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

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 R2 = 0.94) and the highest for the
Italian Spinone dataset (mean R2 = 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.