Significant sparse polygenic risk scores across 813 traits in UK Biobank

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

  • Yosuke Tanigawa
  • Junyang Qian
  • Guhan Venkataraman
  • Justesen, Johanne Marie
  • Ruilin Li
  • Robert Tibshirani
  • Trevor Hastie
  • Manuel A Rivas

We present a systematic assessment of polygenic risk score (PRS) prediction across more than 1,500 traits using genetic and phenotype data in the UK Biobank. We report 813 sparse PRS models with significant (p < 2.5 x 10-5) incremental predictive performance when compared against the covariate-only model that considers age, sex, types of genotyping arrays, and the principal component loadings of genotypes. We report a significant correlation between the number of genetic variants selected in the sparse PRS model and the incremental predictive performance (Spearman's ⍴ = 0.61, p = 2.2 x 10-59 for quantitative traits, ⍴ = 0.21, p = 9.6 x 10-4 for binary traits). The sparse PRS model trained on European individuals showed limited transferability when evaluated on non-European individuals in the UK Biobank. We provide the PRS model weights on the Global Biobank Engine (https://biobankengine.stanford.edu/prs).

OriginalsprogEngelsk
Artikelnummere1010105
TidsskriftPLOS Genetics
Vol/bind18
Udgave nummer3
Antal sider21
ISSN1553-7390
DOI
StatusUdgivet - 2022
Eksternt udgivetJa

ID: 301160488