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: Dataset
• Language: English
• Published: Dryad 2019
• Subjects: whole genome sequencing; Imputation; Canis lupus familiaris; domestic dog; Genome-wide association study; Canis lupus
• Online Access: https://dx.doi.org/10.5061/dryad.jk9504s; https://datadryad.org/stash/dataset/doi: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 ... : chr_prephased.bimPLINK binary format (.bim files) of genotype data, by chromosomebim.tar.gzchr_prephased.bedPLINK binary format (.bed files) of genotype data, by chromosomebed.tar.gzphenotype filebreed and body size phenotypes for each dogsize_phenos.txtchr_prephased.famPLINK binary format (.fam files) of genotype data, by chromosomefam.tar.gzchr1 phased vcf filephased vcf file of variants on chr1 from 365 canid WGSchr1.new.filtered.phased.vcf.gzchr2 phased vcf filephased vcf file of variants on chr2 from 365 canid WGSchr2.new.filtered.phased.vcf.gzchr3 phased vcf filephased vcf file of variants on chr3 from 365 canid WGSchr3.new.filtered.phased.vcf.gzchr4 phased vcf filephased vcf file of variants on chr4 from 365 canid WGSchr4.new.filtered.phased.vcf.gzchr5 phased vcf filephased vcf file of variants on chr5 from 365 canid WGSchr5.new.filtered.phased.vcf.gzchr6 phased vcf filephased vcf file of variants on chr6 from 365 canid WGSchr6.new.filtered.phased.vcf.gzchr7 phased vcf filephased vcf file of variants ...