Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression
Urmo Võsa
1, 2
,
Annique Claringbould
1, 3, 4
,
Harm Jan Westra
1, 3
,
Marc Jan Bonder
1, 5
,
Patrick Deelen
1, 3, 6, 7
,
Biao Zeng
8
,
Holger Kirsten
9, 10
,
Ashis Saha
11
,
Roman Kreuzhuber
12, 13, 14
,
Seyhan Yazar
15
,
Harm Brugge
1, 3
,
Roy Oelen
1, 3
,
Dylan H De Vries
1, 3
,
Monique G P Van Der Wijst
1, 3
,
Silva Kasela
2
,
Natalia Pervjakova
2
,
Isabel Alves
16, 17
,
Marie Julie Favé
16
,
Mawusse Agbessi
16
,
Mark W Christiansen
18
,
Rick Jansen
19
,
Ilkka Seppälä
20
,
Tong Lin
21
,
Alexander Teumer
22, 23
,
Katharina Schramm
24, 25
,
Gibran Hemani
26
,
Joost A M Verlouw
27
,
Hanieh Yaghootkar
28, 29, 30
,
Reyhan Sönmez Flitman
31, 32
,
Andrew A Brown
33, 34
,
Viktorija Kukushkina
2
,
Anette Kalnapenkis
2
,
Sina Rüeger
35
,
Eleonora Porcu
35
,
Jaanika Kronberg
2
,
Johannes Kettunen
36, 37, 38, 39
,
Bernett Lee
40
,
Futao Zhang
41
,
TING QI
41
,
Jose Alquicira Hernandez
15
,
Wibowo Arindrarto
42
,
Frank Beutner
43
,
PETER A. C. 'T HOEN
44
,
Jenny van Dongen
45
,
Morris A Swertz
42
,
Marc Jan Bonder
46, 47
,
Julia Dmitrieva
48
,
Mahmoud Elansary
11, 49
,
Benjamin P. Fairfax
45
,
M. Georges
50
,
Bastiaan T. Heijmans
51
,
Alex W Hewitt
1, 6
,
Mika Kähönen
9, 10
,
Yungil Kim
8, 52, 53
,
Julian C Knight
54
,
Peter Kovacs
44, 55
,
Knut Krohn
24, 25, 56
,
Shuang Li
23, 57
,
Markus Loeffler
58
,
Urko M. Marigorta
19
,
Hailang Mei
59, 60
,
Yukihide Momozawa
61, 62, 63
,
Matthias Nauck
42
,
M.J.M Nivard
64
,
Brenda W. J. H. Penninx
65
,
Jonathan Pritchard
66
,
Olli T. Raitakari
67
,
Olaf Rötzschke
10, 68
,
P. Eline Slagboom
65
,
Coen D.A. Stehouwer
69
,
Michael Stumvoll
42
,
Patrick Sullivan
70
,
Peter A.C. 't Hoen
71
,
Joachim Thiery
1, 3
,
Anke Tönjes
1
,
Jenny van Dongen
6
,
Maarten van Iterson
40
,
J. H. Veldink
41
,
Uwe Völker
72, 73, 74
,
Robert Warmerdam
75
,
Cisca Wijmenga
76
,
Morris A. Swertz
32, 33, 77
,
Anand Kumar Andiappan
31, 32
,
Grant W. Montgomery
28
,
Samuli Ripatti
27
,
Markus Perola
78, 79
,
Zoltán Kutalik
21
,
Emmanouil K. Dermitzakis
21
,
Sven Bergmann
20
,
Timothy M Frayling
69
,
Joyce Van Meurs
80
,
Holger Prokisch
18, 81
,
Habibul Ahsan
16
,
Brandon L. Pierce
2
,
Terho Lehtimäki
12, 13, 82
,
Dorret I. Boomsma
12, 13
,
B Psaty
5, 14, 83
,
Sina A. Gharib
11, 84
,
Philip Awadalla
41
,
Lili Milani
41, 85, 86
,
W. Ouwehand
9, 10
,
Kate Downes
15, 87
,
Oliver Stegle
8
,
Alexis Battle
2
,
P. B. Visscher
1, 3
3
Oncode Institute, Amsterdam, the Netherlands
|
4
17
19
27
Department of Internal medicine, Erasmus Medical Center, Rotterdam, The Netherlands
|
40
47
49
52
62
69
72
75
86
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
|
Publication type: Journal Article
Publication date: 2021-09-03
scimago Q1
wos Q1
SJR: 16.586
CiteScore: 45.1
Impact factor: 29.0
ISSN: 10614036, 15461718
PubMed ID:
34475573
Genetics
Abstract
Trait-associated genetic variants affect complex phenotypes primarily via regulatory mechanisms on the transcriptome. To investigate the genetics of gene expression, we performed cis- and trans-expression quantitative trait locus (eQTL) analyses using blood-derived expression from 31,684 individuals through the eQTLGen Consortium. We detected cis-eQTL for 88% of genes, and these were replicable in numerous tissues. Distal trans-eQTL (detected for 37% of 10,317 trait-associated variants tested) showed lower replication rates, partially due to low replication power and confounding by cell type composition. However, replication analyses in single-cell RNA-seq data prioritized intracellular trans-eQTL. Trans-eQTL exerted their effects via several mechanisms, primarily through regulation by transcription factors. Expression of 13% of the genes correlated with polygenic scores for 1,263 phenotypes, pinpointing potential drivers for those traits. In summary, this work represents a large eQTL resource, and its results serve as a starting point for in-depth interpretation of complex phenotypes. Analyses of expression profiles from whole blood of 31,684 individuals identify cis-expression quantitative trait loci (eQTL) effects for 88% of genes and trans-eQTL effects for 37% of trait-associated variants.
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Võsa U. et al. Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression // Nature Genetics. 2021. Vol. 53. No. 9. pp. 1300-1310.
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Võsa U. et al. Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression // Nature Genetics. 2021. Vol. 53. No. 9. pp. 1300-1310.
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@article{2021_Võsa,
author = {Urmo Võsa and Annique Claringbould and Harm Jan Westra and Marc Jan Bonder and Patrick Deelen and Biao Zeng and Holger Kirsten and Ashis Saha and Roman Kreuzhuber and Seyhan Yazar and Harm Brugge and Roy Oelen and Dylan H De Vries and Monique G P Van Der Wijst and Silva Kasela and Natalia Pervjakova and Isabel Alves and Marie Julie Favé and Mawusse Agbessi and Mark W Christiansen and Rick Jansen and Ilkka Seppälä and Tong Lin and Alexander Teumer and Katharina Schramm and Gibran Hemani and Joost A M Verlouw and Hanieh Yaghootkar and Reyhan Sönmez Flitman and Andrew A Brown and Viktorija Kukushkina and Anette Kalnapenkis and Sina Rüeger and Eleonora Porcu and Jaanika Kronberg and Johannes Kettunen and Bernett Lee and Futao Zhang and TING QI and Jose Alquicira Hernandez and Wibowo Arindrarto and Frank Beutner and PETER A. C. 'T HOEN and Jenny van Dongen and Morris A Swertz and Marc Jan Bonder and Julia Dmitrieva and Mahmoud Elansary and Benjamin P. Fairfax and M. Georges and others},
title = {Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression},
journal = {Nature Genetics},
year = {2021},
volume = {53},
publisher = {Springer Nature},
month = {sep},
url = {https://doi.org/10.1038/s41588-021-00913-z},
number = {9},
pages = {1300--1310},
doi = {10.1038/s41588-021-00913-z}
}
Cite this
MLA
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Võsa, Urmo, et al. “Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression.” Nature Genetics, vol. 53, no. 9, Sep. 2021, pp. 1300-1310. https://doi.org/10.1038/s41588-021-00913-z.