Data from: Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose
Contains unprocessed and processed phenotype data. Covariates specific to each trait contain the same prefix in the raw phenotype file. For example, bmi_w_tail_age and bmi_w_tail_technician are age and technician initials for the trait bmi_w_tail. Residuals (processed phenotype data) used for GWAS were produced using the following approach: Each trait within each research site was quantile normalized separately for males and females, this approach is similar to using sex as a covariate. Other relevant covariates (including age and dissector) were identified for each trait, and covariate effects were regressed out if they were significant and explained more than 2% of the variance. (Please note that each technician is specific to each center. Phenotyping center information is in column “center”). Residuals were then quantile normalized again, after which the data for each sex and site was pooled prior to further analysis. Trait_ontology.xlsx contains phenotype descriptions and InterLex IDs.
LD pruned genotype data
LD pruned genotype data in PLINK binary and BIMBAM file formats. Command used to LD-prune the genotype data in PLINK v1.90 : --indep-pairwise 50 5 0.95. The 50 is the number of variants to look at in a window, the 5 is the number of variants to shift the windows side way each step, and the 0.95 is the r2 threshold for trimming SNPs.
Unpruned genotype data in Oxford file format
Genotype data in the form of genotype probabilities.
Genetic Relatedness Matrix (GRM)
gcta v1.26.0 was used to produce the GRM using the following command: gcta --bfile genotype --autosome-num 20 --autosome --thread-num 1 --make-grm-bin --out obesity_published_grm
- Cite This Work
Chitre, Apurva S.; Polesskaya, Oksana; Holl, Katie; Gao, Jianjun; Cheng, Riyan; Bimschleger, Hannah; Garcia Martinez, Angel; George, Anthony; Gileta, Alexander F.; Han, Wenyan; Horvath, Aidan; Hughson, Alesa; Ishiwari, Keita; King, Christopher P.; Lamparelli, Alexander; Versaggi, Cassandra L.; Martin, Connor; St. Pierre, Celine L.; Tripi, Jordan A.; Wang, Tengfei; Chen, Hao; Flagel, Shelly B.; Meyer, Paul; Richards, Jerry; Robinson, Terry E.; Palmer, Abraham A.; Solberg Woods, Leah C. (2022). Data from: Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose. In The Center for GWAS in Outbred Rats Database (C-GORD). UC San Diego Library Digital Collections. https://doi.org/10.6075/J0Q240F0
The data in this object comes from the publication titled “Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose”, authored by Chitre et al. The majority of the object is dedicated to the phenotypic and genetic data presented throughout the publication. However, this object also contains additional information beyond what is presented, including (1) a genetic relatedness matrix generated from LD pruned set of genotypes, (2) Summary files for the GWAS results for all phenotypes, (3) Trait descriptions. Details on how these files were generated can all be found in the Methods section of the associated publication.
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- 2014 to 2020
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- Technical Details
All relevant tools and software used to generate the data in this object are noted below and in the Methods section of the associated publication.
GWAS: GEMMA v0.97
Converting genotype probabilities into dosages: QCTOOL v2
Converting genotype probabilities into Hard-Called Genotypes: PLINK v2.0
LD pruning of the genotype data : PLINK v1.90
Command used to LD-prune the genotype data in PLINK v1.90 : --indep-pairwise 50 5 0.95
The 50 is the number of variants to look at in a window, the 5 is the number of variants to shift the windows side way each step, and the 0.95 is the r2 threshold for trimming SNPs.
This work was supported by the National Institute on Drug Abuse (P50 DA037844) and the National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK106386).
View formats within this collection
Bimschleger, Hannah: https://orcid.org/0000-0001-6578-7201
Chen, Hao: https://orcid.org/0000-0002-2680-6921
Cheng, Riyan: https://orcid.org/0000-0002-8670-795X
Chitre, Apurva S.: https://orcid.org/0000-0003-1709-9214
Flagel, Shelly B.: https://orcid.org/0000-0002-7309-9908
George, Anthony: https://orcid.org/0000-0002-3700-5003
Gileta, Alexander F.: https://orcid.org/0000-0002-7793-8043
Han, Wenyan: https://orcid.org/0000-0003-0886-1430
Ishiwari, Keita: https://orcid.org/0000-0002-6190-2249
King, Christopher P.: https://orcid.org/0000-0002-6641-237X
Lamparelli, Alexander: https://orcid.org/0000-0003-1908-9562
Meyer, Paul: https://orcid.org/0000-0001-5665-2292
Palmer, Abraham A.: https://orcid.org/0000-0003-3634-0747
Polesskaya, Oksana: https://orcid.org/0000-0003-3024-114X
Robinson, Terry E.: https://orcid.org/0000-0001-7861-3737
Solberg Woods, Leah C.: https://orcid.org/0000-0002-7943-798X
St. Pierre, Celine L.: https://orcid.org/0000-0001-5465-6601
Wang, Tengfei: https://orcid.org/0000-0003-3527-3394
- Related Resources
- Chitre, A. S., Polesskaya, O., Holl, K., Gao, J., Cheng, R., Bimschleger, H., Garcia Martinez, A., George, T., Gileta, A. F., Han, W., Horvath, A., Hughson, A., Ishiwari, K., King, C. P., Lamparelli, A., Versaggi, C. L., Martin, C., St. Pierre, C. L., Tripi, J. A., … Solberg Woods, L. C. (2020). Genome‐Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose. Obesity, 28(10), 1964–1973. https://doi.org/10.1002/oby.22927
- NCBI SRA repository of Heterogeneous stock rats sequencing data and alignments: https://www.ncbi.nlm.nih.gov/sra/
- Wright, Sarah N.; Leger, Brittany S.; Rosenthal, Sara B.; Liu, Sophie; Jia, Tongqiu; Chitre, Apurva S.; Polesskaya, Oksana; Holl, Katie; Gao, Jianjun; Cheng, Riyan; Martinez, Angel G.; George, Anthony; Gileta, Alexander F.; Han, Wenyan; Netzley, Alesa H.; King, Christopher P.; Lamparelli, Alexander; Martin, Connor; St. Pierre, Celine L.; Wang, Tengfei; Bimschleger, Hannah; Richards, Jerry; Ishiwari, Keita; Chen, Hao; Flagel, Shelly B.; Meyer, Paul; Robinson, Terry E.; Solberg Woods, Leah C.; Kreisberg, Jason F.; Ideker, Trey; Palmer, Abraham A. (2023). Data from: Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks. In The Center for GWAS in Outbred Rats Database (C-GORD). UC San Diego Library Digital Collections. https://doi.org/10.6075/J0NV9JFT
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