LD reference panels - All of Us and UK Biobank

All of Us Reference Panels LD reference panels construction Select genetic variants that are available in the All of Us (CDRv7, Controlled Tier) array genotype dataset. The following variant filtering/removing criteria were applied: (a) located on sex chromosomes; (b) missing value frequency > 0.03; and (c) MAF < 0.01. LD blocks were defined according to the LD block definition in PRS-CSx [Ref] (the start and end base pair position of the blocks of the LD reference panels used in PRS-CSx). LD blocks were saved in matrices with the "dgCMatrix" class and in "RDS" file format, together compressed with map files including the variant information. Sample size African American: 62,331 Hispanic: 59,640 Number of variants African American: 993,783 Hispanic: 875,221 UK Biobank Reference Panels LD reference panels construction Select genetic variants that are available in both 1000 Genomes and the UK Biobank genotyped dataset. The following variant filtering/removing criteria were applied: (a) located on sex chromosomes; (b) missing value frequency > 0.02; and (c) MAF < 0.05. LD blocks were saved in matrices with the "dgCMatrix" class and in "RDS" file format, together compressed with map files including the variant information. Sample size AFR:7,507 AMR: 687 Number of variants AFR: 1,234,911 AMR: 1,183,556