Replication of past candidate loci for common diseases and phenotypes in 100 genome-wide association studies

European Journal of Human Genetics

Volumn 18, Issue 7, 2010, Pages 832-837

  Siontis, Konstantinos C M ^a   Patsopoulos, Nikolaos A ^a   Ioannidis, John P A ^a,b,c  

^a UNIVERSITY OF IOANNINA   (Greece)

^b TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c INSTITUTE OF COMPUTER SCIENCE   (Greece)

Author keywords

Candidate loci; Common diseases phenotypes; Genome wide association studies; Replication; Single nucleotide polymorphisms

Indexed keywords

ARTICLE; CAUCASIAN; GENE FREQUENCY; GENE LOCUS; GENE REPLICATION; GENETIC ASSOCIATION; GENETIC SCREENING; GENETIC VARIABILITY; HEREDITY; HUMAN; PHENOTYPE; PRIORITY JOURNAL; RELIABILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

BAYES THEOREM; DATABASES, GENETIC; DISEASE; GENETIC LOCI; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; ODDS RATIO; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 77953774727     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2010.26     Document Type: Article

References (38)

1. Cordell HJ, Clayton DG: Genetic association studies. Lancet 2005; 366: 1121-1131.
2. Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K: A comprehensive review of genetic association studies. Genet Med 2002; 4: 45-61.
3. Lin BK, Clyne M, Walsh M et al: Tracking the epidemiology of human genes in the literature: the HuGE Published Literature database. Am J Epidemiol 2006; 164: 1-4.
4. Ioannidis JP, Ntzani EE, Trikalinos TA, Contopoulos-Ioannidis DG: Replication validity of genetic association studies. Nat Genet 2001; 29: 306-309.
5. Ioannidis JP: Genetic associations: false or true? Tr e n d s M o l M e d 2003; 9: 135-138.
6. Cardon LR: Genetics. Delivering new disease genes. Science 2006; 314: 1403-1405.
7. McCarthy MI, Abecasis GR, Cardon LR et al: Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 2008; 9: 356-369.
8. Manolio TA, Brooks LD, Collins FS: A HapMap harvest of insights into the genetics of common disease. J Clin Invest 2008; 118: 1590-1605.
9. Barrett JC, Cardon LR: Evaluating coverage of genome-wide association studies. Nat Genet 2006; 38: 659-662.
10. Yu W, Gwinn M, Clyne M, Yesupriya A, Khoury MJ: A navigator for human genome epidemiology. Nat Genet 2008; 40: 124-125.
11. Bertram L, McQueen MB, Mullin K, Blacker D, Tanzi RE: Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat Genet 2007; 39: 17-23.
12. Allen NC, Bagade S, McQueen MB et al: Systematic meta-analyses and field synopsis of genetic association studies in schizophrenia: the SzGene database. Nat Genet 2008; 40: 827-834.
13. Ioannidis JP: Calibration of credibility of agnostic genome-wide associations. Am J Med Genet B Neuropsychiatr Genet 2008; 147B: 964-972.
14. Ioannidis JP: Effect of formal statistical significance on the credibility of observational associations. Am J Epidemiol 2008; 168: 374-383.
15. Kehoe P, Wavrant-De Vrieze F, Crook R et al: A full genome scan for late onset Alzheimer's disease. Hum Mol Genet 1999; 8: 237-245.
16. Gaffney PM, Kearns GM, Shark KB et al: A genome-wide search for susceptibility genes in human systemic lupus erythematosus sib-pair families. Proc Natl Acad Sci USA 1998; 95: 14875-14879.
17. Jawaheer D, Seldin MF, Amos CI et al: Screening the genome for rheumatoid arthritis susceptibility genes: a replication study and combined analysis of 512 multicase families. Arthritis Rheum 2003; 48: 906-916.
18. Gudbjartsson DF, Arnar DO, Helgadottir A et al: Variants conferring risk of atrial fibrillation on chromosome 4q25. Nature 2007; 448: 353-357.
19. Haiman CA, Patterson N, Freedman ML et al: Multiple regions within 8q24 independently affect risk for prostate cancer. Nat Genet 2007; 39: 638-644.
20. Graham RR, Kyogoku C, Sigurdsson S et al: Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Proc Natl Acad Sci USA 2007; 104: 6758-6763.
21. Ioannidis JP, Gwinn M, Little J et al: A road map for efficient and reliable human genome epidemiology. Nat Genet 2006; 38: 3-5.
22. Pe¢er I, Yelensky R, Altshuler D, Daly MJ: Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet Epidemiol 2008; 32: 381-385.
23. Hoggart CJ, Clark TG, De Iorio M, Whittaker JC, Balding DJ: Genome-wide significance for dense SNP and resequencing data. Genet Epidemiol 2008; 32: 179-185.
24. Ioannidis JP: Why most discovered true associations are inflated. Epidemiology 2008; 19: 640-648.
25. Zollner S, Pritchard JK: Overcoming the winner's curse: estimating penetrance parameters from case-control data. Am J Hum Genet 2007; 80: 605-615.
26. Zeggini E, Weedon MN, Lindgren CM et al: Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 2007; 316: 1336-1341.
27. Zeggini E, Scott LJ, Saxena R et al: Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 2008; 40: 638-645.
28. Manolio TA, Collins FS, Cox NJ et al: Finding the missing heritability of complex diseases. Nature 2009; 461: 747-753.
29. Dong LM, Potter JD, White E, Ulrich CM, Cardon LR, Peters U: Genetic susceptibility to cancer: the role of polymorphisms in candidate genes. JAMA 2008; 299: 2423-2436.
30. Vineis P, Manuguerra M, Kavvoura FK et al: A field synopsis on low-penetrance variants in DNA repair genes and cancer susceptibility. J Natl Cancer Inst 2009; 101: 24-36.
31. Ntzani EE, Rizos EC, Ioannidis JP: Genetic effects versus bias for candidate polymorphisms in myocardial infarction: case study and overview of large-scale evidence. Am J Epidemiol 2007; 165: 973-984.
32. Morgan TM, Krumholz HM, Lifton RP, Spertus JA: Nonvalidation of reported genetic risk factors for acute coronary syndrome in a large-scale replication study. JAMA 2007; 297: 1551-1561.
33. Wang L, Weinshilboum RM: Pharmacogenomics: candidate gene identification, functional validation and mechanisms. Hum Mol Genet 2008; 17: R174-R179.
34. Bodmer W, Bonilla C: Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 2008; 40: 695-701.
35. Ioannidis JP, Thomas T, Daly MJ: Validating, augmenting and refining genome-wide association signals. Nat Rev Genet 2009; 10: 318-329.
36. McCarthy MI, Hirschhorn JN: Genome-wide association studies: potential next steps on a genetic journey. Hum Mol Genet 2008; 17 (R2): R156-R165.
37. Zeggini E, Ioannidis JP: Meta-analysis in genome-wide association studies. Pharmaco-genomics 2009; 10: 191-201.
38. Richards JB, Kavvoura FK, Rivadeneira F et al: Collaborative meta-analysis: associations of 150 candidate genes with osteoporosis and osteoporotic fracture. Ann Intern Med 2009; 151: 528-537.