The road to genome-wide association studies

Nature Reviews Genetics

Volumn 9, Issue 4, 2008, Pages 314-318

  Kruglyak, Leonid ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCE; GENE FREQUENCY; GENE FUNCTION; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC MARKER; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; INTRAHEPATIC CHOLESTASIS; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; RNA TRANSLATION; SINGLE NUCLEOTIDE POLYMORPHISM;

CASE-CONTROL STUDIES; CHROMOSOME MAPPING; GENOME, HUMAN; GENOMICS; HISTORY, 18TH CENTURY; HISTORY, 20TH CENTURY; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; VARIATION (GENETICS);

EID: 40849096166     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg2316     Document Type: Review

References (56)

1. Altshuler, D. & Daly, M. Guilt beyond a reasonable doubt. Nature Genet. 39, 813-815 (2007).
2. Bowcock, A. M. Genomics: guilt by association. Nature 447, 645-646 (2007).
3. Gibson, G. & Goldstein, D. B. Human genetics: the hidden text of genome-wide associations. Curr. Biol. 17, R929-R932 (2007).
4. Topol, E. J., Murray, S. S. & Frazer, K. A. The genomics gold rush. JAMA 298, 218-221 (2007).
5. The International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003).
6. Botstein, D., White, D. L., Skolnick, M. & Davis, R. W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314-331 (1980).
7. Solomon, E. & Bodmer, W. F. Evolution of sickle variant gene. Lancet 1, 923 (1979).
8. Lander, E. S. & Botstein, D. Mapping complex genetic traits in humans: new methods using a complete RFLP linkage map. Cold Spring Harb. Symp. Quant. Biol. 51, 49-62 (1986).
9. Kan, Y. W. & Dozy, A. M. Polymorphism of DNA sequence adjacent to human beta-globin structural gene: relationship to sickle mutation. Proc. Natl Acad. Sci. USA 75, 5631-5635 (1978).
10. Bodmer, W. F. Human genetics: the molecular challenge. Cold Spring Harb. Symp. Quant. Biol. 51, 1-13 (1986).
11. Donis-Keller, H. et al. A genetic linkage map of the human genome. Cell 51, 319-337 (1987).
12. Weissenbach, J. et al. A second-generation linkage map of the human genome. Nature 359, 794-801 (1992).
13. Kerem, B. -S. et al. Identification of the cystic fibrosis gene: genetic analysis. Science 245, 1073-1080 (1989).
14. Houwen, R. H. J. et al. Genome scanning by searching for shared segments: mapping a gene for benign recurrent intrahepatic cholestasis. Nature Genet. 8, 380-386 (1994).
15. Puffenberger, E. G. et al. Identity-by-descent and association mapping of a recessive gene for Hirschsprung disease on human chromosome 13q22. Hum. Mol. Genet. 3, 1217-1225 (1994).
16. Risch, N. Linkage strategies for genetically complex traits. III. The effect of marker polymorphism on analysis of affected relative pairs. Am. J. Hum. Genet. 46, 242-253 (1990).
17. Risch, N. Linkage strategies for genetically complex traits. II. The power of affected relative pairs. Am. J. Hum. Genet. 46, 229-241 (1990).
18. Risch, N. Linkage strategies for genetically complex traits. I. Multilocus models. Am. J. Hum. Genet. 46, 222-228 (1990).
19. Kruglyak, L. & Lander, E. S. Complete multipoint sib-pair analysis of qualitative and quantitative traits. Am. J. Hum. Genet. 57, 439-454 (1995).
20. Risch, N. & Merikangas, K. The future of genetic studies of complex human diseases. Science 273, 1516-1517 (1996).
21. Lander, E. S. The new genomics: global views of biology. Science 274, 536-539 (1996).
22. Collins, F. S., Guyer, M. S. & Chakravarti, A. Variations on a theme: cataloging human DNA sequence variation. Science 278, 1580-1581 (1997).
23. Wang, D. G. et al. Large-scale identification, mapping and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077-1082 (1998).
24. The International SNP Map Working Group. A map of human genome sequence variation containing 1 million single nucleotide polymorphisms. Nature 409, 928-933 (2001).
25. Kruglyak, L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genet. 22, 139-144 (1999).
26. Collins, F. S. et al. New goals for the US human genome project: 1998-2003. Science 282, 682-689 (1998).
27. Pe'er, I. et al. Biases and reconciliation in estimates of linkage disequilibrium in the human genome. Am. J. Hum. Genet. 78, 588-603 (2006).
28. Reich, D. E. et al. Human genome sequence variation and the influence of gene history, mutation and recombination. Nature Genet. 32, 135-142 (2002).
29. The International HapMap Consortium. A second generation human haplotype map of over 3 million SNPs. Nature 449, 851-861 (2007).
30. Lonjou, C., Collins, A. & Morton, N. E. Allelic association between marker loci. Proc. Natl Acad. Sci. USA 96, 1621-1626 (1999).
31. Kruglyak, L. Genetic isolates: separate but equal? Proc. Natl Acad. Sci. USA 96, 1170-1172 (1999).
32. Carlson, C. S. et al. Additional SNPs and linkage-disequilibrium analyses are necessary for wholegenome association studies in humans. Nature Genet. 33, 518-521 (2003).
33. Gabriel, S. B. et al. The structure of haplotype blocks in the human genome. Science 296, 2225-2229 (2002).
34. Reich, D. E., Gabriel, S. B. & Altshuler, D. Quality and completeness of SNP databases. Nature Genet. 33, 457-458 (2003).
35. Daly, M. J., Rioux, J. D., Schaffner, S. F., Hudson, T. J. & Lander, E. S. High-resolution haplotype structure in the human genome. Nature Genet. 29, 229-232 (2001).
36. Hinds, D. A. et al. Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072-1079 (2005).
37. The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
38. Hirschhorn, J. N. & Daly, M. J. Genome-wide association studies for common diseases and complex traits. Nature Rev. Genet. 6, 95-108 (2005).
39. Sulem, P. et al. Genetic determinants of hair, eye and skin pigmentation in Europeans. Nature Genet. (2007).
40. Weedon, M. N. et al. A common variant of HMGA2 is associated with adult and childhood height in the general population. Nature Genet. 39, 1245-1250 (2007).
41. Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661-678 (2007).
42. Albert, T. J. et al. Direct selection of human genomic loci by microarray hybridization. Nature Methods 4, 903-905 (2007).
43. Hodges, E. et al. Genome-wide in situ exon capture for selective resequencing. Nature Genet. (2007).
44. Porreca, G. J. et al. Multiplex amplification of large sets of human exons. Nature Methods 4, 931-936 (2007).
45. Legendre, M., Pochet, N., Pak, T. & Verstrepen, K. J. Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Res. 17, 1787-1796 (2007).
46. Kruglyak, L. & Nickerson, D. A. Variation is the spice of life. Nature Genet. 27, 234-236 (2001).
47. Estivill, X. & Armengol, L. Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies. PLoS Genet. 3, 1787-1799 (2007).
48. Sinha, H., Nicholson, B. P., Steinmetz, L. M. & McCusker, J. H. Complex genetic interactions in a quantitative trait locus. PLoS Genet. 2, e13 (2006).
49. Brenner, S. E. Common sense for our genomes. Nature 449, 783-784 (2007).
50. Levy, S. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007).
51. Anonymous. Risky business. Nature Genet. 39, 1415 (2007).
52. McGuire, A. L., Cho, M. K., McGuire, S. E. & Caulfield, T. Medicine. The future of personal genomics. Science 317, 1687 (2007).
53. Gusella, J. F. et al. A polymorphic DNA marker genetically linked to Huntington's disease. Nature 306, 234-238 (1983).
54. Wyman, A. R. & White, R. W. A highly polymorphic locus in human DNA. Proc. Natl. Acad. Sci. USA 77, 6754-6758 (1980).
55. Weber, J. L. & May, P. E. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44, 388-396 (1989).
56. Kruglyak, L. The use of a genetic map of biallelic markers in linkage studies. Nature Genet. 17, 21-24 (1997).