10.5061/DRYAD.8G7H7
Huang, Meng
Washington State University
Hayward, Jessica J.
Cornell University
Corey, Elizabeth
Cornell University
Garrison, Susan J.
Cornell University
Wagner, Gabriela R.
Cornell University
Krotscheck, Ursula
Cornell University
Hayashi, Kei
Cornell University
Schweitzer, Peter A.
Cornell University
Lust, George
Cornell University
Boyko, Adam R.
Cornell University
Todhunter, Rory J.
Cornell University
Data from: A novel iterative mixed model to remap three complex orthopedic
traits in dogs
Dryad
dataset
2018
FarmCPU
elbow dysplasia
Canis lupus familiaris
Genome-wide association study
hip dysplasia
2018-04-26T00:00:00Z
2018-04-26T00:00:00Z
en
https://doi.org/10.1371/journal.pone.0176932
50983677 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Hip dysplasia (HD), elbow dysplasia (ED), and rupture of the cranial
(anterior) cruciate ligament (RCCL) are the most common complex orthopedic
traits of dogs and all result in debilitating osteoarthritis. Herein we
reanalyzed previously reported data: the Norberg angle (a quantitative
measure of HD) in 921 dogs, ED in 113 cases and 633 controls, and RCCL in
271 cases and 399 controls and their genotypes at ~185,000 single
nucleotide polymorphisms. A novel fixed and random model with a
circulating probability unification (FarmCPU) function, with marker-based
principal components and a kinship matrix to correct for population
stratification, was used. A Bonferroni correction at p<0.01
resulted in a pgenome of 6.96 ×10-8. Six loci were identified; three for
HD and three for RCCL. An associated locus at CFA28:34,369,342 for HD was
described in the same dogs using a conventional mixed model. No loci were
identified for RCCL in the previous report but the two loci for ED in the
previous report did not reach genome-wide significance using the FarmCPU
model. These results were supported by simulation which demonstrated that
the FarmCPU held no power advantage over the linear mixed model for the ED
sample but provided additional power for the HD and RCCL samples.
Candidate genes for HD and RCCL are discussed. When using FarmCPU
software, we recommend a resampling test, that a positive control be used
to determine the optimum pseudo quantitative trait nucleotide-based
covariate structure of the model, and a negative control be used
consisting of permutation testing and the identical resampling test as for
the non-permuted phenotypes.
RCCL .bedrccl.bed.gzRCCL .famrccl.fam.gzRCCL .bimrccl.bim.gzHD
.bedHD.bed.gzHD .bimHD.bim.gzHD .famHD.fam.gzED .famED.fam.gzED
.bedED.bed.gzED .bimED.bim.gz