Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds.

Dog Biomedical Variant Database Consortium; Division of Population Health, Health Services Research & Primary Care, University of Manchester, Manchester, UK.

Publisher: Wiley-Blackwell Country of Publication: England NLM ID: 8605704 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1365-2052 (Electronic) Linking ISSN: 02689146 NLM ISO Abbreviation: Anim Genet Subsets: MEDLINE

Publication: Oxford, England : Wiley-Blackwell
Original Publication: Oxford, England : Published by Blackwell Scientific Publications for the International Society for Animal Blood Group Research, c1986-

Genotype*; Dogs/*genetics ; Genetic Association Studies/*veterinary ; Genomics/*methods; Animals ; Breeding ; Polymorphism, Single Nucleotide

Genotype imputation using a reference panel that combines high-density array data and publicly available whole genome sequence consortium variant data is potentially a cost-effective method to increase the density of extant lower-density array datasets. In this study, three datasets (two Border Collie; one Italian Spinone) generated using a legacy array (Illumina CanineHD, 173 662 SNPs) were utilised to assess the feasibility and accuracy of this approach and to gather additional evidence for the efficacy of canine genotype imputation. The cosmopolitan reference panels used to impute genotypes comprised dogs of 158 breeds, mixed breed dogs, wolves and Chinese indigenous dogs, as well as breed-specific individuals genotyped using the Axiom Canine HD array. The two Border Collie reference panels comprised 808 individuals including 79 Border Collies and 426 326 or 426 332 SNPs; and the Italian Spinone reference panel comprised 807 individuals including 38 Italian Spinoni and 476 313 SNPs. A high accuracy for imputation was observed, with the lowest accuracy observed for one of the Border Collie datasets (mean R ²  = 0.94) and the highest for the Italian Spinone dataset (mean R ²  = 0.97). This study's findings demonstrate that imputation of a legacy array study set using a reference panel comprising both breed-specific array data and multi-breed variant data derived from whole genomes is effective and accurate. The process of canine genotype imputation, using the valuable growing resource of publicly available canine genome variant datasets alongside breed-specific data, is described in detail to facilitate and encourage use of this technique in canine genetics.
(© 2021 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.)

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Kennel Club Charitable Trust; K01 OD019912 United States OD NIH HHS; K01 OD027051 United States OD NIH HHS; Italian Spinone Club of Great Britain; S18-688-726 Petplan Charitable Trust; United Kingdom WT_ Wellcome Trust

Keywords: Border Collie; Italian Spinone; genome-wide association study; imputation accuracy; whole genome sequencing

Date Created: 20210712 Date Completed: 20210923 Latest Revision: 20221005

20221213

PMC8514152

10.1111/age.13117

34252218