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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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Autor principal: Privé, Florian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
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
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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.
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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
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