Version: V7 Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
The All of Us Research Program is a
large-scale biomedical research initiative launched by the U.S. National Institutes of Health (NIH)
in 2018. Its goal is to build one of the most diverse health databases, enrolling over one
million participants who reflect the full diversity of the United States, including groups that
have been historically underrepresented in biomedical research. Participants contribute health
surveys, electronic health records (EHR), physical measurements, and biosamples for genomic
analysis.
This track shows allele frequencies from the v7 short-read whole-genome sequencing (srWGS)
release of 245,388 participants. A minimum allele count filter of ≥20 was applied.
Frequencies are provided both overall and broken down by genetic ancestry using local ancestry
inference: European (EUR), East Asian (EAS), African (AFR), Indigenous American (AMR),
Oceanian (OCE), and South Asian (SAS). Some variants are flagged with an "NW" tag
(not in window) when the variant was not within a genomic window covered by the ancestry
reference files; in these cases the closest available position was used for ancestry assignment.
Data Access
Due to license restrictions, the data for this track cannot be downloaded from the UCSC
Genome Browser. The Table Browser, Data Integrator, and download server are not available
for this track.
Variant data and individual-level data are accessible through the
All of Us Researcher Workbench,
which requires registration and completion of a training program. Aggregate allele frequency
data is freely available.
Methods
Whole-genome sequencing was performed on the Illumina NovaSeq 6000 platform with PCR-free library
preparation targeting 30x coverage. Reads were aligned to GRCh38 and variants were called using
the Illumina DRAGEN (Dynamic Read Analysis for GENomics) pipeline, which performs mapping,
alignment, sorting, duplicate marking, and variant calling (SNVs and indels) in a single
hardware-accelerated workflow. Joint genotyping was performed across all samples. Quality control
included sample-level filtering for contamination, sex discordance, and relatedness, and
variant-level filtering using VQSR.
Population-specific allele frequencies were determined using local ancestry inference at UCSC by the Ioannidis group.
The ancestry breakdown into European, East Asian, African, Indigenous American, Oceanian,
and South Asian components is part of a pending publication.
The conversion of all source files for the varFreqs track is documented in the makeDoc file of the track.
For some tracks, python scripts were needed and are also available from GitHub.
Credits
The All of Us Research Program is supported by the National Institutes of Health. We thank the
participants and the program for making frequency data available.
The local ancestry inference was performed by Qudsi Aljabiri and Cole Shanks under
Prof. Alexander Ioannidis, UC Santa Cruz.