The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
On the advantage of haplotype analysis in the presence of multiple disease susceptibility alleles
Abstract
We investigated the effect of multiple susceptibility alleles at a single disease locus on the statistical power of a likelihood ratio test to detect association between alleles at a marker locus and a disease phenotype in a case-control design. Using simplifying assumptions to obtain the joint frequency distribution of marker and disease locus alleles, we present numerical results that illustrate the impact of historical variation of initial associations between marker alleles and susceptibility alleles on the power of a likelihood ratio test for association. Our results show that an increase in the number of susceptibility alleles produces a decrease in power of the likelihood ratio test. The decrease in power in the presence of multiple susceptibility alleles, however, is less for markers with multiple alleles than for markers with two alleles. We investigate the implications of this observation for tests of association based on haplotypes made up of tightly linked single-nucleotide polymorphisms (SNPs). Our results suggest that an analysis based on haplotypes can be advantageous over an analysis based on individual SNPs in the presence of multiple susceptibility alleles, particularly when linkage disequilibria between SNPs is weak. The results provide motivation for further development of statistical methods based on haplotypes for assessing the potential for association methods to identify and locate complex disease genes.
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“Compared to SNP-based studies, haplotype analysis can increase the statistical power of genetic analysis and identify key disease-associated SNPs or haplotypes [46].”
From Association of SPI1 haplotypes with altered SPI1 gene expression and Alzheimer’s disease risk (2022) · cites this paper as [46]
Citations
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Haplotypes vs single marker linkage disequilibrium tests: what do we gain?
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Nyholt, D. R. (2004) · The American Journal of Human Genetics · doi:10.1086/383251 · Cited by 1,699
An evaluation of statistical approaches to rare variant analysis in genetic association studies
Morris, A. P., & Zeggini, E. (2010) · Genetic Epidemiology · doi:10.1002/gepi.20450 · Cited by 481
The role of haplotypes in candidate gene studies
Clark, A. G. (2004) · Genetic Epidemiology · doi:10.1002/gepi.20025 · Cited by 428
Evaluating associations of haplotypes with traits
Schaid, D. J. (2004) · Genetic Epidemiology · doi:10.1002/gepi.20037 · Cited by 315
Rare Variant Association Analysis Methods for Complex Traits
Asimit, J. L., & Zeggini, E. (2010) · Annual Review of Genetics · doi:10.1146/annurev-genet-102209-163421 · Cited by 281
Metadata
- Authors
- Morris, R. W., & Kaplan, N. L.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Morris, Richard W.
- Venue
- Genetic Epidemiology
- Publisher
- Wiley
- Published
- 2002-10
- Volume
- 23
- Issue
- 3
- Pages
- 221-233
- ISSN
- 0741-0395 (ISSN-L)
- 1098-2272
- OpenAlex
- W2029361834
- Cited by
- 369
- References
- 24
- Citations by year
- 2026: 2 · 2025: 4 · 2024: 7 · 2023: 7 · 2022: 8 · 2021: 3 · 2020: 8 · 2019: 23 · 2018: 11 · 2017: 8 · 2016: 15 · 2015: 17 · 2014: 21 · 2013: 16 · 2012: 18
- FWCI
- 10.96
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Genetic Epidemiology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- haplotype analysis, statistical power, likelihood ratio test, genetic association testing, case-control study, linkage disequilibrium, single nucleotide polymorphisms, marker alleles
- MeSH terms
- Alleles, Chromosome Mapping, Gene Frequency, Genetic Markers, Genetic Testing, Haplotypes, Humans, Reproducibility of Results, Linkage Disequilibrium, Likelihood Functions, Case-Control Studies, Risk Assessment, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genetic Diseases, Inborn
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