A Simple Correction for Multiple Testing for Single-Nucleotide Polymorphisms in Linkage Disequilibrium with Each Other
Open accessAbstract
In this report, we describe a simple correction for multiple testing of single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between SNPs. This method provides a useful alternative to more computationally intensive permutation tests. A user-friendly interface (SNPSpD) for performing this correction is available online (http://genepi.qimr.edu.au/general/daleN/SNPSpD/). Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor "loadings" after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.
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Before meta-analysis, all study-specific files underwent quality control procedures to check for completeness and plausible descriptive statistics on all variables as well as for compliance of allele frequencies with HapMap.
“Before meta-analysis, all study-specific files underwent quality control procedures to check for completeness and plausible descriptive statistics on all variables as well as for compliance of allele frequencies with HapMap59.”
From Seven new loci associated with age-related macular degeneration (2013) · cites this paper as [59]
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Billings, L. K., Jablonski, K. A., Warner, A. S., Cheng, Y.-C., McAteer, J. B., Tipton, L., Shuldiner, A. R., Ehrmann, D. A., Manning, A. K., Dabelea, D., et al. (2017) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2016-3429 · Cited by 20 · see citing works
FKBP5 interacts with maltreatment in children with extreme, pervasive, and persistent aggression
Bryushkova, L., Zai, C., Chen, S., Pappa, I., Mileva, V., Tiemeier, H., Bakermans-Kranenburg, M., Kennedy, J. L., & Beitchman, J. H. (2016) · Psychiatry Research · doi:10.1016/j.psychres.2015.09.052 · Cited by 13 · see citing works
Test-based versus parent ratings of executive function in pediatric Obsessive-Compulsive Disorder
Negreiros, J., Best, J. R., Yamin, D. F., Belschner, L., Lin, S., & Stewart, S. E. (2020) · Journal of Obsessive-Compulsive and Related Disorders · doi:10.1016/j.jocrd.2019.100495 · Cited by 8 · see citing works
- Authors
- Nyholt, D. R.
- Affiliations
- QIMR Berghofer Medical Research Institute (AU)
- Corresponding author
- Nyholt, Dale R.
- ORCID
- Nyholt, Dale R.
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2004-04
- Volume
- 74
- Issue
- 4
- Pages
- 765-769
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC1181954
- OpenAlex
- W2030705868
- Cited by
- 1,699
- References
- 30
- Citations by year
- 2026: 27 · 2025: 36 · 2024: 42 · 2023: 37 · 2022: 40 · 2021: 71 · 2020: 58 · 2019: 56 · 2018: 67 · 2017: 49 · 2016: 81 · 2015: 101 · 2014: 106 · 2013: 111 · 2012: 136
- FWCI
- 38.08
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Faculty of Health; Institute of Health and Biomedical Innovation
- Funders
- National Health and Medical Research Council
- National Medical Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- multiple testing correction, single nucleotide polymorphisms, linkage disequilibrium, spectral decomposition, principal component analysis, factor analysis, varimax rotation
- MeSH terms
- Gene Frequency, Haplotypes, Humans, Probability, Research Design, Software, Linkage Disequilibrium, Internet, Polymorphism, Single Nucleotide
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