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 variants on chr5 from 365 canid WGS
chr5.new.filtered.phased.vcf.gz
chr6 phased vcf file
phased vcf file of variants on chr6 from 365 canid WGS
chr6.new.filtered.phased.vcf.gz
chr7 phased vcf file
phased vcf file of variants on chr7 from 365 canid WGS
chr7.new.filtered.phased.vcf.gz
chr8 phased vcf file
phased vcf file of variants on chr8 from 365 canid WGS
chr8.new.filtered.phased.vcf.gz
chr9 phased vcf file
phased vcf file of variants on chr9 from 365 canid WGS
chr9.new.filtered.phased.vcf.gz
chr10 phased vcf file
phased vcf file of variants on chr10 from 365 canid WGS
chr10.new.filtered.phased.vcf.gz
chr11 phased vcf file
phased vcf file of variants on chr11 from 365 canid WGS
chr11.new.filtered.phased.vcf.gz
chr12 phased vcf file
phased vcf file of variants on chr12 from 365 canid WGS
chr12.new.filtered.phased.vcf.gz
chr13 phased vcf file
phased vcf file of variants on chr13 from 365 canid WGS
chr13.new.filtered.phased.vcf.gz
chr14 phased vcf file
phased vcf file of variants on chr14 from 365 canid WGS
chr14.new.filtered.phased.vcf.gz
chr15 phased vcf file
phased vcf file of variants on chr15 from 365 canid WGS
chr15.new.filtered.phased.vcf.gz
chr16 phased vcf file
phased vcf file of variants on chr16 from 365 canid WGS
chr16.new.filtered.phased.vcf.gz
chr17 phased vcf file
phased vcf file of variants on chr17 from 365 canid WGS
chr17.new.filtered.phased.vcf.gz
chr18 phased vcf file
phased vcf file of variants on chr18 from 365 canid WGS
chr18.new.filtered.phased.vcf.gz
chr19 phased vcf file
phased vcf file of variants on chr19 from 365 canid WGS
chr19.new.filtered.phased.vcf.gz
chr20 phased vcf file
phased vcf file of variants on chr20 from 365 canid WGS
chr20.new.filtered.phased.vcf.gz
chr21 phased vcf file
phased vcf file of variants on chr21 from 365 canid WGS
chr21.new.filtered.phased.vcf.gz
chr22 phased vcf file
phased vcf file of variants on chr22 from 365 canid WGS
chr22.new.filtered.phased.vcf.gz
chr23 phased vcf file
phased vcf file of variants on chr23 from 365 canid WGS
chr23.new.filtered.phased.vcf.gz
chr24 phased vcf file
phased vcf file of variants on chr24 from 365 canid WGS
chr24.new.filtered.phased.vcf.gz
chr25 phased vcf file
phased vcf file of variants on chr25 from 365 canid WGS
chr25.new.filtered.phased.vcf.gz
chr26 phased vcf file
phased vcf file of variants on chr26 from 365 canid WGS
chr26.new.filtered.phased.vcf.gz
chr27 phased vcf file
phased vcf file of variants on chr27 from 365 canid WGS
chr27.new.filtered.phased.vcf.gz
chr28 phased vcf file
phased vcf file of variants on chr28 from 365 canid WGS
chr28.new.filtered.phased.vcf.gz
chr29 phased vcf file
phased vcf file of variants on chr29 from 365 canid WGS
chr29.new.filtered.phased.vcf.gz
chr30 phased vcf file
phased vcf file of variants on chr30 from 365 canid WGS
chr30.new.filtered.phased.vcf.gz
chr31 phased vcf file
phased vcf file of variants on chr31 from 365 canid WGS
chr31.new.filtered.phased.vcf.gz
chr32 phased vcf file
phased vcf file of variants on chr32 from 365 canid WGS
chr32.new.filtered.phased.vcf.gz
chr33 phased vcf file
phased vcf file of variants on chr33 from 365 canid WGS
chr33.new.filtered.phased.vcf.gz
chr34 phased vcf file
phased vcf file of variants on chr34 from 365 canid WGS
chr34.new.filtered.phased.vcf.gz
chr35 phased vcf file
phased vcf file of variants on chr35 from 365 canid WGS
chr35.new.filtered.phased.vcf.gz
chr36 phased vcf file
phased vcf file of variants on chr36 from 365 canid WGS
chr36.new.filtered.phased.vcf.gz
chr37 phased vcf file
phased vcf file of variants on chr37 from 365 canid WGS
chr37.new.filtered.phased.vcf.gz
chr38 phased vcf file
phased vcf file of variants on chr38 from 365 canid WGS
chr38.new.filtered.phased.vcf.gz
chrX phased vcf file
phased vcf file of variants on chrX from 365 canid WGS
chrX.new.filtered.phased.vcf.gz
215k_accuracy.fam
ID and sex information for each dog (215k array data used to calculate the imputation accuracy)
215k_accuracy
chromosome, name, bp location, alleles for each SNP (215k array data used to calculate the imputation accuracy)
215k_accuracy
genotypes for each dog at each SNP (215k array data used to calculate the imputation accuracy)
README
Short description of the files included in this submission (prephased PLINK files, phased variant data from WGS, and 215k array PLINK files used for imputation accuracy)