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- Title
Family-specific genotype arrays increase the accuracy of pedigree-based imputation at very low marker densities.
- Authors
Whalen, Andrew; Gorjanc, Gregor; Hickey, John M.
- Abstract
Background: In this paper, we evaluate the performance of using family-specific low-density genotype arrays to increase the accuracy of pedigree-based imputation. Genotype imputation is a widely used tool that decreases the costs of genotyping a population by genotyping the majority of individuals on a low-density array and using statistical regularities between the low-density and high-density individuals to fill in the missing genotypes. Previous work on population-based imputation has found that it is possible to increase the accuracy of imputation by maximizing the number of informative markers on an array. In the context of pedigree-based imputation, where the informativeness of a marker depends only on the genotypes of an individual's parents, it may be beneficial to select the markers on each low-density array on a family-by-family basis. Results: In this paper, we examined four family-specific low-density marker selection strategies and evaluated their performance in the context of a real pig breeding dataset. We found that family-specific or sire-specific arrays could increase imputation accuracy by 0.11 at one marker per chromosome, by 0.027 at 25 markers per chromosome and by 0.007 at 100 markers per chromosome. Conclusions: These results suggest that there may be room to use family-specific genotyping for very-low-density arrays particularly if a given sire or sire-dam pairing have a large number of offspring.
- Subjects
GENOTYPES; EXPONENTIAL families (Statistics); GENETIC markers; MISSING data (Statistics)
- Publication
Genetics Selection Evolution, 2019, Vol 51, Issue 1, pN.PAG
- ISSN
0999-193X
- Publication type
Article
- DOI
10.1186/s12711-019-0478-2