Data from: Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies

• Main Authors: Hayward, Jessica J., White, Michelle E., Boyle, Michael, Shannon, Laura M, Casal, Margret L., Castelhano, Marta G., Center, Sharon A., Meyers-Wallen, Vicki N., Simpson, Kenneth W., Sutter, Nathan B., Todhunter, Rory J., Boyko, Adam R.
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 2020
• Subjects: whole genome sequencing; Imputation; Canis lupus familiaris; domestic dog; Genome-wide association study; Canis lupus
• Online Access: https://doi.org/10.5061/dryad.jk9504s

Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying potentially novel associations, including a locus on CFA20 significantly associated with cranial cruciate ligament disease, and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes. chr_prephased.bim PLINK binary format (.bim files) of genotype data, by chromosome bim.tar.gz chr_prephased.bed PLINK binary format (.bed files) of genotype data, by chromosome bed.tar.gz phenotype file breed and body size phenotypes for each dog size_phenos.txt chr_prephased.fam PLINK binary format (.fam files) of genotype data, by chromosome fam.tar.gz chr1 phased vcf file phased vcf file of variants on chr1 from 365 canid WGS chr1.new.filtered.phased.vcf.gz chr2 phased vcf file phased vcf file of variants on chr2 from 365 canid WGS chr2.new.filtered.phased.vcf.gz chr3 phased vcf file phased vcf file of variants on chr3 from 365 canid WGS chr3.new.filtered.phased.vcf.gz chr4 phased vcf file phased vcf file of variants on chr4 from 365 canid WGS chr4.new.filtered.phased.vcf.gz chr5 phased vcf file phased vcf file of ...