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Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics
MOTIVATION: Measuring genetic diversity is an important problem because increasing genetic diversity is a key to making new genetic discoveries, while also being a major source of confounding to be aware of in genetics studies. RESULTS: Using the UK Biobank data, a prospective cohort study with deep...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9237724/ https://www.ncbi.nlm.nih.gov/pubmed/35604078 http://dx.doi.org/10.1093/bioinformatics/btac348 |
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author | Privé, Florian |
author_facet | Privé, Florian |
author_sort | Privé, Florian |
collection | PubMed |
description | MOTIVATION: Measuring genetic diversity is an important problem because increasing genetic diversity is a key to making new genetic discoveries, while also being a major source of confounding to be aware of in genetics studies. RESULTS: Using the UK Biobank data, a prospective cohort study with deep genetic and phenotypic data collected on almost 500 000 individuals from across the UK, we carefully define 21 distinct ancestry groups from all four corners of the world. These ancestry groups can serve as a global reference of worldwide populations, with a handful of applications. Here, we develop a method that uses allele frequencies and principal components derived from these ancestry groups to effectively measure ancestry proportions from allele frequencies of any genetic dataset. AVAILABILITY AND IMPLEMENTATION: This method is implemented in function snp_ancestry_summary of R package bigsnpr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-9237724 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-92377242022-06-29 Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics Privé, Florian Bioinformatics Applications Note MOTIVATION: Measuring genetic diversity is an important problem because increasing genetic diversity is a key to making new genetic discoveries, while also being a major source of confounding to be aware of in genetics studies. RESULTS: Using the UK Biobank data, a prospective cohort study with deep genetic and phenotypic data collected on almost 500 000 individuals from across the UK, we carefully define 21 distinct ancestry groups from all four corners of the world. These ancestry groups can serve as a global reference of worldwide populations, with a handful of applications. Here, we develop a method that uses allele frequencies and principal components derived from these ancestry groups to effectively measure ancestry proportions from allele frequencies of any genetic dataset. AVAILABILITY AND IMPLEMENTATION: This method is implemented in function snp_ancestry_summary of R package bigsnpr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2022-05-23 /pmc/articles/PMC9237724/ /pubmed/35604078 http://dx.doi.org/10.1093/bioinformatics/btac348 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Privé, Florian Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics |
title | Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics |
title_full | Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics |
title_fullStr | Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics |
title_full_unstemmed | Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics |
title_short | Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics |
title_sort | using the uk biobank as a global reference of worldwide populations: application to measuring ancestry diversity from gwas summary statistics |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9237724/ https://www.ncbi.nlm.nih.gov/pubmed/35604078 http://dx.doi.org/10.1093/bioinformatics/btac348 |
work_keys_str_mv | AT priveflorian usingtheukbiobankasaglobalreferenceofworldwidepopulationsapplicationtomeasuringancestrydiversityfromgwassummarystatistics |