All of Us Research Program Sequencing

Sequencing was performed by the Genome Centers funded by the All of Us Research Program^{14 (link),15 (link)}. All centers used the same sequencing protocols that consisted of PCR-free 150 bp, paired-end libraries sequenced on the Illumina NovaSeq 6000 platform and processed using DRAGEN v3.4.12 (Illumina) software. The GRCh38 reference genome was used for alignment^{16 (link)}. Phenotypic data, ancestry features, and principal components were annotated using Hail through the All of Us Researcher Workbench¹⁷ . Low-quality variants with a call rate of less than 0.95, multiallelic variants, and variants significantly departed from Hardy-Weinberg equilibrium in the control cohort (P ≤ 1.0 × 10⁻¹⁰) were removed. Common variants in autosomal chromosomes with a minor allele frequency of higher than 0.005 were included in the association test. Sex concordance was part of the All of Us upstream genomic data quality control process, and all samples within the released genomic data have passed the sex concordance check. Ancestry annotation and relatedness were inferred by the PC-relate method in Hail. Duplicate samples and one of the related participant pairs were excluded¹⁷ .