A gene-centric approach to genome-wide association studies

Nature Reviews Genetics

Volumn 7, Issue 11, 2006, Pages 885-891

  Jorgenson, Eric ^a   Witte, John S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS; GENE; GENE FUNCTION; GENETIC VARIABILITY; GENOME; GENOTYPE; HUMAN; PRIORITY JOURNAL; REVIEW; RISK; SINGLE NUCLEOTIDE POLYMORPHISM;

DATABASES, GENETIC; GENETIC PREDISPOSITION TO DISEASE; GENETIC TECHNIQUES; GENETIC VARIATION; GENOME, HUMAN; GENOMICS; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; VARIATION (GENETICS);

EID: 33750211858     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg1962     Document Type: Review

References (29)

1. Risch, N. & Merikangas, K. The future of genetic studies of complex human diseases. Science 273, 1516-1517 (1996).
2. Kruglyak, L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genet. 22, 139-144 (1999).
3. Collins, F. S., Brooks, L. D. & Chakravarti, A. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8, 1229-1231 (1998).
4. Olds, L. C. & Sibley, E. Lactase persistence DNA variant enhances lactase promoter activity in vitro: functional role as a cis regulatory element. Hum. Mol. Genet. 12, 2333-2340 (2003).
5. The International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003).
6. Altshuler, D. et al. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
7. Ozaki, K. et al. Functional SNPs in the lymphotoxin-α gene that are associated with susceptibility to myocardial infarction. Nature Genet. 32, 650-654 (2002).
8. Klein, R. J. et al. Complement factor H polymorphism in age-related macular degeneration. Science 308, 385-389 (2005).
9. Maraganore, D. M. et al. High-resolution whole-genome association study of Parkinson disease. Am. J. Hum. Genet. 77, 685-693 (2005).
10. Conley, Y. P. et al. Candidate gene analysis suggests a role for fatty acid biosynthesis and regulation of the complement system in the etiology of age-related maculopathy. Hum. Mol. Genet. 14, 1991-2002 (2005).
11. Rivera, A. et al. Hypothetical LOC387715 is a second major susceptibility gene for age-related macular degeneration, contributing independently of complement factor H to disease risk. Hum. Mol. Genet. 14, 3227-3236 (2005).
12. Terwilliger, J. D. & Hiekkalinna, T. An utter refutation of the "Fundamental Theorem of the HapMap". Eur. J. Hum. Genet. 14, 426-437 (2006).
13. Botstein, D. & Risch, N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nature Genet. 33, 228-237 (2003).
14. Palmer L. J., Cardon, L. R. Shaking the tree: Mapping complex disease genes using linkage disequilibrium. Lancet 336, 1223-1234 (2005).
15. Tabor, H. K., Risch, N. J. & Myers, R. M. Candidate-gene approaches for studying complex genetic traits: practical considerations. Nature Rev. Genet. 3, 391-397 (2002).
16. Smith, A. V., Thomas, D. J., Munro, H. M. & Abecasis, G. R. Sequence features in regions of weak and strong linkage disequilibrium. Genome Res. 15, 1519-1534 (2005).
17. McVean, G. A. et al. The fine-scale structure of recombination rate variation in the human genome. Science 304, 581-584 (2004).
18. Tsunoda, T. et al. Variation of gene-based SNPs and linkage disequilibrium patterns in the human genome. Hum. Mol. Genet. 13, 1623-1632 (2004).
19. Goddard, K. A., Hopkins, P. J., Hall, J. M. & Witte, J. S. Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms in five populations. Am. J. Hum. Genet. 66, 216-234 (2000).
20. Stephens, J. C. et al. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293, 489-493 (2001).
21. Hill, W. G. & Robertson, A. The effect of linkage on limits to artificial selection. Genet. Res. 8, 269-294 (1966).
22. Pe'er, I. et al. Evaluating and improving power in whole-genome association studies using fixed marker sets. Nature Genet. 38, 663-667 (2006).
23. Barrett, J. C. & Cardon, L. R. Evaluating coverage of genome-wide association studies. Nature Genet. 38, 659-662 (2006).
24. de Bakker, P. I. et al. Efficiency and power in genetic association studies. Nature Genet. 37, 1217-1223 (2005).
25. Jorgenson, E. & Witte, J. S. Coverage and power in genome-wide association studies. Am. J. Hum. Genet. 78, 884-889 (2006).
26. Pennisi, E. Human genome. A low number wins the GeneSweep Pool. Science 300, 1484 (2003).
27. Livingston, R. J. et al. Pattern of sequence variation across 213 environmental response genes. Genome Res. 14, 1821-1831 (2004).
28. Crawford, D. C. et al. Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am. J. Hum. Genet. 74, 610-622 (2004).
29. 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).