Getting started with biomedical and genomic data in the All of Us Researcher Workbench

The NIH's All of Us data is a significant source of biomedical and genomic data with 245,400 short-read whole genome sequences (WGS), 1,040 long-read WGS, 11,400 short-read WGS with structural variant calls, and 312,940 genotyping arrays. The genomic data are from participants who have also shared phenotypic data, including from electronic health records, drug exposures, procedures, physical measurements, Fitbits, and surveys. New data are released every year with ongoing engagement of one million participants planned. Researchers from institutions with Data Use and Registration Agreements (DURAs) access and analyze the data on the online platform, the All of Us Researcher Workbench. This workshop will take attendees through interactive exercises to become familiar with the All of Us data and begin research with it. First, attendees will perform a data quest on the All of Us Research Hub to browse and query the available data and to examine current projects. Then attendees will complete an exercise to learn the unique tools of the Researcher Workbench and how they are used to access and analyze the data. We will demonstrate a GWAS in interactive Jupyter Notebooks using Hail, a cloud-compatible genomic data analytic tool with efficiency and scalability to handle the large dataset. Example notebooks will be provided to the attendees. We will also address importing external (local or cloud-based) data in the Researcher Workbench. The close of the workshop will be a Q&A session.

Please note: This item is only available as part of the ASHG 2024 Annual Meeting Digital Pass.