Transcriptome-wide association study in UK biobank Europeans identifies associations with blood cell traits
File(s)yun_li_transcriptome_wide_analysis.pdf (1.46 MB)
Accepted version
Author(s)
Type
Journal Article
Abstract
Previous genome-wide association studies (GWAS) of hematological traits have identified over 10 000 distinct trait-specific risk loci. However, at these loci, the underlying causal mechanisms remain incompletely characterized. To elucidate novel biology and better understand causal mechanisms at known loci, we performed a transcriptome-wide association study (TWAS) of 29 hematological traits in 399 835 UK Biobank (UKB) participants of European ancestry using gene expression prediction models trained from whole blood RNA-seq data in 922 individuals. We discovered 557 gene-trait associations for hematological traits distinct from previously reported GWAS variants in European populations. Among the 557 associations, 301 were available for replication in a cohort of 141 286 participants of European ancestry from the Million Veteran Program (MVP). Of these 301 associations, 108 replicated at a strict Bonferroni adjusted threshold ($\alpha$ = 0.05/301). Using our TWAS results, we systematically assigned 4261 out of 16 900 previously identified hematological trait GWAS variants to putative target genes. Compared to coloc, our TWAS results show reduced specificity and increased sensitivity in external datasets to assign variants to target genes.
Date Issued
2022-07-15
Date Acceptance
2022-02-01
Citation
Human Molecular Genetics, 2022, 31 (14), pp.2333-2347
ISSN
0964-6906
Publisher
Oxford University Press
Start Page
2333
End Page
2347
Journal / Book Title
Human Molecular Genetics
Volume
31
Issue
14
Copyright Statement
© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). This is a pre-copy-editing, author-produced version of an article accepted for publication in Human Molecular Genetics following peer review. The definitive publisher-authenticated version Bryce Rowland, Sanan Venkatesh, Manuel Tardaguila, Jia Wen, Jonathan D Rosen, Amanda L Tapia, Quan Sun, Mariaelisa Graff, Dragana Vuckovic, Guillaume Lettre, Vijay G Sankaran, Georgios Voloudakis, Panos Roussos, Jennifer E Huffman, Alexander P Reiner, Nicole Soranzo, Laura M Raffield, Yun Li, Transcriptome-wide association study in UK biobank Europeans identifies associations with blood cell traits, Human Molecular Genetics, 2022;, ddac011 is available online at: https://doi.org/10.1093/hmg/ddac011
This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model). This is a pre-copy-editing, author-produced version of an article accepted for publication in Human Molecular Genetics following peer review. The definitive publisher-authenticated version Bryce Rowland, Sanan Venkatesh, Manuel Tardaguila, Jia Wen, Jonathan D Rosen, Amanda L Tapia, Quan Sun, Mariaelisa Graff, Dragana Vuckovic, Guillaume Lettre, Vijay G Sankaran, Georgios Voloudakis, Panos Roussos, Jennifer E Huffman, Alexander P Reiner, Nicole Soranzo, Laura M Raffield, Yun Li, Transcriptome-wide association study in UK biobank Europeans identifies associations with blood cell traits, Human Molecular Genetics, 2022;, ddac011 is available online at: https://doi.org/10.1093/hmg/ddac011
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/35138379
PII: 6524829
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemistry & Molecular Biology
Genetics & Heredity
ADAPTER PROTEIN
GENOME
MUTATIONS
LIME
EQTL
Biological Specimen Banks
Blood Cells
Genetic Predisposition to Disease
Genome-Wide Association Study
Humans
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Transcriptome
United Kingdom
Blood Cells
Humans
Genetic Predisposition to Disease
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Biological Specimen Banks
Genome-Wide Association Study
Transcriptome
United Kingdom
Genetics & Heredity
06 Biological Sciences
11 Medical and Health Sciences
Publication Status
Published
Coverage Spatial
England
Date Publish Online
2022-02-09