Sifting the wheat from the chaff: Prioritizing GWAS results by identifying consistency across analytical methods

Genetic Epidemiology

Volumn 35, Issue 8, 2011, Pages 745-754

  Oldmeadow, Christopher ^a,b   Riveros, Carlos ^b,c   Holliday, Elizabeth G ^a,b   Scott, Rodney ^b   Moscato, Pablo ^b,c,d   Wang, Jie Jin ^e,f   Mitchell, Paul ^e   Buitendijk, Gabrielle H S ^g   Vingerling, Johannes R ^g   Klaver, Caroline C W ^g   Klein, Ronald ^h   Attia, John ^a,b  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b JOHN HUNTER HOSPITAL   (Australia)

^c NEWCASTLE UNIVERSITY   (United Kingdom)

^d Australian Government Australian Research Council   (Australia)

^e UNIVERSITY OF SYDNEY   (Australia)

^f UNIVERSITY OF MELBOURNE   (Australia)

^g ERASMUS MEDICAL CENTER   (Netherlands)

^h UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Age related macular degeneration; Genome wide association study

Indexed keywords

ADULT; ARTICLE; CHROMOSOME 10P; CHROMOSOME 2P; GENE LOCUS; GENETIC ASSOCIATION; HAPLOTYPE; HUMAN; RETINA MACULA AGE RELATED DEGENERATION; SINGLE NUCLEOTIDE POLYMORPHISM;

AUSTRALIA; CASE-CONTROL STUDIES; CHROMOSOMES, HUMAN, PAIR 10; CHROMOSOMES, HUMAN, PAIR 2; GENOME-WIDE ASSOCIATION STUDY; HAPLOTYPES; HUMANS; LOGISTIC MODELS; MACULAR DEGENERATION; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEINS; SAMPLE SIZE; SERINE ENDOPEPTIDASES;

EID: 82355170604     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20622     Document Type: Article

References (34)

1. Barrett JC, Clayton D, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, and others. 2009. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet 41:703-707.
2. Cantor RM, Lange K, Sinsheimer JS. 2010. Prioritizing GWAS results: a review of statistical methods and recommendations for their application. Am J Hum Genet 86:6-22.
3. Edwards AO, Ritter R, Abel KJ, Manning A, Panhuysen C, Farrer LA. 2005. Complement factor H polymorphism and age-related macular degeneration. Science 308:421-424.
4. Fisher SA, Abecasis GR, Yashar BM, Zareparsi S, Swaroop A, Iyengar SK, Klein BEK, Klein R, Lee KE, Majewski J and others. 2005. Meta-analysis of genome scans of age-related macular degeneration. Human Molecular Genetics 14:2257-2264.
5. Gold B, Merriam JE, Zernant J, Hancox LS, Taiber AJ, Gehrs K, Cramer K, Neel J, Bergeron J, Barile GR and others. 2006. Variation in factor B (BF) and complement component 2 (C2) genes is associated with age-related macular degeneration. Nat Genet 38:458-462.
6. Haines JL, Hauser MA, Schmidt S, Scott WK, Olson LM, Gallins P, Spencer KL, Kwan SY, Noureddine M, Gilbert JR and others. 2005. Complement factor H variant increases the risk of age-related macular degeneration. Science 308:419-421.
7. Hofman A, Breteler MMB, Van Duijn CM, Janssen HLA, Krestin GP, Kuipers EJ, Stricker BHC, Tiemeier H, Uitterlinden AG, Vingerling JR. 2009. The Rotterdam study: 2010 objectives and design update. Eur J epidemiol 24:553-572.
8. Hoggart CJ, Clark TG, De Iorio M, Whittaker JC, Balding DJ. 2008. Genome-wide significance for dense SNP and resequencing data. Genet Epidemiol 32:179-185.
9. Iyengar SK, Song D, Klein BEK, Klein R, Schick JH, Humphrey J, Millard C, Liptak R, Russo K, Jun G, and others. 2004. Dissection of genomewide-scan data in extended families reveals a major locus and oligogenic susceptibility for age-related macular degeneration. Am J Hum Genet 74:20-39.
10. Kenealy SJ, Schmidt S, Agarwal A, Postel EA, De La Paz MA, Pericak-Vance MA, Haines JL. 2004. Linkage analysis for age-related macular degeneration supports a gene on chromosome 10q26. Mol Vis 10:57-61.
11. Klaver CC, Wolfs RC, Assink JJ, van Duijn CM, Hofman A, de Jong PT. 1998. Genetic risk of age-related maculopathy. Population-based familial aggregation study. Arch Ophthalmol 116:1646-1651.
12. Klein RJ, Zeiss C, Chew EY, Tsai J-Y, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST and others. 2005. Complement factor H polymorphism in age-related macular degeneration. Science 308:385-389.
13. Kooperberg C, LeBlanc M, Dai JY, Rajapakse I. 2009. Structures and assumptions: strategies to harness Gene×Gene and Gene×Environment interactions in GWAS. Stat Sci 24:472-488.
14. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. 2010. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34:816-834.
15. Liu JZ, McRae AF, Nyholt DR, Medland SE, Wray NR, Brown KM, Hayward NK, Montgomery GW, Visscher PM, Martin NG and others. 2010. A versatile gene-based test for genome-wide association studies. Am J Hum Genet 87:139-145.
16. Majewski J, Schultz DW, Weleber RG, Schain MB, Edwards AO, Matise TC, Acott TS, Ott J, Klein ML. 2003. Age-related macular degeneration-a genome scan in extended families. Am J Hum Genet 73:540-550.
17. Maller J, George S, Purcell S, Fagerness J, Altshuler D, Daly MJ, Seddon JM. 2006. Common variation in three genes, including a noncoding variant in CFH, strongly influences risk of age-related macular degeneration. Nat Genet 38:1055-1059.
18. Neale BM, Sham PC. 2004. The future of association studies: gene-based analysis and replication. Am J Hum Genet 75:353-362.
19. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904-909.
20. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, and others. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559-575.
21. Rivera A, Fisher SA, Fritsche LG, Keilhauer CN, Lichtner P, Meitinger T, Weber BHF. 2005. 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.
22. Ruczinski I. 2004. Exploring interactions in high-dimensional genomic data: an overview of logic regression, with applications. J Multivariate Anal 90:178-195.
23. Santangelo SL, Haddad S, Chen C, Seddon JM. 2005. A genome scan for age-related macular degeneration with investigation of genetic heterogeneity using OSA analysis. Invest Ophthalmol Vis Sci 46:3205-3205.
24. Schaid DJ. 2006. Power and sample size for testing associations of haplotypes with complex traits. Ann Hum Genet 70:116-130.
25. Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. 2002. Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70:425-434.
26. Seddon JM, Ajani UA, Mitchell BD. 1997. Familial aggregation of age-related maculopathy. Am J Ophthalmol 123:199-206.
27. Seddon JM, Santangelo SL, Book K, Chong S, Cote J. 2003. A genomewide scan for age-related macular degeneration provides evidence for linkage to several chromosomal regions. Am J Hum Genet 73:780-790.
28. Stephens M, Smith NJ, Donnelly P. 2001. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989.
29. Wan X, Yang C, Yang Q, Xue H, Fan X, Tang NLS, Yu W. 2010. BOOST: a fast approach to detecting gene-gene interactions in genome-wide case-control studies. Am J Hum Genet 87:325-340.
30. Wang JJ, Rochtchina E, Lee AJ, Chia E-M, Smith W, Cumming RG, Mitchell P. 2007. Ten-year incidence and progression of age-related maculopathy: the Blue Mountains Eye Study. Ophthalmology 114:92-98.
31. Weeks DE, Conley YP, Mah TS, Paul TO, Morse L, Ngo-Chang J, Dailey JP, Ferrell RE, Gorin MB. 2000. A full genome scan for age-related maculopathy. Hum Mol Genet 9:1329-1349.
32. Weeks DE, Conley Y, Tsai H, Mah TS, Schmidt S, Postel EA, Agarwal A, Haines J, Pericak-Vance MA, Rosenfeld P and others. 2004. Age-related maculopathy: a genomewide scan with continued evidence of susceptibility loci within the 1q31, 10q26, and 17q25 regions. Am J Hum Genet 75:174-189.
33. Yang Z, Camp NJ, Sun H, Tong Z, Gibbs D, Cameron DJ, Chen H, Zhao Y, Pearson E, Li X, and others. 2006. A variant of the HTRA1 gene increases susceptibility to age-related macular degeneration. Science 314:992-993.
34. Zeggini E, Scott LJ, Saxena R, Voight BF, Marchini JL, Hu T, de Bakker PIW, Abecasis GR, Almgren P, Andersen G and others. 2008. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 40:638-645.