Technical Reproducibility of Genotyping SNP Arrays Used in Genome-Wide Association Studies

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Hong, Huixiao ^a   Xu, Lei ^a   Liu, Jie ^a   Jones, Wendell D ^b   Su, Zhenqiang ^a   Ning, Baitang ^a   Perkins, Roger ^a   Ge, Weigong ^a   Miclaus, Kelci ^c   Zhang, Li ^a   Park, Kyunghee ^d   Green, Bridgett ^a   Han, Tao ^a   Fang, Hong ^a   Lambert, Christophe G ^e   Vega, Silvia C ^f   Lin, Simon M ^g   Jafari, Nadereh ^h   Czika, Wendy ^c   Wolfinger, Russell D ^c   Goodsaid, Federico ^a,i   Tong, Weida ^a   Shi, Leming ^a   more..

^a CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^b Expression Analysis Inc   (United States)

^c SAS INSTITUTE INC   (United States)

^d Samsung Advanced Institute of Technology (SAIT)   (South Korea)

^e GOLDEN HELIX INC   (United States)

^f MICROSOFT   (United States)

^g MARSHFIELD CLINIC   (United States)

^h NORTHWESTERN UNIVERSITY   (United States)

ⁱ VERTEX PHARMACEUTICALS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; DNA MICROARRAY; GENE FREQUENCY; GENE TECHNOLOGY; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPING TECHNIQUE; HUMAN; INTERMETHOD COMPARISON; LABORATORY TEST; MATHEMATICAL COMPUTING; QUALITY CONTROL; REPRODUCIBILITY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 84866081687     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0044483     Document Type: Article

References (42)

1. The International HapMap Consortium, (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-862.
2. Manolio TA, Brooks LD, Collins FS, (2008) A HapMap harvest of insights into the genetics of common disease. J Clin Invest 118: 1590-1605.
3. Zeggini E, Weedon MN, Lindgren CM, Frayling TM, Elliott KS, et al. (2007) Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 316: 1336-1341.
4. Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, et al. (2007) A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316: 1341-1345.
5. Sladek R, Rocheleau G, Rung J, Dina C, Shen L, et al. (2007) A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445: 881-885.
6. Steinthorsdottir V, Thorleifsson G, Reynisdottir I, Benediktsson R, Jonsdottir T, et al. (2007) A variant in CDKAL1 influences insulin response and risk of type 2 diabetes. Nat Genet 39: 770-775.
7. Rung J, Cauchi S, Albrechtsen A, Shen L, Rocheleau G, et al. (2009) Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistence and hyperinsulinemia. Nat Genet 41: 1110-1115.
8. Wellcome Trust Case Control Consortium, (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
9. Raelson JV, Little RD, Ruether A, Fournier H, Paquin B, et al. (2007) Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci. Proc Natl Acad Sci USA 104: 14747-14752.
10. Smyth DJ, Cooper JD, Bailey R, Field S, Burren O, et al. (2006) A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat Genet 38: 617-619.
11. Gudmundsson J, Sulem P, Manolescu A, Amundadottir LT, Gudbjartsson D, et al. (2007) Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat Genet 39: 631-637.
12. van Heel DA, Franke L, Hunt KA, Gwilliam R, Zhernakova A, et al. (2007) A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nat Genet 39: 827-829.
13. Tomlinson I, Webb E, Carvajal-Carmona L, Broderick P, Kemp Z, et al. (2007) A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat Genet 39: 984-988.
14. Buch S, Schafmayer C, Völzke H, Becker C, Franke A, et al. (2007) A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease. Nat Genet 39: 995-999.
15. Winkelmann J, Schormair B, Lichtner P, Ripke S, Xiong L, et al. (2007) Genome-wide association study of restless legs syndrome identifies common variants in three genomic regions. Nat Genet 39: 1000-1006.
16. Grupe A, Abraham R, Li Y, Rowland C, Hollingworth P, et al. (2007) Evidence for novel susceptibility genes for late-onset Alzheimer's disease from a genome-wide association study of putative functional variants. Hum Mol Genet 16: 865-873.
17. Cargill M, Schrodi SJ, Chang M, Garcia VE, Brandon R, et al. (2007) A large-scale genetic association study confirms IL12B and leads to the identification of IL23R as psoriasis-risk genes. Am J Hum Genet 80: 273-290.
18. Arking DE, Cutler DJ, Brune CW, Teslovich TM, West K, et al. (2008) A common genetic variant in the neurexin superfamily member CNTNAP2 increases familial risk of autism. Am J Hum Genet 82: 160-164.
19. Gold B, Kirchhoff T, Stefanov S, Lautenberger J, Viale A, et al. (2008) A genome-wide association study provides evidence for a breast cancer risk at 6q22.33. Proc Natl Acad Sci USA 105: 4340-4345.
20. Knauff EA, Franke L, van Es MA, van den Berg LH, van der Schouw YT, et al. (2009) Genome-wide association study in premature ovarian failure patients suggests ADAMTS19 as a possible candidate gene. Hum Reprod 24: 2372-2378.
21. Lyssenko V, Groop L, (2009) Genome-wide association study for type 2 diabetes- clinical applications. Curr Opin Lipidol 20: 87-91.
22. Landi MT, Chatterjee N, Yu K, Goldin LR, Goldstein AM, et al. (2009) A Genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. Am J Hum Genet 85: 679-691.
23. Kerkhof HJ, Lories RJ, Meulenbelt I, Jonsdottir I, Valdes AM, et al. (2010) A Genome-wide association study identifies an osteoarthritis susceptibility locus on chromosome 7q22. Arthritis Rheum 62: 499-510.
24. Petersen GM, Amundadottir L, Fuchs CS, Kraft P, Stolzenberg-Solomon RZ, et al. (2010) A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. Nat Genet 42: 224-228.
25. Azzato EM, Pharoah PD, Harrington P, Easton DF, Greenberg D, et al. (2010) A Genome-Wide association study of prognosis in breast cancer. Cancer Epidemiol Biomarkers Prev 19: 1140-1143.
26. Pfeufer A, van Noord C, Marciante KD, Arking DE, Larson MG, et al. (2007) Genome-wide association study of PR interval. Nat Genet 42: 153-159.
27. Hirschhorn JN, (2009) Genomewide association studies - illuminating biological pathways. N Engl J Med 360: 1699-1701.
28. Kraft P, Hunter DJ, (2009) Genetic risk prediction - are we there yet? N Engl J Med 360: 1701-1703.
29. Reich DE, Lander ES, (2001) On the allelic spectrum of human disease. Trends Genet 17: 502-510.
30. Pearson TA, Manolio TA, (2008) How to interpret a genome-wide association study. J Am Med Assoc 82: 411-423.
31. Dewan A, Liu M, Hartman S, Zhang SS, Liu DT, et al. (2006) HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 314: 989-992.
32. Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM, et al. (2007) A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 316: 889-894.
33. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal component analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
34. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, et al. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9: 356-369.
35. Hong H, Su Z, Ge W, Shi L, Perkins R, et al. (2010) Evaluating Variations of Genotype Calling: A potential source of spurious associations in genome-wide association studies. J Genet 89: 55-64.
36. Hong H, Shi L, Su Z, Ge W, Jones WD, et al. (2010) Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples. Pharmacogenomics J 10: 364-374.
37. Hong H, Su Z, Ge W, Shi L, Perkins R, et al. (2008) Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500K array set using 270 HapMap samples. BMC Bioinformatics 9: S17.
38. Hong H, Shi L, Fuscoe JC, Goodsaid F, Mendrick D, Tong W (2009) Potential sources of spurious associations and batch effects in genome-wide association studies. In: Scherer A, editor. Batch Effects and Noise in Microarray Experiments: Sources and Solutions. West Sussex, United Kingdom: John Wiley & Sons. 191-201.
39. Miclaus K, Chierici M, Lambert C, Zhang L, Vega S, et al. (2010) Variability in GWAS analysis: the impact of genotype calling algorithm inconsistencies. Pharmacogenomics J 10: 324-335.
40. Miclaus K, Wolfinger R, Vega S, Chierici M, Furlanello C, et al. (2010) Batch effects in the brlmm genotype calling algorithm influence gwas results for the Affymetrix 500K array. Pharmacogenomics J 10: 336-346.
41. Zhang L, Yin S, Miclaus K, Chierici M, Vega S, et al. (2010) Assessment of variability in GWAS with CRLMM genotyping algorithm on WTCCC coronary artery disease. Pharmacogenomics J 10: 347-354.
42. Zeggini E, Scott LJ, Saxena R, Voight BF, Marchini JL, et al. (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.