DOI: 10.5061/dryad.jk9504s
title: Data from: Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies

description: 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.
description: 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 on chr7 from 365 canid WGSchr7.new.filtered.phased.vcf.gzchr8 phased vcf filephased vcf file of variants on chr8 from 365 canid WGSchr8.new.filtered.phased.vcf.gzchr9 phased vcf filephased vcf file of variants on chr9 from 365 canid WGSchr9.new.filtered.phased.vcf.gzchr10 phased vcf filephased vcf file of variants on chr10 from 365 canid WGSchr10.new.filtered.phased.vcf.gzchr11 phased vcf filephased vcf file of variants on chr11 from 365 canid WGSchr11.new.filtered.phased.vcf.gzchr12 phased vcf filephased vcf file of variants on chr12 from 365 canid WGSchr12.new.filtered.phased.vcf.gzchr13 phased vcf filephased vcf file of variants on chr13 from 365 canid WGSchr13.new.filtered.phased.vcf.gzchr14 phased vcf filephased vcf file of variants on chr14 from 365 canid WGSchr14.new.filtered.phased.vcf.gzchr15 phased vcf filephased vcf file of variants on chr15 from 365 canid WGSchr15.new.filtered.phased.vcf.gzchr16 phased vcf filephased vcf file of variants on chr16 from 365 canid WGSchr16.new.filtered.phased.vcf.gzchr17 phased vcf filephased vcf file of variants on chr17 from 365 canid WGSchr17.new.filtered.phased.vcf.gzchr18 phased vcf filephased vcf file of variants on chr18 from 365 canid WGSchr18.new.filtered.phased.vcf.gzchr19 phased vcf filephased vcf file of variants on chr19 from 365 canid WGSchr19.new.filtered.phased.vcf.gzchr20 phased vcf filephased vcf file of variants on chr20 from 365 canid WGSchr20.new.filtered.phased.vcf.gzchr21 phased vcf filephased vcf file of variants on chr21 from 365 canid WGSchr21.new.filtered.phased.vcf.gzchr22 phased vcf filephased vcf file of variants on chr22 from 365 canid WGSchr22.new.filtered.phased.vcf.gzchr23 phased vcf filephased vcf file of variants on chr23 from 365 canid WGSchr23.new.filtered.phased.vcf.gzchr24 phased vcf filephased vcf file of variants on chr24 from 365 canid WGSchr24.new.filtered.phased.vcf.gzchr25 phased vcf filephased vcf file of variants on chr25 from 365 canid WGSchr25.new.filtered.phased.vcf.gzchr26 phased vcf filephased vcf file of variants on chr26 from 365 canid WGSchr26.new.filtered.phased.vcf.gzchr27 phased vcf filephased vcf file of variants on chr27 from 365 canid WGSchr27.new.filtered.phased.vcf.gzchr28 phased vcf filephased vcf file of variants on chr28 from 365 canid WGSchr28.new.filtered.phased.vcf.gzchr29 phased vcf filephased vcf file of variants on chr29 from 365 canid WGSchr29.new.filtered.phased.vcf.gzchr30 phased vcf filephased vcf file of variants on chr30 from 365 canid WGSchr30.new.filtered.phased.vcf.gzchr31 phased vcf filephased vcf file of variants on chr31 from 365 canid WGSchr31.new.filtered.phased.vcf.gzchr32 phased vcf filephased vcf file of variants on chr32 from 365 canid WGSchr32.new.filtered.phased.vcf.gzchr33 phased vcf filephased vcf file of variants on chr33 from 365 canid WGSchr33.new.filtered.phased.vcf.gzchr34 phased vcf filephased vcf file of variants on chr34 from 365 canid WGSchr34.new.filtered.phased.vcf.gzchr35 phased vcf filephased vcf file of variants on chr35 from 365 canid WGSchr35.new.filtered.phased.vcf.gzchr36 phased vcf filephased vcf file of variants on chr36 from 365 canid WGSchr36.new.filtered.phased.vcf.gzchr37 phased vcf filephased vcf file of variants on chr37 from 365 canid WGSchr37.new.filtered.phased.vcf.gzchr38 phased vcf filephased vcf file of variants on chr38 from 365 canid WGSchr38.new.filtered.phased.vcf.gzchrX phased vcf filephased vcf file of variants on chrX from 365 canid WGSchrX.new.filtered.phased.vcf.gz215k_accuracy.famID and sex information for each dog (215k array data used to calculate the imputation accuracy)215k_accuracychromosome, name, bp location, alleles for each SNP (215k array data used to calculate the imputation accuracy)215k_accuracygenotypes for each dog at each SNP (215k array data used to calculate the imputation accuracy)READMEShort 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)