ComPaSS-GWAS: A method to reduce type I error in genome-wide association studies when replication data are not available.
| Title: | ComPaSS-GWAS: A method to reduce type I error in genome-wide association studies when replication data are not available. |
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| Authors: | Sabourin JA; Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute/National Institutes of Health (NHGRI/NIH), Baltimore, Maryland.; Cropp CD; Statistical Genetics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute/National Institutes of Health (NHGRI/NIH), Baltimore, Maryland.; Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona.; McWhorter School of Pharmacy, Samford University, Birmingham, Alabama.; Sung H; Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute/National Institutes of Health (NHGRI/NIH), Baltimore, Maryland.; Brody LC; Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute/National Institutes of Health (NHGRI/NIH), Bethesda, Maryland.; Bailey-Wilson JE; Statistical Genetics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute/National Institutes of Health (NHGRI/NIH), Baltimore, Maryland.; Wilson AF; Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute/National Institutes of Health (NHGRI/NIH), Baltimore, Maryland. |
| Source: | Genetic epidemiology [Genet Epidemiol] 2019 Feb; Vol. 43 (1), pp. 102-111. Date of Electronic Publication: 2018 Oct 18. |
| Publication Type: | Journal Article; Research Support, N.I.H., Intramural |
| Language: | English |
| Journal Info: | Publisher: Wiley-Liss Country of Publication: United States NLM ID: 8411723 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1098-2272 (Electronic) Linking ISSN: 07410395 NLM ISO Abbreviation: Genet Epidemiol Subsets: MEDLINE |
| Imprint Name(s): | Publication: New York, NY : Wiley-Liss; Original Publication: New York, N.Y. : Alan R. Liss, c1984- |
| MeSH Terms: | Genome-Wide Association Study*; Polymorphism, Single Nucleotide/genetics ; Computer Simulation ; Humans ; Models, Genetic ; Phenotype ; Reproducibility of Results |
| Abstract: | Results from association studies are traditionally corroborated by replicating the findings in an independent data set. Although replication studies may be comparable for the main trait or phenotype of interest, it is unlikely that secondary phenotypes will be comparable across studies, making replication problematic. Alternatively, there may simply not be a replication sample available because of the nature or frequency of the phenotype. In these situations, an approach based on complementary pairs stability selection for genome-wide association study (ComPaSS-GWAS), is proposed as an ad-hoc alternative to replication. In this method, the sample is randomly split into two conditionally independent halves multiple times (resamples) and a GWAS is performed on each half in each resample. Similar in spirit to testing for association with independent discovery and replication samples, a marker is corroborated if its p-value is significant in both halves of the resample. Simulation experiments were performed for both nongenetic and genetic models. The type I error rate and power of ComPaSS-GWAS were determined and compared to the statistical properties of a traditional GWAS. Simulation results show that the type I error rate decreased as the number of resamples increased with only a small reduction in power and that these results were comparable with those from a traditional GWAS. Blood levels of vitamin pyridoxal 5'-phosphate from the Trinity Student Study (TSS) were used to validate this approach. The results from the validation study were compared to, and were consistent with, those obtained from previously published independent replication data and functional studies.; (© 2018 Wiley Periodicals Inc.) |
| References: | Genet Epidemiol. 2011 Nov;35(7):722-8. (PMID: 22009793); Am J Hum Genet. 2010 Jan;86(1):6-22. (PMID: 20074509); Genet Epidemiol. 2011;35 Suppl 1:S107-14. (PMID: 22128050); Nat Protoc. 2015 Oct;10(10):1556-66. (PMID: 26379229); Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):588-93. (PMID: 23267103); Genet Epidemiol. 2018 Jun;42(4):405-414. (PMID: 29682794); Genet Epidemiol. 2015 Feb;39(2):77-88. (PMID: 25417853); Nat Genet. 2010 Apr;42(4):348-54. (PMID: 20208533); Genet Epidemiol. 2007 Nov;31(7):776-88. (PMID: 17549752); Am J Hum Genet. 2016 May 5;98(5):869-882. (PMID: 27132595); Hum Mol Genet. 2009 Dec 1;18(23):4677-87. (PMID: 19744961); BMC Proc. 2016 Oct 18;10(Suppl 7):385-388. (PMID: 27980666); Genome Res. 2002 Jun;12(6):996-1006. (PMID: 12045153); J Nutr. 2015 Jul;145(7):1386-93. (PMID: 25972531); Genetics. 2009 Aug;182(4):1263-77. (PMID: 19474203); Am J Hum Genet. 2008 Oct;83(4):520-8. (PMID: 18940312); Genet Epidemiol. 2012 Jul;36(5):451-62. (PMID: 22549815); Front Public Health. 2014 Aug 06;2:112. (PMID: 25147783); Am J Hum Genet. 2007 Sep;81(3):559-75. (PMID: 17701901); Nat Rev Genet. 2008 May;9(5):356-69. (PMID: 18398418); Nucleic Acids Res. 2012 May;40(9):3777-84. (PMID: 22241776); BMC Proc. 2011 Nov 29;5 Suppl 9:S15. (PMID: 22373501) |
| Grant Information: | ZIA HG000200 United States ImNIH Intramural NIH HHS; United States HG NHGRI NIH HHS |
| Contributed Indexing: | Keywords: GWAS; corroboration; power; replication; type I error |
| Entry Date(s): | Date Created: 20181019 Date Completed: 20190218 Latest Revision: 20250530 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC6330131 |
| DOI: | 10.1002/gepi.22168 |
| PMID: | 30334581 |
| Database: | MEDLINE |
Journal Article; Research Support, N.I.H., Intramural