Workshop: Accessing and analyzing All of Us biomedical and genomic data via the Researcher Workbench

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The NIH’s All of Us data is one of the largest health data resources available and includes demographic, survey, electronic health record (EHR), Fitbit, genomic, and other data from over 400,000 participants with a target to grow to 1,000,000 participants. The data is extensive, currently including EHR data from over 378,000 participants, survey data from over 409,000 participants, short-read whole genomic sequencing (WGS) data from 245,400 participants, long-read WGS data from 1,040 participants, short-read WGS structural variant data from 11,400 participants, and genotyping arrays from 312,940 participants.

The All of Us data is also one of the most diverse health data resources available, with over 50% of participants from racial and ethnic minorities and 80% of participants underrepresented in biomedical research. The All of Us Evenings with Genetics (AoUEwG) Research Program of the Department of Molecular and Human Genetics at Baylor College of Medicine is training the next generation of biomedical researchers on the platform and tools available to be used for projects leveraging data from All of Us.

The training provided at this workshop includes the topics below:

  • An introduction to the All of Us Researcher Workbench as the online platform for accessing and analyzing the All of Us data
  • A demonstration of starting a project on the Researcher Workbench by creating a workspace and retrieving the desired datasets
  • A review of best practices for cleaning and analyzing retrieved datasets in All of Us Jupyter Notebooks that support Python and R programming languages, limited bash commands, and genomic analysis software, including Hail and Plink
  • A discussion of analyzing the genomic data in a genome-wide association study (GWAS) using Hail that is scalable and efficient, and includes principal component analyses (PCA)
  • Supplementary material to review after the workshop for continued practice and learning

Julie R. Coleman

Lead Bioinformatics Programmer of the All of Us Evenings with Genetics Research Program

Department of Molecular of Human Genetics, Baylor College of Medicine

Dr. Julie R. Coleman is the Lead Bioinformatics Programmer of the All of Us Evenings with Genetics (AoUEwG) Research Program in the Department of Molecular of Human Genetics at Baylor College of Medicine (BCM). Her PhD is in Plant Breeding and Genetics from Texas A&M University, followed by working in the seed industry for five years in breeding Brassica genetics. She then transitioned to medicine and biotechnology, briefly working in the drug discovery industry with data science and software, before joining BCM in January 20222. While at BCM, she has focused on training biomedical researchers from across the United States on the All of Us Researcher Workbench through the AoUEwG’s annual All of Us Biomedical Researcher (BR) Scholars Program. She also provides continual data science support for these researchers as they complete their projects on the Researcher Workbench.

Shamika Ketkar

Assistant Professor

Department of Molecular and Human Genetics, Baylor College of Medicine

Dr. Shamika Ketkar is an Assistant Professor in the Department of Molecular and Human Genetics at Baylor College of Medicine (BCM). She completed her doctoral training in Statistical and Human Genetics and masters training in Genetic Epidemiology from Washington University School of Medicine in St Louis Missouri (WashU). Her core research interests include understanding the genomics, transcriptomics and epigenomics of genetic disorders with an emphasis on rare undiagnosed diseases and cancers with a special focus on hematologic and bone cancers. She has a broad background in translational bioinformatics, genomics, and genetics with more than a decade of extensive experience in genomic data science at Harvard School of Public Health, WashU and BCM. She supports the All of Us Evening with Genetics Research Program as an educator and data scientist.

Jinyoung Byun

Assistant Professor, Institute of Clinical and Translational Research and Section of Epidemiology and Population Sciences

Department of Medicine, Baylor College of Medicine

Dr. Jinyoung Byun is an Assistant Professor in the Institute of Clinical and Translational Research and Section of Epidemiology and Population Sciences, Department of Medicine, at Baylor College of Medicine (BCM). She completed her postdoctoral training at the Department of Biomedical Science in the Geisel School of Medicine at Dartmouth and joined BCM in 2018. Her research focuses on understanding genetic etiology in lung cancer, liver cancer, and rare diseases in diverse populations. She joined the All of Us Evening with Genetics Research Program in 2022 and has supported the Community Engagement Partners with the All of Us Research Program introduction sessions.

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Live Workshop Event
09/21/2023 at 12:00 PM (EDT)  |  Recorded On: 09/22/2023
09/21/2023 at 12:00 PM (EDT)  |  Recorded On: 09/22/2023
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