The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Genome‐wide significance for dense SNP and resequencing data
Abstract
The problem of multiple testing is an important aspect of genome‐wide association studies, and will become more important as marker densities increase. The problem has been tackled with permutation and false discovery rate procedures and with Bayes factors, but each approach faces difficulties that we briefly review. In the current context of multiple studies on different genotyping platforms, we argue for the use of truly genome‐wide significance thresholds, based on all polymorphisms whether or not typed in the study. We approximate genome‐wide significance thresholds in contemporary West African, East Asian and European populations by simulating sequence data, based on all polymorphisms as well as for a range of single nucleotide polymorphism (SNP) selection criteria. Overall we find that significance thresholds vary by a factor of >20 over the SNP selection criteria and statistical tests that we consider and can be highly dependent on sample size. We compare our results for sequence data to those derived by the HapMap Consortium and find notable differences which may be due to the small sample sizes used in the HapMap estimate. Genet. Epidemiol. 32:179–185, 2008. © 2007 Wiley‐Liss, Inc.
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Cites
Statistical significance for genomewide studies
Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
The Wellcome Trust Case Control Consortium, Management Committee, Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., et al. (2007) · Nature · doi:10.1038/nature05911 · Cited by 9,442
A simple correction for multiple comparisons in interval mapping genome scans
Cheverud, J. M. (2001) · Heredity · doi:10.1046/j.1365-2540.2001.00901.x · Cited by 421
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Genome-wide association studies for complex traits: consensus, uncertainty and challenges
McCarthy, M. I., Abecasis, G. R., Cardon, L. R., Goldstein, D. B., Little, J., Ioannidis, J. P. A., & Hirschhorn, J. N. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2344 · Cited by 2,891
Diamanti-Kandarakis, E., & Dunaif, A. (2012) · Endocrine Reviews · doi:10.1210/er.2011-1034 · Cited by 1,947
Thirty years of Alzheimer's disease genetics: the implications of systematic meta-analyses
Bertram, L., & Tanzi, R. E. (2008) · Nature Reviews Neuroscience · doi:10.1038/nrn2494 · Cited by 747
Statistical power and significance testing in large-scale genetic studies
Sham, P. C., & Purcell, S. M. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3706 · Cited by 573
Genomewide Association Studies of Stroke
Ikram, M. A., Seshadri, S., Bis, J. C., Fornage, M., DeStefano, A. L., Aulchenko, Y. S., Debette, S., Lumley, T., Folsom, A. R., van den Herik, E. G., et al. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0900094 · Cited by 458
Metadata
- Authors
- Hoggart, C. J., Clark, T. G., De Iorio, M., Whittaker, J. C., & Balding, D. J.
- Venue
- Genetic Epidemiology
- Publisher
- Wiley
- Published
- 2008-01-16
- Volume
- 32
- Issue
- 2
- Pages
- 179-185
- ISSN
- 0741-0395 (ISSN-L)
- 1098-2272
- OpenAlex
- W2013524758
- Cited by
- 209
- References
- 3
- FWCI
- 15.29
- Type
- journal article
- Language
- en
- Open access
- closed
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- Hoggart, C. J., Clark, T. G., De Iorio, M., Whittaker, J. C., & Balding, D. J. (2008). Genome‐wide significance for dense SNP and resequencing data. Genetic Epidemiology. https://doi.org/10.1002/gepi.20292
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