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

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Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds
 
Dog Biomedical Variant Database Consortium
(2021) Animal Genetics, volume 52, issue 5, pp. 703 - 713
(Article)
Abstract
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 ... read more
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Keywords: Border Collie, Italian Spinone, genome-wide association study, imputation accuracy, whole genome sequencing, Animal Science and Zoology, Genetics
DOI: https://doi.org/10.1111/age.13117
ISSN: 0268-9146
Publisher: Wiley-Blackwell
Note: Funding Information: The Petplan Charitable Trust funded this study in the Border Collie (project number S18-688-726). Generation of datasets for the Italian Spinone were funded by the Italian Spinone Club of Great Britain. C.A.J., S.L.R., C.S.M. and E.C.S. are supported by the Kennel Club Charitable Trust. We thank the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (funded by Wellcome Trust grant reference 203141/Z/16/Z) for the generation and initial processing of the Axiom array data. Illumina genotyping was conducted by GeneSeek (Neogen Genomics, Lincoln, NE, USA). We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (funded by Wellcome Trust grant reference 090532/Z/09/Z and MRC Hub grant G090074791070) for the whole genomes of 24 dogs. The sequencing of the whole genomes of four dogs was carried out by the University of Cambridge. The whole genomes of 157 other dogs were sequenced by Edinburgh Genomics Laboratories, University of Edinburgh. The whole genome sequencing of 82 of the dogs was part of the Give a Dog a Genome project. We also thank Natasha Olby for sharing whole genome data. We acknowledge all canine researchers who deposited dog whole genome sequencing data into public databases. We thank Dr Janine Lamb, University of Manchester, for critical review of the manuscript. We would like to thank all owners who provided samples from their dogs, whose data contributed to this study. Funding Information: The Petplan Charitable Trust funded this study in the Border Collie (project number S18‐688‐726). Generation of datasets for the Italian Spinone were funded by the Italian Spinone Club of Great Britain. C.A.J., S.L.R., C.S.M. and E.C.S. are supported by the Kennel Club Charitable Trust. We thank the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (funded by Wellcome Trust grant reference 203141/Z/16/Z) for the generation and initial processing of the Axiom array data. Illumina genotyping was conducted by GeneSeek (Neogen Genomics, Lincoln, NE, USA). We thank the High‐Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics (funded by Wellcome Trust grant reference 090532/Z/09/Z and MRC Hub grant G090074791070) for the whole genomes of 24 dogs. The sequencing of the whole genomes of four dogs was carried out by the University of Cambridge. The whole genomes of 157 other dogs were sequenced by Edinburgh Genomics Laboratories, University of Edinburgh. The whole genome sequencing of 82 of the dogs was part of the Give a Dog a Genome project. We also thank Natasha Olby for sharing whole genome data. We acknowledge all canine researchers who deposited dog whole genome sequencing data into public databases. We thank Dr Janine Lamb, University of Manchester, for critical review of the manuscript. We would like to thank all owners who provided samples from their dogs, whose data contributed to this study. Publisher Copyright: © 2021 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics
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