All of Us Genomics & Multi-omics Quality Report

  • Updated

On June 26, 2026, the All of Us Research Program released the genomic and multi-omic data of 553,949 array samples, 535,662 srWGS samples with SNP & Indel calls, 96,405 srWGS samples with SV calls, 8,980 RNA Seq samples, 9,969 proteomics samples and 14,521 lrWGS samples in the Researcher Workbench (RW) for use by researchers registered for Controlled Tier access. As described previously [2], this high-quality genetic data along with comprehensive health data will enable health research and catalog the genetic variation that leads to human health and disease. For a snapshot of the data, see Table 1.

DatasetNumber of participantsHighlights
Array553,949
  • More than 1.9 million variants
  • We added more than 100,000 new participants in CDRv9
Short-read WGS SNP and Indel535,662
  • More than 1.3 billion variants
  • We added more than 120,000 new participants with srWGS data in CDRv9
  • There are more than 125 million new variants as compared to the previous All of Us dataset
  • The All of Us srWGS dataset is now one of the largest srWGS datasets
Short-read WGS structural variants (SVs) 96,405
  • Nearly 1.5 million variants
Long-read WGS14,521
  • We added more than 11,000 new participants with long-read WGS data in CDRv9 (more than 2.5 million variants)
RNA Seq8,980
  • NEW data type in the CDRv9 release
  • Gene counts and per-ancestry quantitative trait loci (QTL) analyses
Proteomic samples9,969
  • NEW data type in the CDRv9 release
  • Expression counts for more than 5,000 proteins
Table 1 - Snapshot of All of Us CDRv9 genomics and multi-omics data

In addition to variant calls, raw data (IDAT files for array data, CRAM files for srWGS data, BAM files for lrWGS data and RNA data), and auxiliary files (including variant annotations, pharmacogenomics, genetic ancestry categories, relatedness/kinship scores, HLA variant calls, and challenging medically relevant gene calls) are available in the RW through Controlled Tier access. Quality control processes, performed both independently and across samples, indicate that these data are ready for general analysis. We suggest researchers, at a minimum, read the Known Issues and FAQ sections below before using the data.

Was this article helpful?

0 out of 0 found this helpful

Have more questions? Submit a request

Comments

0 comments

Article is closed for comments.