The Impact of Improved Microarray Coverage and Larger Sample Sizes on Future Genome-Wide Association Studies

Genetic Epidemiology

Volumn 37, Issue 4, 2013, Pages 383-392

  Lindquist, Karla J ^a,b   Jorgenson, Eric ^c   Hoffmann, Thomas J ^a,b   Witte, John S ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c DIVISION OF RESEARCH   (United States)

Author keywords

Complex disease; Genetic association studies; Heritability; Single nucleotide polymorphisms

Indexed keywords

ARTICLE; CHRONIC DISEASE; GENETIC ASSOCIATION; GENOME; GENOTYPE; HERITABILITY; MICROARRAY ANALYSIS; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM;

CHRONIC DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; ODDS RATIO; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; RESEARCH DESIGN; SAMPLE SIZE;

EID: 84876417113     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21724     Document Type: Article

References (42)

1. Begum F, Ghosh D, Tseng GC, Feingold E. 2012. Comprehensive literature review and statistical considerations for GWAS meta-analysis. Nucleic Acids Res 40:3777-84.
2. Bustamante CD, Burchard EG, De la Vega FM. 2011. Genomics for the world. Nature 13:163-165.
3. 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.
4. Capen EC, Clapp RV, Campbell WM. 1971. Competitive bidding in high-risk situations. J Pet Technol 23:641-653.
5. Das SK, Elbein SC. 2006. The genetic basis of Type 2 diabetes. Cellscience 2:100-131.
6. Gibson G. 2010. Hints of hidden heritability in GWAS. Nat Genet 42:558-560.
7. Girard SL, Gauthier J, Noreau A, Xiong L, Zhou S, Jouan L, Dionne-Laporte A, Spiegelman D, Henrion E, Diallo O and others. 2011. Increased exonic de novo mutation rate in individuals with schizophrenia. Nat Genet 10:860-863.
8. Hao K, Di X, Cawley S. 2007. LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage. Bioinformatics 23:252-54.
9. Harley JB, Alarcon-Riquelme ME, Criswell LA, Jacob CO, Kimberly RP, Moser KL, Tsao BP, Vyse TJ, Langefeld CD, Nath SK and others. 2008. Genome-wide association scan in women with systemic lupus erythema- tosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet 40:204-210.
10. Harney S, Wordsworth BP. 2002. Genetic epidemiology of rheumatoid arthritis. Tissue Antigens 60:465-473.
11. Hemminki K, Li X, Sundquist K, Sundquist J. 2007. Familial risks for asthma among twins and other siblings based on hospitalizations in Sweden. Clin Exp Allergy 37:1320-1325.
12. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106:9362-9367.
13. Hoffmann TJ, Zhan Y, Kvale MN, Hesselson SE, Gollub J, Iribarren C, Lu Y, Mei G, Purdy MM, Quesenberry C and others. 2011a. Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian African American and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm. Genomics 98:422-430.
14. Hoffmann TJ, Kvale MN, Hesselson SE, Zhan Y, Aquino C, Cao Y, Cawley S, Chung E, Connell S, Eshragh J and others. 2011b. Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array. Genomics 98:79-89.
15. Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. 2012. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet 44:955-995.
16. Howie BN, Donnelly P, Marchini J. 2009. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5:e1000529.
17. Iles MM. 2008. What can genome-wide association studies tell us about the genetics of common disease?. PLoS Genet 4:e33.
18. International HapMap Consortium. 2003. The International HapMap Project. Nature 18:789-796.
19. Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O'Donnell CJ, de Bakker PI. 2008. SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics 24(24):2938-2939.
20. Jorgenson E, Witte JS. 2006. Coverage and power in genomewide association studies. Am J Hum Genet 78:884-888.
21. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A and others. 2009. Finding the missing heritability of complex diseases. Nature 461:747-753.
22. Marchini J, Howie B. 2010. Genotype imputation for genome-wide association studies. Nat Rev Genet 11:499-511.
23. Marenberg ME, Risch N, Berkman LF, Floderus B, Defaire U. 1994. Genetic susceptibility to death from coronary heart disease in a study of twins. N Engl J Med 330:1041-1046.
24. Park JH, Wacholder S, Gail MH, Peters U, Jacobs KB, Chanock SJ, Chatterjee N. 2010. Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat Genet 42:570-575.
25. Pawitan Y, Seng KC, Magnusson PK. 2009. How many genetic variants remain to be discovered?. PLoS One 4:e7969.
26. Pritchard JK. 2001. Are rare variants responsible for susceptibility to complex diseases?. Am J Hum Genet 69:124-137.
27. Reich DE, Lander ES. 2001. On the allelic spectrum of human disease. Trends Genet 17:502-510.
28. Risch N. 2001. The genetic epidemiology of cancer: interpreting family and twin studies and their implications for molecular genetic approaches. Cancer Epidemiol Biomarkers Prev 10:733-741.
29. Sebastiani P, Timofeev N, Dworkis DA, Perls TT, Steinberg MH. 2009. Genome-wide association studies and the genetic dissection of complex traits. Am J Hematol 84:504-515.
30. Skol AD, Scott LJ, Abecasis GR, Boehnke M. 2006. Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 38:209-213.
31. Sladek R, Rocheleau G, Rung J, Dina C, Shen L, Serre D, Boutin P, Vincent D, Belisle A, Hadjadj S and others. 2007. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 22:881-885.
32. Sollid LM, Jabri B. 2005. Is celiac disease an autoimmune disorder?. Curr Opin Immunol 17:595-600.
33. Study of the Effectiveness of Additional Reductions in Cholesterol and Homocysteine (SEARCH) Collaborative Group. 2008. SLCO1B1 variants and statin-induced myopathy-a genomewide study. N Engl J Med 21:789-799.
34. The 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-1073.
35. Visscher PM, Brown MA, McCarthy MI, Yang J. 2012. Five Years of GWAS Discovery. Am J Hum Genet 13:7-24.
36. Williams SM, Haines JL. 2011. Correcting away the hidden heritability. Ann Hum Genet 75:348-50.
37. Witte JS. 2010. Genome-wide association studies and beyond. Annu Rev Public Health 31:9-20.
38. WTCCC. 2007. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 447:661-678.
39. Xu B, Roos JL, Dexheimer P, Boone B, Plummer B, Levy S, Gogos JA, Karayiorgou M. 2011. Exome sequencing supports a de novo mutational paradigm for schizophrenia. Nat Genet 7:864-868.
40. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW and others. 2010. Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42:565-569.
41. Yang J, Ferreira T, Morris AP, Medland SE, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, DIAbetes Genetics Replication and Meta-analysis (DIAGRAM) Consortium, Madden PA, Heath AC, Martin NG, Montgomery GW and others. 2012. Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nat Genet 44:369-378.
42. Zuk O, Hechter E, Sunyaev SR, Lander ES. 2012. The mystery of missing heritability: genetic interactions create phantom heritability. Proc Natl Acad Sci USA 109:1193-1198.