10.5061/DRYAD.JK9504S
Hayward, Jessica J.
Cornell University
White, Michelle E.
Cornell University
Boyle, Michael
Cornell University
Shannon, Laura M
University of Minnesota
Casal, Margret L.
University of Pennsylvania
Castelhano, Marta G.
Cornell University
Center, Sharon A.
Cornell University
Meyers-Wallen, Vicki N.
Cornell University
Simpson, Kenneth W.
Cornell University
Sutter, Nathan B.
La Sierra University
Todhunter, Rory J.
Cornell University
Boyko, Adam R.
Cornell University
Data from: Imputation of canine genotype array data using 365 whole-genome
sequences improves power of genome-wide association studies
Dryad
dataset
2019
whole genome sequencing
Imputation
Canis lupus familiaris
domestic dog
Genome-wide association study
2020-08-30T00:00:00Z
2019-10-08T00:00:00Z
en
https://doi.org/10.1371/journal.pgen.1008003
11329856417 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.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)