title: Genotype imputation to increase sample size in pedigreed populations.
abstract: Genotype imputation is a cost-effective way to increase the power of genomic selection or genome-wide association studies. While several genotype imputation algorithms are available, this chapter focuses on a heuristic algorithm, as implemented in the AlphaImpute software. This algorithm combines long-range phasing, haplotype library imputation, and segregation analysis and it is specifically designed to work with pedigreed populations.The chapter is organized in different sections. First the challenges related to genotype imputation in pedigreed populations are described, along with the specifics of the imputation algorithm used in AlphaImpute. In the second section, factors affecting the accuracy of genotype imputation using this algorithm are discussed. The different parameters that control AlphaImpute are detailed and examples of how to apply AlphaImpute are given.
authors.affiliation: School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia.
authors.forename: John M
authors.initials: JM
authors.lastname: Hickey
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Cleveland
authors.forename: Christian
authors.initials: C
authors.lastname: Maltecca
authors.forename: Gregor
authors.initials: G
authors.lastname: Gorjanc
authors.forename: Birgit
authors.initials: B
authors.lastname: Gredler
authors.forename: Andreas
authors.initials: A
authors.lastname: Kranis
mesh_terms: D000465:Algorithms; D000483:Alleles; D000818:Animals; D001947:Breeding; D005787:Gene Frequency; D005828:Genetics, Population; D016678:Genome; D055106:Genome-Wide Association Study / Q000706:statistics & numerical data*; D006239:Haplotypes; D006801:Humans; D008957:Models, Genetic; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D018401:Sample Size; D012984:Software