Direct inference and control of genetic population structure from RNA sequencing data.

Humans Retrospective Studies Genetics, Population Genotype Base Sequence Sequence Analysis, RNA

Journal

Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179

Informations de publication

Date de publication:
02 08 2023
Historique:
received: 09 11 2022
accepted: 24 07 2023
medline: 4 8 2023
pubmed: 3 8 2023
entrez: 2 8 2023
Statut: epublish

Résumé

RNAseq data can be used to infer genetic variants, yet its use for estimating genetic population structure remains underexplored. Here, we construct a freely available computational tool (RGStraP) to estimate RNAseq-based genetic principal components (RG-PCs) and assess whether RG-PCs can be used to control for population structure in gene expression analyses. Using whole blood samples from understudied Nepalese populations and the Geuvadis study, we show that RG-PCs had comparable results to paired array-based genotypes, with high genotype concordance and high correlations of genetic principal components, capturing subpopulations within the dataset. In differential gene expression analysis, we found that inclusion of RG-PCs as covariates reduced test statistic inflation. Our paper demonstrates that genetic population structure can be directly inferred and controlled for using RNAseq data, thus facilitating improved retrospective and future analyses of transcriptomic data.

Identifiants

DOI: 10.1038/s42003-023-05171-9 PMID: 37532769 PMC: PMC10397182
pubmed: 37532769
doi: 10.1038/s42003-023-05171-9
pii: 10.1038/s42003-023-05171-9
pmc: PMC10397182
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

804

Subventions

Organisme : Department of Health
ID : BRC-1215-20014
Pays : United Kingdom
Organisme : Medical Research Council
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 106158/Z/14/Z
Pays : United Kingdom
Organisme : Department of Health
ID : NIHR203312
Pays : United Kingdom
Organisme : British Heart Foundation
ID : RG/18/13/33946
Pays : United Kingdom

Investigateurs

Anup Adhikari (A)
Happy Chimphako Banda (HC)
Christoph Blohmke (C)
Thomas C Darton (TC)
Yama Farooq (Y)
Maheshwar Ghimire (M)
Jennifer Hill (J)
Nhu Tran Hoang (NT)
Tikhala Makhaza Jere (TM)
Moses Kamzati (M)
Yu-Han Kao (YH)
Clemens Masesa (C)
Maurice Mbewe (M)
Harrison Msuku (H)
Patrick Munthali (P)
Tran Vu Thieu Nga (TVT)
Rose Nkhata (R)
Neil J Saad (NJ)
Trinh Van Tan (T)
Deus Thindwa (D)
Farhana Khanam (F)
James Meiring (J)
John D Clemens (JD)
Gordon Dougan (G)
Virginia E Pitzer (VE)
Firdausi Qadri (F)
Robert S Heyderman (RS)
Melita A Gordon (MA)
Merryn Voysey (M)

Informations de copyright

© 2023. The Author(s).

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Auteurs

Muhamad Fachrul (M)

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia. fachrul.mhmd@gmail.com.
Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia. fachrul.mhmd@gmail.com.
School of BioSciences, The University of Melbourne, Parkville, VIC, Australia. fachrul.mhmd@gmail.com.
ORCID: 0000-0003-2199-5900

Abhilasha Karkey (A)

Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal.

Mila Shakya (M)

Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal.

Louise M Judd (LM)

Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.

Taylor Harshegyi (T)

Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
ORCID: 0000-0001-9620-8735

Kar Seng Sim (KS)

Genome Institute of Singapore, Singapore, Singapore.

Susan Tonks (S)

Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK.

Sabina Dongol (S)

Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal.

Rajendra Shrestha (R)

Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal.

Agus Salim (A)

Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia.
School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, Australia.
Department of Population Health, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.

Stephen Baker (S)

Department of Medicine, University of Cambridge, Cambridge, UK.

Andrew J Pollard (AJ)

Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK.
ORCID: 0000-0001-7361-719X

Chiea Chuen Khor (CC)

Genome Institute of Singapore, Singapore, Singapore.
ORCID: 0000-0002-1128-4729

Christiane Dolecek (C)

Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.
Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.

Buddha Basnyat (B)

Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal.
Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.

Sarah J Dunstan (SJ)

The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
ORCID: 0000-0001-7873-933X

Kathryn E Holt (KE)

Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
ORCID: 0000-0003-3949-2471

Michael Inouye (M)

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia. mi336@medschl.cam.ac.uk.
Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia. mi336@medschl.cam.ac.uk.
Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. mi336@medschl.cam.ac.uk.
Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK. mi336@medschl.cam.ac.uk.
British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. mi336@medschl.cam.ac.uk.
British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK. mi336@medschl.cam.ac.uk.
Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK. mi336@medschl.cam.ac.uk.
ORCID: 0000-0001-9413-6520

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