A framework for research into continental ancestry groups of the UK Biobank

Andrei-Emil Constantinescu; Ruth E. Mitchell; Jie Zheng; Caroline J. Bull; Nicholas J. Timpson; Borko Amulic; Emma E. Vincent; David A. Hughes

doi:10.1186/s40246-022-00380-5

A framework for research into continental ancestry groups of the UK Biobank

Andrei-Emil Constantinescu, Ruth E. Mitchell, Jie Zheng, Caroline J. Bull, Nicholas J. Timpson, Borko Amulic, Emma E. Vincent, David A. Hughes^*

^*Corresponding author for this work

Research output: Contribution to journal › Article (Academic Journal) › peer-review

16 Citations (Scopus)

149 Downloads (Pure)

Abstract

Background
The UK Biobank is a large prospective cohort, based in the UK, that has deep phenotypic and genomic data on roughly a half a million individuals. Included in this resource are data on approximately 78,000 individuals with “non-white British ancestry.” While most epidemiology studies have focused predominantly on populations of European ancestry, there is an opportunity to contribute to the study of health and disease for a broader segment of the population by making use of the UK Biobank’s “non-white British ancestry” samples. Here, we present an empirical description of the continental ancestry and population structure among the individuals in this UK Biobank subset.

Results
Reference populations from the 1000 Genomes Project for Africa, Europe, East Asia, and South Asia were used to estimate ancestry for each individual. Those with at least 80% ancestry in one of these four continental ancestry groups were taken forward (N = 62,484). Principal component and K-means clustering analyses were used to identify and characterize population structure within each ancestry group. Of the approximately 78,000 individuals in the UK Biobank that are of “non-white British” ancestry, 50,685, 6653, 2782, and 2364 individuals were associated to the European, African, South Asian, and East Asian continental ancestry groups, respectively. Each continental ancestry group exhibits prominent population structure that is consistent with self-reported country of birth data and geography.

Conclusions
Methods outlined here provide an avenue to leverage UK Biobank’s deeply phenotyped data allowing researchers to maximize its potential in the study of health and disease in individuals of non-white British ancestry.

Original language	English
Article number	3
Number of pages	14
Journal	Human Genomics
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s40246-022-00380-5
Publication status	Published - 29 Jan 2022

Bibliographical note

Funding Information:
AC acknowledges funding from a Medical Research Council PhD studentship (MR/N013794/1). NJT and REM acknowledge funding from the Medical Research Council (MC_UU_00011/1). NJT is the PI of the Avon Longitudinal Study of Parents and Children (Medical Research Council & Wellcome Trust 217065/Z/19/Z) and is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215-2001). EEV, CJB, NJT, and DH acknowledge funding from the Wellcome Trust (202802/Z/16/Z). EEV, CJB, and NJT also acknowledge funding by the CRUK Integrative Cancer Epidemiology Programme (C18281/A29019). EEV and CJB are supported by Diabetes UK (17/0005587) and the World Cancer Research Fund (WCRF UK), as part of the World Cancer Research Fund International grant program (IIG_2019_2009). JZ is supported by the Academy of Medical Sciences (AMS) Springboard Award, the Wellcome Trust, the Government Department of Business, Energy and Industrial Strategy (BEIS), the British Heart Foundation and Diabetes UK (SBF006\1117). JZ is funded by the Vice-Chancellor Fellowship from the University of Bristol and is supported by Shanghai Thousand Talents Program. BA acknowledges funding from the Medical Research Council (MR/R02149x/1). The funders of the study had no role in the study design, data collection, data analysis, data interpretation, or writing of the report.

Publisher Copyright:
© 2022, The Author(s).

Research Groups and Themes

ICEP

Keywords

Ancestry
UK Biobank
Population structure

Access to Document

10.1186/s40246-022-00380-5Licence: Unspecified

Full-text PDF (final published version)
This is the final published version of the article (version of record). It first appeared online via BMC at https://doi.org/10.1186/s40246-022-00380-5. Please refer to any applicable terms of use of the publisher.
Final published version, 3.58 MBLicence: CC BY

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Persistent link

8074 (C18281/A29019) ICEP2 - Programme Award: Towards improved casual evidence and enhanced prediction of cancer risk and survival
Martin, R. M. (Principal Investigator)
1/10/20 → 30/09/25
Project: Research

Using genetic data to determine the effect of routinely measured blood cell traits on disease
Constantinescu, A. (Author), Vincent, E. (Supervisor), Timpson, N. (Supervisor), Bull, C. (Supervisor) & Dayan, C. (Supervisor), 3 Oct 2023
Student thesis: Doctoral Thesis › Doctor of Philosophy (PhD)

File

Additional file 1 of A framework for research into continental ancestry groups of the UK Biobank
Constantinescu, A. (Creator), Mitchell, R. E. (Creator), Zheng, J. (Creator), Bull, C. J. (Creator), Timpson, N. J. (Creator), Amulic, B. (Creator), Vincent, E. E. (Creator) & Hughes, D. A. (Creator), figshare, 2022
DOI: 10.6084/m9.figshare.19092280.v1, https://springernature.figshare.com/articles/dataset/Additional_file_1_of_A_framework_for_research_into_continental_ancestry_groups_of_the_UK_Biobank/19092280/1 and one more link, https://springernature.figshare.com/articles/dataset/Additional_file_1_of_A_framework_for_research_into_continental_ancestry_groups_of_the_UK_Biobank/19092280 (show fewer)
Dataset
UK Biobank Genetic Data: MRC-IEU Quality Control, version 2
Mitchell, R. (Creator), Hemani, G. (Creator), Dudding, T. (Creator), Corbin, L. (Creator), Harrison, S. (Creator) & Paternoster, L. (Creator), University of Bristol, 22 Jan 2019
DOI: 10.5523/bris.1ovaau5sxunp2cv8rcy88688v, http://data.bris.ac.uk/data/dataset/1ovaau5sxunp2cv8rcy88688v
Dataset

HPC (High Performance Computing) and HTC (High Throughput Computing) Facilities
Alam, S. R. (Manager), Williams, D. A. G. (Manager), Eccleston, P. E. (Manager) & Greene, D. (Manager)
Facility/equipment: Facility

Cite this

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title = "A framework for research into continental ancestry groups of the UK Biobank",

abstract = "BackgroundThe UK Biobank is a large prospective cohort, based in the UK, that has deep phenotypic and genomic data on roughly a half a million individuals. Included in this resource are data on approximately 78,000 individuals with “non-white British ancestry.” While most epidemiology studies have focused predominantly on populations of European ancestry, there is an opportunity to contribute to the study of health and disease for a broader segment of the population by making use of the UK Biobank{\textquoteright}s “non-white British ancestry” samples. Here, we present an empirical description of the continental ancestry and population structure among the individuals in this UK Biobank subset.ResultsReference populations from the 1000 Genomes Project for Africa, Europe, East Asia, and South Asia were used to estimate ancestry for each individual. Those with at least 80% ancestry in one of these four continental ancestry groups were taken forward (N = 62,484). Principal component and K-means clustering analyses were used to identify and characterize population structure within each ancestry group. Of the approximately 78,000 individuals in the UK Biobank that are of “non-white British” ancestry, 50,685, 6653, 2782, and 2364 individuals were associated to the European, African, South Asian, and East Asian continental ancestry groups, respectively. Each continental ancestry group exhibits prominent population structure that is consistent with self-reported country of birth data and geography.ConclusionsMethods outlined here provide an avenue to leverage UK Biobank{\textquoteright}s deeply phenotyped data allowing researchers to maximize its potential in the study of health and disease in individuals of non-white British ancestry.",

keywords = "Ancestry, UK Biobank, Population structure",

author = "Andrei-Emil Constantinescu and Mitchell, {Ruth E.} and Jie Zheng and Bull, {Caroline J.} and Timpson, {Nicholas J.} and Borko Amulic and Vincent, {Emma E.} and Hughes, {David A.}",

note = "Funding Information: AC acknowledges funding from a Medical Research Council PhD studentship (MR/N013794/1). NJT and REM acknowledge funding from the Medical Research Council (MC_UU_00011/1). NJT is the PI of the Avon Longitudinal Study of Parents and Children (Medical Research Council & Wellcome Trust 217065/Z/19/Z) and is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215-2001). EEV, CJB, NJT, and DH acknowledge funding from the Wellcome Trust (202802/Z/16/Z). EEV, CJB, and NJT also acknowledge funding by the CRUK Integrative Cancer Epidemiology Programme (C18281/A29019). EEV and CJB are supported by Diabetes UK (17/0005587) and the World Cancer Research Fund (WCRF UK), as part of the World Cancer Research Fund International grant program (IIG_2019_2009). JZ is supported by the Academy of Medical Sciences (AMS) Springboard Award, the Wellcome Trust, the Government Department of Business, Energy and Industrial Strategy (BEIS), the British Heart Foundation and Diabetes UK (SBF006\1117). JZ is funded by the Vice-Chancellor Fellowship from the University of Bristol and is supported by Shanghai Thousand Talents Program. BA acknowledges funding from the Medical Research Council (MR/R02149x/1). The funders of the study had no role in the study design, data collection, data analysis, data interpretation, or writing of the report. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = jan,

day = "29",

doi = "10.1186/s40246-022-00380-5",

language = "English",

volume = "16",

journal = "Human Genomics",

issn = "1479-7364",

publisher = "BioMed Central",

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TY - JOUR

T1 - A framework for research into continental ancestry groups of the UK Biobank

AU - Constantinescu, Andrei-Emil

AU - Mitchell, Ruth E.

AU - Zheng, Jie

AU - Bull, Caroline J.

AU - Timpson, Nicholas J.

AU - Amulic, Borko

AU - Vincent, Emma E.

AU - Hughes, David A.

N1 - Funding Information: AC acknowledges funding from a Medical Research Council PhD studentship (MR/N013794/1). NJT and REM acknowledge funding from the Medical Research Council (MC_UU_00011/1). NJT is the PI of the Avon Longitudinal Study of Parents and Children (Medical Research Council & Wellcome Trust 217065/Z/19/Z) and is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215-2001). EEV, CJB, NJT, and DH acknowledge funding from the Wellcome Trust (202802/Z/16/Z). EEV, CJB, and NJT also acknowledge funding by the CRUK Integrative Cancer Epidemiology Programme (C18281/A29019). EEV and CJB are supported by Diabetes UK (17/0005587) and the World Cancer Research Fund (WCRF UK), as part of the World Cancer Research Fund International grant program (IIG_2019_2009). JZ is supported by the Academy of Medical Sciences (AMS) Springboard Award, the Wellcome Trust, the Government Department of Business, Energy and Industrial Strategy (BEIS), the British Heart Foundation and Diabetes UK (SBF006\1117). JZ is funded by the Vice-Chancellor Fellowship from the University of Bristol and is supported by Shanghai Thousand Talents Program. BA acknowledges funding from the Medical Research Council (MR/R02149x/1). The funders of the study had no role in the study design, data collection, data analysis, data interpretation, or writing of the report. Publisher Copyright: © 2022, The Author(s).

PY - 2022/1/29

Y1 - 2022/1/29

N2 - BackgroundThe UK Biobank is a large prospective cohort, based in the UK, that has deep phenotypic and genomic data on roughly a half a million individuals. Included in this resource are data on approximately 78,000 individuals with “non-white British ancestry.” While most epidemiology studies have focused predominantly on populations of European ancestry, there is an opportunity to contribute to the study of health and disease for a broader segment of the population by making use of the UK Biobank’s “non-white British ancestry” samples. Here, we present an empirical description of the continental ancestry and population structure among the individuals in this UK Biobank subset.ResultsReference populations from the 1000 Genomes Project for Africa, Europe, East Asia, and South Asia were used to estimate ancestry for each individual. Those with at least 80% ancestry in one of these four continental ancestry groups were taken forward (N = 62,484). Principal component and K-means clustering analyses were used to identify and characterize population structure within each ancestry group. Of the approximately 78,000 individuals in the UK Biobank that are of “non-white British” ancestry, 50,685, 6653, 2782, and 2364 individuals were associated to the European, African, South Asian, and East Asian continental ancestry groups, respectively. Each continental ancestry group exhibits prominent population structure that is consistent with self-reported country of birth data and geography.ConclusionsMethods outlined here provide an avenue to leverage UK Biobank’s deeply phenotyped data allowing researchers to maximize its potential in the study of health and disease in individuals of non-white British ancestry.

AB - BackgroundThe UK Biobank is a large prospective cohort, based in the UK, that has deep phenotypic and genomic data on roughly a half a million individuals. Included in this resource are data on approximately 78,000 individuals with “non-white British ancestry.” While most epidemiology studies have focused predominantly on populations of European ancestry, there is an opportunity to contribute to the study of health and disease for a broader segment of the population by making use of the UK Biobank’s “non-white British ancestry” samples. Here, we present an empirical description of the continental ancestry and population structure among the individuals in this UK Biobank subset.ResultsReference populations from the 1000 Genomes Project for Africa, Europe, East Asia, and South Asia were used to estimate ancestry for each individual. Those with at least 80% ancestry in one of these four continental ancestry groups were taken forward (N = 62,484). Principal component and K-means clustering analyses were used to identify and characterize population structure within each ancestry group. Of the approximately 78,000 individuals in the UK Biobank that are of “non-white British” ancestry, 50,685, 6653, 2782, and 2364 individuals were associated to the European, African, South Asian, and East Asian continental ancestry groups, respectively. Each continental ancestry group exhibits prominent population structure that is consistent with self-reported country of birth data and geography.ConclusionsMethods outlined here provide an avenue to leverage UK Biobank’s deeply phenotyped data allowing researchers to maximize its potential in the study of health and disease in individuals of non-white British ancestry.

KW - Ancestry

KW - UK Biobank

KW - Population structure

U2 - 10.1186/s40246-022-00380-5

DO - 10.1186/s40246-022-00380-5

M3 - Article (Academic Journal)

C2 - 35093177

SN - 1479-7364

VL - 16

JO - Human Genomics

JF - Human Genomics

IS - 1

M1 - 3

ER -

A framework for research into continental ancestry groups of the UK Biobank

Abstract

Bibliographical note

Research Groups and Themes

Keywords

Access to Document

Handle.net

Fingerprint

Projects

8074 (C18281/A29019) ICEP2 - Programme Award: Towards improved casual evidence and enhanced prediction of cancer risk and survival

Student theses

Using genetic data to determine the effect of routinely measured blood cell traits on disease

Datasets

Additional file 1 of A framework for research into continental ancestry groups of the UK Biobank

UK Biobank Genetic Data: MRC-IEU Quality Control, version 2

Equipment

HPC (High Performance Computing) and HTC (High Throughput Computing) Facilities

Cite this