human genome

Nature Genetics

Volumn 37, Issue 7, 2005, Pages 727-732

  Tuzun, Eray ^a   Sharp, Andrew J ^a   Bailey, Jeffrey A ^b   Kaul, Rajinder ^c   Morrison, V Anne ^a   Pertz, Lisa M ^b   Haugen, Eric ^c   Hayden, Hillary ^c   Albertson, Donna ^d   Pinkel, Daniel ^d   Olson, Maynard V ^c   Eichler, Evan E ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

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

^c UNIVERSITY OF WASHINGTON   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DISEASE PREDISPOSITION; GENE MAPPING; GENETIC POLYMORPHISM; GENOTYPE; HUMAN; HUMAN GENOME; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; BASE PAIRING; BIOLOGY; DNA MICROARRAY; DNA SEQUENCE; GENOME; GENOMIC INSTABILITY; MUTATION; REFERENCE VALUE; TUMOR CELL LINE;

BASE PAIRING; CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; GENOME, HUMAN; GENOMIC INSTABILITY; HUMANS; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, GENETIC; REFERENCE VALUES; SEQUENCE ANALYSIS, DNA;

EID: 22844451617     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1562     Document Type: Article

References (27)

1. Botstein, D. & Risch, N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat. Genet. 33 Suppl, 228-237 (2003).
2. Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525-528 (2004).
3. Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949-951 (2004).
4. Gonzalez, E. et al. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307, 1434-1440 (2005).
5. Stefansson, H. et al. A common inversion under selection in Europeans. Nat. Genet. 37, 129-137 (2005).
6. International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004).
7. She, X. et al. Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431, 927-930 (2004).
8. Buckland, P.R. Polymorphically duplicated genes: their relevance to phenotypic variation in humans. Ann. Med. 35, 308-315 (2003).
9. Small, K., Iber, J. & Warren, S. Emerin deletion revais a common X-chromosome inversion mediated by inverted repeats. Nat. Genet. 16, 96-99 (1997).
10. Colin, Y. et al. Genetic basis of the RhD-positive and RhD-negative blood group polymorphism as determined by Southern analysis. Blood 78, 2747-2752 (1991).
11. Lackner, C., Cohen, J.C. & Hobbs, H.H. Molecular definition of the extreme size polymorphism in apolipoprotem(a). Hum. Mol. Genet. 2. 933-940 (1993)
12. Kruglyak, L. & Nickerson, D.A. Variation is the spice of life. Nat. Genet. 27, 234-236 (2001).
13. Bailey, J.A. et al. Recent segmental duplications in the human genome. Science 297, 1003-1007 (2002).
14. Locke, D.P. et al. Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster. Genome Biol. 4, R50 (2003).
15. Brewer, C., Holloway, S., Zawalnyski, P., Schinzel, A. & FitzPatnck, D. A chromosomal duplication map of malformations: regions of suspected haplo- and triplolethality-and tolerance of segmental aneuploidy-in humans. Am. J. Hum. Genet. 64, 1702-1708 (1999).
16. Lindsley, D.L. et al. Segmental aneuploidy and the genetic gross structure of the Drosophila genome. Genetics 71, 157-184 (1972).
17. Snijders, A.M. et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet. 29, 263-264 (2001).
18. Horvath, J., Schwartz, S. & Eichler, E. The mosaic structure of a 2p11 pericentromeric segment: A strategy for characterizing complex regions of the human genome. Genome Res. 10, 839-852 (2000).
19. Eichler, E.E. et al. Length of uninterrupted CGG repeats determines stability in the FMR1 gene. Nat. Genet. 8, 88-94 (1994).
20. Badge, P.M., Alisch, R.S. & Moran, J.V. ATLAS: a system to selectively identify human-specific L1 insertions. Am. J. Hum. Genet. 72, 823-838 (2003).
21. Wong, G.K., Yu, J., Thayer, E.C. & Olson, M.V. Multiple-complete- digest restriction fragment mapping: generating sequence-ready maps for large-scale DNA sequencing. Proc. Natl. Acad. Sci. USA 94, 5225-5230 (1997).
22. Thompson, J.D., Higgins, D.G. & Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).
23. Sprenger, R. et al. Characterization of the glutathione S-transferase GSTT1 deletion: discrimination of all genotypes by polymerase chain reaction indicates a trimodular genotype-phenotype correlation. Pharmacogenetics 10, 557-565 (2000).
24. McLellan, R.A., Oscarson, M., Seidegard, J., Evans, D.A. & Ingelman-Sundberg, M. Frequent occurrence of CYP2D6 gene duplication in Saudi Arabians. Pharmacogenetics 7, 187-191 (1997).
25. Aklillu, E. et al. Frequent distribution of ultrarapid metabolizers of debrisoquine in an ethiopian population carrying duplicated and multiduplicated functional CYP2D6 alleles. J. Pharmacol. Exp. Ther. 278, 441-446 (1996).
26. Koppens, P.F., Hoogenboezem, T. & Degenhart, H.J. Duplication of the CYP21A2 gene complicates mutation analysis of steroid 21-hydroxylase deficiency: characteristics of three unusual haplotypes. Hum. Genet. 111, 405-410 (2002).
27. Lee, E.J., Wong, J.Y., Yeoh, P.N. & Gong, N.H. Glutathione S-transferase-θ (GSTT1) genetic polymorphism among Chinese, Malays and Indians in Singapore. Pharmacogenetics 5, 332-334 (1995).