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UK Biobank Pharma Proteomics Project

Identifier

Section titled “Identifier”
ukb_ppp

License

Section titled “License”

CC BY

Citation

Section titled “Citation”
Sun BB, Chiou J, Traylor M, et al. Plasma proteomic associations with genetics and health in the UK Biobank. Nature 2023;622:329-338. doi:10.1038/s41586-023-06592-6

Overview

Section titled “Overview”

Large-scale pQTL (protein quantitative trait loci) study with associations between genetic variants from the UK Biobank and measurements of approximately 3,000 proteins.

The study cohort contains individuals from six ancestry populations (AFR=African, AMR=Admixed American, CSA=Central-South Asian, EAS=East Asian, EUR=European, MID=Middle Eastern).

There are also pQTL associations for the ALL ancestry group (a combination of all six ancestries).

Harmonization procedure for variants:

  • No liftover necessary; source files already include GRCh37 and GRCh38 coordinates.
  • Variants were aligned to dbSNP (build 157, GRCh38 coordinates), so that effect_allele == dbSNP alt_allele and other_allele == dbSNP ref_allele.

The forward strand in ukb_ppp.variants table refers to the dbSNP allele orientation.

  • Where effect_allele and other_allele were swapped (was_swapped = True in ukb_ppp.variants table), beta and effect_allele_frequency values were adjusted appropriately (-beta, 1 - effect_allele_frequency).
  • Variants without an exact dbSNP allele match (in_dbsnp = False).

Domain: genetics.

Source: https://doi.org/10.7303/syn51364943.

Always use ancestry codes (AFR, ALL, AMR, CSA, EAS, EUR, MID) to filter, not full names. protein_id values are UniProt accession IDs. gene_id values are Ensembl gene IDs (ENSG*). gene_symbol values are HGNC (Hugo) symbols.

Tables

Section titled “Tables”