Significant sparse polygenic risk scores across 813 traits in UK Biobank.
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-on...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-03-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1010105 |
| _version_ | 1797990905017270272 |
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| author | Yosuke Tanigawa Junyang Qian Guhan Venkataraman Johanne Marie Justesen Ruilin Li Robert Tibshirani Trevor Hastie Manuel A Rivas |
| author_facet | Yosuke Tanigawa Junyang Qian Guhan Venkataraman Johanne Marie Justesen Ruilin Li Robert Tibshirani Trevor Hastie Manuel A Rivas |
| author_sort | Yosuke Tanigawa |
| collection | DOAJ |
| description | 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). |
| first_indexed | 2024-04-11T08:42:55Z |
| format | Article |
| id | doaj.art-40b16052b1c54592a901ecc6fce1d7d0 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-11T08:42:55Z |
| publishDate | 2022-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-40b16052b1c54592a901ecc6fce1d7d02022-12-22T04:34:02ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042022-03-01183e101010510.1371/journal.pgen.1010105Significant sparse polygenic risk scores across 813 traits in UK Biobank.Yosuke TanigawaJunyang QianGuhan VenkataramanJohanne Marie JustesenRuilin LiRobert TibshiraniTrevor HastieManuel A RivasWe 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).https://doi.org/10.1371/journal.pgen.1010105 |
| spellingShingle | Yosuke Tanigawa Junyang Qian Guhan Venkataraman Johanne Marie Justesen Ruilin Li Robert Tibshirani Trevor Hastie Manuel A Rivas Significant sparse polygenic risk scores across 813 traits in UK Biobank. PLoS Genetics |
| title | Significant sparse polygenic risk scores across 813 traits in UK Biobank. |
| title_full | Significant sparse polygenic risk scores across 813 traits in UK Biobank. |
| title_fullStr | Significant sparse polygenic risk scores across 813 traits in UK Biobank. |
| title_full_unstemmed | Significant sparse polygenic risk scores across 813 traits in UK Biobank. |
| title_short | Significant sparse polygenic risk scores across 813 traits in UK Biobank. |
| title_sort | significant sparse polygenic risk scores across 813 traits in uk biobank |
| url | https://doi.org/10.1371/journal.pgen.1010105 |
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