A quality control algorithm for filtering SNPs in genome-wide association studies

Bioinformatics

Volumn 26, Issue 14, 2010, Pages 1731-1737

  Pongpanich, Monnat ^a   Sullivan, Patrick F ^b   Tzeng, Jung Ying ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; GENETIC ASSOCIATION; GENOME; METHODOLOGY; QUALITY CONTROL; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD;

ALGORITHMS; GENOME; GENOME-WIDE ASSOCIATION STUDY; POLYMORPHISM, SINGLE NUCLEOTIDE; QUALITY CONTROL;

EID: 77954531945     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq272     Document Type: Article

References (30)

1. Anney, R. et al. (2008) Non-random error in genotype calling procedures: implications for family-based and case-control genome-wide association studies. Am. J. Med. Genet., 147B, 1379-1386.
2. Barrett, J.C. et al. (2008) Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat. Genet., 40, 955-962.
3. Clayton, D.G. et al. (2005) Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat. Genet., 37, 1243-1246.
4. Cox, D.G. and Kraft, P. (2006) Quantification of the power of Hardy-Weinberg equilibrium testing to detect genotyping error. Hum. Hered., 61, 10-14.
5. Devlin, B. and Roeder, K. (1999) Genomic control for association studies. Biometrics, 55, 997-1004.
6. Donnelly, P. (2008) Progress and challenges in genome-wide association studies in humans. Nature, 456, 728-731.
7. Ester, M. et al. (1996) A density-based algorithm for discovering clusters in large spatial databases with noise. In Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining, AAAI Press, Portland, OR, pp. 226-231.
8. Fardo, D.W. et al. (2009) On quality control measures in genome-wide association studies: a test to assess the genotyping quality of individual probands in family- based association studies and an application to the HapMap data. PLoS Genet., 5, e1000572.
9. GAIN Collaborative Research Group (2007) New models of collaboration in genome- wide association studies: the Genetic Association Information Network. Nat. Genet., 39, 1045-1051.
10. Gordon, D. et al. (2001) A transmission/disequilibrium test that allows for genotyping errors in the analysis of single-nucleotide polymorphism data. Am. J. Hum. Genet., 69, 371-380.
11. Gordon, D. and Ott, J. (2001) Assessment and management of single nucleotide polymorphism genotype errors in genetic association analysis. Pac. Symp. Biocomput., 6, 18-29.
12. Hao, K. and Wang, X. (2004) Incorporating individual error rate into association test of unmatched case-control design. Hum. Hered., 58, 154-163.
13. Hindorff, L.A. et al. (2009) Potential etiologic and functional implications of genomewide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362-9367.
14. Hugot, J.P. et al. (2001) Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature, 411, 599-603.
15. McCarthy, M.I. (2004) Progress in defining the molecular basis of type 2 diabetes mellitus through susceptibility-gene identification. Hum. Mol. Genet., 13, R33-R41.
16. Miyagawa, T. et al. (2008) Appropriate data cleaning methods for genome-wide association study. J. Hum. Genet., 53, 886-893.
17. Neale, B.M. and Purcell, S. (2008) The positives, protocols, and perils of genome-wide association. Am. J. Med. Genet., 147B, 1288-1294.
18. Pettersson, F. et al. (2008) Goldsurfer2 (Gs2): a comprehensive tool for the analysis and visualization of genome wide association studies. BMC Bioinformatics, 9, 1-11.
19. Plagnol, V. et al. (2007)Amethod to address differential bias in genotyping in large-scale association studies. PLoS Genet., 3, 0759-0767.
20. Pompanon, F. et al. (2005) Genotyping errors: causes, consequences and solutions. Nat. Rev. Genet., 6, 847-859.
21. Purcell, S. et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am. J. Hum. Genet., 81, 559-875.
22. Rice, K.M. and Holmans, P. (2003) Allowing for genotyping error in analysis of unmatched case-control studies. Ann. Hum. Genet., 67, 165-174.
23. Sladek, R. et al. (2007) A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature, 445, 881-885.
24. Sullivan, P.F. et al. (2009) Genomewide association for major depressive disorder: a possible role for the presynaptic protein piccolo. Mol. Psychiatry, 14, 359-375.
25. Teo, Y.Y. et al. (2007) On the usage of HWE for identifying genotyping errors. Ann. Hum. Genet., 71, 701-703.
26. Teo, Y.Y. (2008) Common statistical issues in genome-wide association studies: a review on power, data quality control, genotype calling and population structure. Curr. Opin. Lipidol., 19, 133-143.
27. Teo, Y.Y. et al. (2008) Perturbation analysis: a simple method for filtering SNPs with erroneous genotyping in genome-wide association studies. Ann. Hum. Genet., 72, 368-374.
28. Unoki, H. et al. (2008) SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. Nat. Genet., 40, 1098-1102.
29. 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.
30. Zeggini, E. 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.