Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs
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 Hip dysplasia (HD), elbow dysplasia (ED), and rupture of the cranial (anterior) cruciate ligament (RCCL) are the most common complex orthopedic...
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Language: | English |
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Dryad
2018
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Online Access: | https://doi.org/10.5061/dryad.8g7h7 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::d12e5bedc26d53163bb3aa39e4e64a7a 2023-05-15T15:51:12+02:00 Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs Huang, Meng Hayward, Jessica J. Corey, Elizabeth Garrison, Susan J. Wagner, Gabriela R. Krotscheck, Ursula Hayashi, Kei Schweitzer, Peter A. Lust, George Boyko, Adam R. Todhunter, Rory J. 2018-04-26 https://doi.org/10.5061/dryad.8g7h7 en eng Dryad http://dx.doi.org/10.5061/dryad.8g7h7 https://dx.doi.org/10.5061/dryad.8g7h7 lic_creative-commons 10.5061/dryad.8g7h7 oai:easy.dans.knaw.nl:easy-dataset:102326 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:102326 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 FarmCPU elbow dysplasia Canis lupus familiaris Genome-wide association study hip dysplasia rupture of the cranial cruciate ligament Life sciences medicine and health care stat lang Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2018 fttriple https://doi.org/10.5061/dryad.8g7h7 2023-01-22T16:52:27Z 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 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. Dataset Canis lupus Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
FarmCPU elbow dysplasia Canis lupus familiaris Genome-wide association study hip dysplasia rupture of the cranial cruciate ligament Life sciences medicine and health care stat lang |
spellingShingle |
FarmCPU elbow dysplasia Canis lupus familiaris Genome-wide association study hip dysplasia rupture of the cranial cruciate ligament Life sciences medicine and health care stat lang Huang, Meng Hayward, Jessica J. Corey, Elizabeth Garrison, Susan J. Wagner, Gabriela R. Krotscheck, Ursula Hayashi, Kei Schweitzer, Peter A. Lust, George Boyko, Adam R. Todhunter, Rory J. Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs |
topic_facet |
FarmCPU elbow dysplasia Canis lupus familiaris Genome-wide association study hip dysplasia rupture of the cranial cruciate ligament Life sciences medicine and health care stat lang |
description |
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 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. |
format |
Dataset |
author |
Huang, Meng Hayward, Jessica J. Corey, Elizabeth Garrison, Susan J. Wagner, Gabriela R. Krotscheck, Ursula Hayashi, Kei Schweitzer, Peter A. Lust, George Boyko, Adam R. Todhunter, Rory J. |
author_facet |
Huang, Meng Hayward, Jessica J. Corey, Elizabeth Garrison, Susan J. Wagner, Gabriela R. Krotscheck, Ursula Hayashi, Kei Schweitzer, Peter A. Lust, George Boyko, Adam R. Todhunter, Rory J. |
author_sort |
Huang, Meng |
title |
Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs |
title_short |
Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs |
title_full |
Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs |
title_fullStr |
Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs |
title_full_unstemmed |
Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs |
title_sort |
data from: a novel iterative mixed model to remap three complex orthopedic traits in dogs |
publisher |
Dryad |
publishDate |
2018 |
url |
https://doi.org/10.5061/dryad.8g7h7 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
10.5061/dryad.8g7h7 oai:easy.dans.knaw.nl:easy-dataset:102326 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:102326 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 |
op_relation |
http://dx.doi.org/10.5061/dryad.8g7h7 https://dx.doi.org/10.5061/dryad.8g7h7 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.8g7h7 |
_version_ |
1766386283353997312 |