GWAS summary statistics for 9 quantitative phenotypes from the UK Biobank (5-fold cross-validation)

This dataset contains GWAS summary statistics for 9 quantitative phenotypes from the UK Biobank.

The phenotypes are:

• HEIGHT: Standing height (Data-Field: 50)
• BMI: Body mass index (Data-Field: 21001)
• WC: Waist circumference (Data-Field: 48)
• HC: Hip circumference (Data-Field: 49)
• BW: Birth weight (Data-Field: 20022)
• FVC: Forced vital capacity (Data-Field: 3062)
• FEV1: Forced expiratory volume in 1-second (Data-Field: 3063)
  
• HDL: HDL cholesterol (Data-Field: 30760)
  
• LDL: LDL cholesterol (Data-Field: 30780)

The GWAS study used data from "White British" samples (N = 337225), which were randomly divided into 5 folds for the purposes of cross-validation. The upload contains, for each fold, GWAS summary statistics for the training, validation, and test set. The validation summary statistics can be used for model selection/tuning. The test summary statistics can be used to evaluate PRS models via pseudo-validation methods. Association testing was done with plink2.

The structure of the data is as follows:

• train
  • fold_1
    • chr_1.PHENO1.glm.linear
    • chr_2.PHENO1.glm.linear
    • ...
  • fold_2
  • fold_3
  • ...
• validation
  • fold_1
  • fold_2
  • fold_3
  • ...
• test
  • fold_1
  • fold_2
  • fold_3
  • ...

For more details about the GWAS study, Quality Control (QC) criteria, or other information, please consult our publication:

Zabad, S., Gravel, S., & Li, Y. (2023). Fast and accurate Bayesian polygenic risk modeling with variational inference. The American Journal of Human Genetics, 110(5), 741–761. https://doi.org/10.1016/j.ajhg.2023.03.009

If you use this data in your work, please cite the publication above.