A complete tool set for molecular QTL discovery and analysis

Nature Communications
Olivier DelaneauEmmanouil T Dermitzakis

Abstract

Population scale studies combining genetic information with molecular phenotypes (for example, gene expression) have become a standard to dissect the effects of genetic variants onto organismal phenotypes. These kinds of data sets require powerful, fast and versatile methods able to discover molecular Quantitative Trait Loci (molQTL). Here we propose such a solution, QTLtools, a modular framework that contains multiple new and well-established methods to prepare the data, to discover proximal and distal molQTLs and, finally, to integrate them with GWAS variants and functional annotations of the genome. We demonstrate its utility by performing a complete expression QTL study in a few easy-to-perform steps. QTLtools is open source and available at https://qtltools.github.io/qtltools/.

References

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Citations

Oct 24, 2017·Nature Genetics·Halit OngenEmmanouil T Dermitzakis
Mar 19, 2019·The New Phytologist·Marshall J WedgerKenneth M Olsen
Apr 21, 2020·PLoS Genetics·Yizhen ZhongMinoli A Perera
Nov 20, 2018·PLoS Genetics·Fabien DelahayeFrancine Hughes
Apr 23, 2019·PLoS Genetics·Vitor R C AguiarDiogo Meyer
Jul 24, 2020·The Journal of Clinical Investigation·Jenny C LinkKaren Reue
Jun 13, 2018·Nature Genetics·Carolina RoselliPatrick T Ellinor
Aug 23, 2020·International Journal of Molecular Sciences·Jae-Ryoung ParkKyung-Min Kim
Nov 9, 2017·Nature Communications·Marco GarieriAlexandre Fort
Oct 21, 2017·Journal of Dental Research·C MasottiM R Passos-Bueno
Feb 23, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Clément GoubertCédric Feschotte
Sep 19, 2019·Nature Communications·Carla Giner-DelgadoMario Cáceres
Sep 7, 2018·Nucleic Acids Research·Qin Qin HuangMichael Inouye
Nov 11, 2020·BMC Dermatology·Marisol Herrera-RiveroStefanie Heilmann-Heimbach
Nov 26, 2020·Scientific Reports·Matthias MunzJeanette Erdmann
Nov 5, 2020·Cancers·Daniel A RodriguezJ William Harbour
Jan 22, 2021·Cell Systems·Jeffrey Molendijk, Benjamin L Parker
Feb 26, 2021·PLoS Genetics·Nana LiuUNKNOWN Alzheimer’s disease Neuroimaging Initiative
Feb 28, 2021·Nature Communications·Ricardo D'Oliveira AlbanusStephen C J Parker
Apr 16, 2020·Trends in Genetics : TIG·Youqiong YeLeng Han
Apr 25, 2021·Nature Communications·Romina J BevacquaSeung K Kim
Apr 30, 2021·Circulation Research·Mark C BlaserElena Aikawa
May 2, 2021·Genome Biology·Sergio Villicaña, Jordana T Bell
Aug 12, 2021·Nature Communications·Diogo M RibeiroOlivier Delaneau

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Methods Mentioned

BETA
RNA-seq
PCA
ChIP-seq
DNA-seq

Software Mentioned

MatrixeQTL
ChromHMM
FastQTL
GENCODE
R
QTLtools
Matrix eQTL
Geuvadis

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