In the November 2024 HSLS Update, we discussed the release of the All by All table data in the All of Us (AoU) Researcher Workbench. Now, researchers can explore these tables in even greater depth through a newly launched interactive website. The publicly available All by All Browser is a powerful platform that allows users to investigate both known and novel genotype-phenotype associations, with access to up to 500 billion associations. By utilizing precomputed genome-wide association study (GWAS) and phenome-wide association study (PheWAS) results based on All of Us data as of July 2022, the browser eliminates the need for researchers to run these complex analyses themselves. This not only saves time and computational resources, but also enables scientists to focus on interpreting results, validating findings, and generating new research questions.
The platform is powered by Hail Tables and SQLite, enabling efficient processing of large-scale genomic and phenotypic data. It currently includes approximately 3,400 phenotypes from 214,216 participants with whole genome sequencing data. To ensure reliable statistical insights, the browser applies multiple association testing methods, including burden tests, sequence kernel association tests (SKAT), and an optimized version combining burden and SKAT tests (SKAT-O). Users can also apply additional filters to focus on specific mutation classes of interest.
The interface features a split-screen layout, with a Results Pane on the left displaying relevant hits for a selected phenotype, gene, or variant, while the right side provides detailed association data. Although the platform offers a wide range of features, new users may need some time to familiarize themselves with its navigation. To assist with this, a comprehensive walkthrough is available to help researchers get started.
In the near future, additional guidance and learning materials will be introduced to support researchers in using the All by All Browser. These resources will offer insights into result interpretation, platform capabilities, and practical applications for research. For those interested in similar genomic research tools, GeneBass, which leverages UK Biobank data, provides another option for exploring PheWAS and GWAS findings based on whole exome sequencing from 394,841 participants. Researchers who prefer to stay within the Researcher Workbench can enhance their analyses by integrating All by All table data with other AoU datasets, enabling deeper exploration of genetic associations, rare diseases, and potential therapeutic targets. Ready to dive in? Visit the home page and enter your gene or phenotype of interest to get started with this powerful new resource!
~Alexis Cenname