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LD reference panels - All of Us and UK Biobank

Domain:

healthcare

Record type:

dataset
Creator:
Wu,
Publisher:
Zenodo
Host:avatar

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

Visit

doi.org

Licenses

info:eu-repo/semantics/openAccessCreative Commons Attribution 4.0 Internationalhttps://creativecommons.org/licenses/by/4.0/legalcodeMIT Licensehttps://opensource.org/licenses/MIT

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