Samples were sequenced by The American Genome Center and processed by the Genome Center for Alzheimer’s Disease (GCAD) at the University of Pennsylvania. This dataset includes (1) sequencing read alignments in CRAM (compressed BAM) format (processed by VCPA v1.1), (2) genomic Variant Call Format (gVCF) files generated by GATK4.1.1 (part of the VCPA v1.1 pipeline), and (3) project-level joint-genotype calls in VCF format (pVCF) across all samples generated using GATK. Quality checks of the dataset have been performed at the sample level.