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A complete tool set for molecular QTL discovery and analysis

Author

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  • Olivier Delaneau

    (University of Geneva
    Swiss Institute of Bioinformatics, University of Geneva
    Institute of Genetics and Genomics in Geneva, University of Geneva)

  • Halit Ongen

    (University of Geneva
    Swiss Institute of Bioinformatics, University of Geneva
    Institute of Genetics and Genomics in Geneva, University of Geneva)

  • Andrew A. Brown

    (University of Geneva
    Swiss Institute of Bioinformatics, University of Geneva
    Institute of Genetics and Genomics in Geneva, University of Geneva)

  • Alexandre Fort

    (University of Geneva)

  • Nikolaos I. Panousis

    (University of Geneva
    Swiss Institute of Bioinformatics, University of Geneva
    Institute of Genetics and Genomics in Geneva, University of Geneva)

  • Emmanouil T. Dermitzakis

    (University of Geneva
    Swiss Institute of Bioinformatics, University of Geneva
    Institute of Genetics and Genomics in Geneva, University of Geneva)

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/ .

Suggested Citation

  • Olivier Delaneau & Halit Ongen & Andrew A. Brown & Alexandre Fort & Nikolaos I. Panousis & Emmanouil T. Dermitzakis, 2017. "A complete tool set for molecular QTL discovery and analysis," Nature Communications, Nature, vol. 8(1), pages 1-7, August.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms15452
    DOI: 10.1038/ncomms15452
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    2. Nikolaos M. R. Lykoskoufis & Evarist Planet & Halit Ongen & Didier Trono & Emmanouil T. Dermitzakis, 2024. "Transposable elements mediate genetic effects altering the expression of nearby genes in colorectal cancer," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
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    13. Fasil Tekola-Ayele & Xuehuo Zeng & Suvo Chatterjee & Marion Ouidir & Corina Lesseur & Ke Hao & Jia Chen & Markos Tesfaye & Carmen J. Marsit & Tsegaselassie Workalemahu & Ronald Wapner, 2022. "Placental multi-omics integration identifies candidate functional genes for birthweight," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    14. James J. Gilchrist & Seiko Makino & Vivek Naranbhai & Piyush K. Sharma & Surya Koturan & Orion Tong & Chelsea A. Taylor & Robert A. Watson & Alba Verge los Aires & Rosalin Cooper & Evelyn Lau & Sara D, 2022. "Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    15. Xena Marie Mapel & Naveen Kumar Kadri & Alexander S. Leonard & Qiongyu He & Audald Lloret-Villas & Meenu Bhati & Maya Hiltpold & Hubert Pausch, 2024. "Molecular quantitative trait loci in reproductive tissues impact male fertility in cattle," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    16. Sébastien Thériault & Zhonglin Li & Erik Abner & Jian’an Luan & Hasanga D. Manikpurage & Ursula Houessou & Pardis Zamani & Mewen Briend & Dominique K. Boudreau & Nathalie Gaudreault & Lily Frenette & , 2024. "Integrative genomic analyses identify candidate causal genes for calcific aortic valve stenosis involving tissue-specific regulation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    17. Miguel Rodriguez de los Santos & Brian H. Kopell & Ariela Buxbaum Grice & Gauri Ganesh & Andy Yang & Pardis Amini & Lora E. Liharska & Eric Vornholt & John F. Fullard & Pengfei Dong & Eric Park & Sara, 2024. "Divergent landscapes of A-to-I editing in postmortem and living human brain," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    18. Jamie L. Everman & Satria P. Sajuthi & Maude A. Liegeois & Nathan D. Jackson & Erik H. Collet & Michael C. Peters & Maurizio Chioccioli & Camille M. Moore & Bhavika B. Patel & Nathan Dyjack & Roger Po, 2024. "A common polymorphism in the Intelectin-1 gene influences mucus plugging in severe asthma," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
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