ArticleHuman heredity2013
Optimal methods for using posterior probabilities in association testing.
Article in Human heredity, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids.The plant genome · 2023Article
- GEN2VCF: a converter for human genome imputation output format to VCF format.Genes & genomics · 2020Article
- A POWERFUL METHOD FOR INCLUDING GENOTYPE UNCERTAINTY IN TESTS OF HARDY-WEINBERG EQUILIBRIUM.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2017Article
- PreCimp: Pre-collapsing imputation approach increases imputation accuracy of rare variants in terms of collapsed variables.Genetic epidemiology · 2017Article
- A novel approach to identify optimal metabotypes of elongase and desaturase activities in prevention of acute coronary syndrome.Metabolomics : Official journal of the Metabolomic Society · 2015Article
- Associations of common variants in the BST2 region with HIV-1 acquisition in African American and European American people who inject drugs.AIDS (London, England) · 2015Article
- Association studies with imputed variants using expectation-maximization likelihood-ratio tests.PloS one · 2014Article
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Authors and funding
3 authors.
Funding
Abstract
objectiveThe use of haplotypes to impute the genotypes of unmeasured single nucleotide variants continues to rise in popularity. Simulation results suggest that the use of the dosage as a one-dimensional summary statistic of imputation posterior probabilities may be optimal both in terms of statistical power and computational efficiency; however, little theoretical understanding is available to explain and unify these simulation results. In our analysis, we provide a theoretical foundation for the use of the dosage as a one-dimensional summary statistic of genotype posterior probabilities from any technology.
methodsWe analytically evaluate the dosage, mode and the more general set of all one-dimensional summary statistics of two-dimensional (three posterior probabilities that must sum to 1) genotype posterior probability vectors.
resultsWe prove that the dosage is an optimal one-dimensional summary statistic under a typical linear disease model and is robust to violations of this model. Simulation results confirm our theoretical findings.
conclusionsOur analysis provides a strong theoretical basis for the use of the dosage as a one-dimensional summary statistic of genotype posterior probability vectors in related tests of genetic association across a wide variety of genetic disease models.
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