Data from: Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks

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

The data in this object relates to the publication titled “Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks”, authored by Wright, Leger, et al. The majority of the object is dedicated to the phenotypic and genetic data presented in figure two of the manuscript, and for related traits collected for this study. This object also included raw phenotypic measurements for each of the 6,147 rats used in this study. GWAS data was collected and analyzed as described in “Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose” by Chitre et al., 2020 in continuation of this study.

File contents:
-- obesity_upublished_data_raw_phenotypes_PalmerLab.csv: raw phenotypes for each of the rats, including the following traits: RFID, BMI without tail, body length with tail, BMI with tail, body length without tail, body weight, sex, and phenotyping center.

-- results.bmi_wo_tail.csv: SNP level summary statistics for rat body mass index (BMI) without tail genome-wide association study.

-- results.length_wo_tail_cm.csv: SNP level summary statistics for rat body length (bl) without tail genome-wide association study, measured and from nose to the base of the tail (cm).

-- results.bmi_w_tail.csv: SNP level summary statistics for rat body mass index (BMI) with tail association study.

-- results.length_w_tail_cm.csv: SNP level summary statistics for rat body length (bl) with tail association study, measured and from nose to the end of the tail (cm).

-- results.body_weight_g.csv: SNP level summary statistics for rat body weight association study (g).

-- Data_Dictionary

• 2014 to 2022

• 2023

• Leger, Brittany S.
• Rosenthal, Sara B.
• Wright, Sarah N.

• Ideker, Trey
• Palmer, Abraham A.

• Chen, Hao
• Flagel, Shelly B.
• Ishiwari, Keita
• Meyer, Paul
• Richards, Jerry
• Robinson, Terry E.
• Solberg Woods, Leah C.

• Bimschleger, Hannah
• George, Anthony
• Han, Wenyan
• Holl, Katie
• King, Christopher P.
• Lamparelli, Alexander
• Leger, Brittany S.
• Martin, Connor
• Martinez, Angel G.
• Netzley, Alesa H.
• Rosenthal, Sara B.
• St. Pierre, Celine L.
• Wang, Tengfei
• Wright, Sarah N.

• Cheng, Riyan
• Chitre, Apurva S.
• Gao, Jianjun
• Gileta, Alexander F.
• Leger, Brittany S.
• Rosenthal, Sara B.
• Wright, Sarah N.

• Polesskaya, Oksana

• Ideker, Trey
• Palmer, Abraham A.

• Kreisberg, Jason F.

• Jia, Tongqiu
• Liu, Sophie

All relevant tools and software used to generate the phenotypic and genetic data included 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 following grants from the National Institutes of Health: NIMH U01 MH115747, NIGMS P41 GM103504, NIDA P50 DA037844, and NIGMS T32 GM008666.

• Body mass index (BMI)
• Complex trait
• Genetics
• Genome-wide association study (GWAS)
• Genotype by sequencing (GBS)
• Heterogeneous stock (HS) rats
• Obesity
• Rat

• data

• English

Identifier: Abraham A. Palmer: https://orcid.org/0000-0003-3634-0747

Identifier: Alesa H. Netzley: https://orcid.org/0000-0003-0171-3363

Identifier: Alexander F. Gileta: https://orcid.org/0000-0002-7793-8043

Identifier: Alexander Lamparelli: https://orcid.org/0000-0003-1908-9562

Identifier: Apurva S. Chitre: https://orcid.org/0000-0003-1709-9214

Identifier: Brittany S. Leger: https://orcid.org/0000-0002-8467-5472

Identifier: Celine L. St. Pierre: https://orcid.org/0000-0001-5465-6601

Identifier: Christopher P. King: https://orcid.org/0000-0002-6641-237X

Identifier: Hannah Bimschleger: https://orcid.org/0000-0001-6578-7201

Identifier: Hao Chen: https://orcid.org/0000-0002-2680-6921

Identifier: Jason F. Kreisberg: https://orcid.org/0000-0002-3616-079X

Identifier: Jianjun Gao: https://orcid.org/0000-0002-7227-1032

Identifier: Keita Ishiwari: https://orcid.org/0000-0002-6190-2249

Identifier: Leah C. Solberg Woods: https://orcid.org/0000-0002-7943-798X

Identifier: Oksana Polesskaya: https://orcid.org/0000-0003-3024-114X

Identifier: Paul Meyer: https://orcid.org/0000-0001-5665-2292

Identifier: Sara B. Rosenthal: https://orcid.org/0000-0002-6548-9658

Identifier: Sarah N. Wright: https://orcid.org/0000-0003-3441-5469

Identifier: Shelly B. Flagel: https://orcid.org/0000-0002-7309-9908

Identifier: Sophie Liu: https://orcid.org/0000-0001-7934-8605

Identifier: Tengfei Wang: https://orcid.org/0000-0003-3527-3394

Identifier: Terry E. Robinson: https://orcid.org/0000-0001-7861-3737

Identifier: Tongqiu Jia: https://orcid.org/0000-0002-6012-6436

Identifier: Trey Ideker: https://orcid.org/0000-0002-1708-8454

Identifier: Wenyan Han: https://orcid.org/0000-0003-0886-1430

Primary associated publication

• Wright, SN, Leger, BS, Rosenthal, SB, Liu, S, Jia, T, Chitre, AS, Polesskaya, O, Holl, K, Gao, J, Cheng, R, Martinez, AG, George, A, Gileta, AF, Han, W, Netzley, AH, King, CP, Lamparelli, A, Martin, C, St. Pierre, CL, Wang, T, Bimschleger, H, Richards, J, Ishiwari, K, Chen, H, Flagel, SB, Meyer, P, Robinson, TE, Solberg Woods, LC, Kreisberg, JF, Ideker, T, Palmer, AA. “Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks”. Waiting on submission to Cell Reports.

Previous version

• 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

Reference

• The genotypes for the HS rats used in this study can be found in: Palmer, Abraham A. (2023). Heterogeneous Stock (HS) Rat Genotypes, Version 1. In Genotype Data from: NIDA Center for GWAS in Outbred Rats. UC San Diego Library Digital Collections. [Pending] https://doi.org/10.6075/J0028RR4

Other resource

• Center for GWAS in Outbred Rats database (cgord.org)

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2023-07-13