all-of-us/ukb-cross-analysis-demo-project

Workbench demo project: cross-analysis of AoU and UKB.

ukb-cross-analysis-demo-project

The code in this repository performs a genome-wide association study on lipids in two ways:

1. A meta-analysis of GWAS results computed separately for the two cohorts:
   • ukb_rap_siloed_analysis holds notebooks for the UK Biobank Research Analysis Platform to perform a GWAS on UK Biobank data.
   • aou_workbench_siloed_analysis holds notebooks for the All of Us Researcher Workbench to perform a GWAS on All of Us data.
   • meta_analysis holds notebooks for the meta-analysis performed via METAL.
2. A GWAS using the two cohorts pooled together as inputs:
   • aou_workbench_pooled_analyses holds notebooks for the All of Us Researcher Workbench to perform a GWAS on All of Us data pooled together with UK Biobank data.

Project context

Please see our preprint on bioRxiv:

Cloud gazing: demonstrating paths for unlocking the value of cloud genomics through cross-cohort analysis Nicole Deflaux, Margaret Sunitha Selvaraj, Henry Robert Condon, Kelsey Mayo, Sara Haidermota, Melissa A. Basford, Chris Lunt, Anthony A. Philippakis, Dan M. Roden, Josh C. Denny, Anjene Musick, Rory Collins, Naomi Allen, Mark Effingham, David Glazer, Pradeep Natarajan, Alexander G. Bick bioRxiv 2022.11.29.518423; doi: https://doi.org/10.1101/2022.11.29.518423