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BMC Bioinformatics . 2020 Jun 12

Deconvolution of bulk blood eQTL effects into immune cell subpopulations

Samuel T Keating, Laszlo Groh, Kathrin Thiem, Siroon Bekkering, Yang Li, Vasiliki Matzaraki, Charlotte D C C van der Heijden, Jelmer H van Puffelen, Ekta Lachmandas, Trees Jansen, Marije Oosting, L Charlotte J de Bree, Valerie A C M Koeken, Simone J C F M Moorlag, Vera P Mourits, Janna van Diepen, Rinke Stienstra, Boris Novakovic, Hendrik G Stunnenberg, Reinout van Crevel, Leo A B Joosten, Mihai G Netea, Niels P Riksen, Charlotte D C C van der Heijden, Rob Ter Horst, Inge C L van den Munckhof, Kiki Schraa, Jacqueline de Graaf, Leo A B Joosten, A H Jan Danser, Mihai G Netea, Jaap Deinum, Joost Rutten, Niels P Riksen, Florian Stöckigt, Lars Eichhorn, Thomas Beiert, Vincent Knappe, Tobias Radecke, Martin Steinmetz, Georg Nickenig, Viktoriya Peeva, Alexei P Kudin, Wolfram S Kunz, Carolin Berwanger, Lisa Kamm, Dorothea Schultheis, Ursula Schlötzer-Schrehardt, Christoph S Clemen, Rolf Schröder, Jan W Schrickel, Valerie A C M Koeken, Eva S van der Pasch, Guus P Leijte, Vera P Mourits, L Charlotte J de Bree, Simone J C F M Moorlag, Isadore Budnick, Nina Idh, Maria Lerm, Matthijs Kox, Arjan van Laarhoven, Mihai G Netea, Reinout van Crevel, Raúl Aguirre-Gamboa, Niek de Klein, Jennifer di Tommaso, Annique Claringbould, Monique Gp van der Wijst, Dylan de Vries, Harm Brugge, Roy Oelen, Urmo Võsa, Maria M Zorro, Xiaojin Chu, Olivier B Bakker, Zuzanna Borek, Isis Ricaño-Ponce, Patrick Deelen, Cheng-Jiang Xu, Morris Swertz, Iris Jonkers, Sebo Withoff, Irma Joosten, Serena Sanna, Vinod Kumar, Hans J P M Koenen, Leo A B Joosten, Mihai G Netea, Cisca Wijmenga, BIOS Consortium, Lude Franke, Yang Li

Background: Expression quantitative trait loci (eQTL) studies are used to interpret the function of disease-associated genetic risk factors. To date, most eQTL analyses have been conducted in bulk tissues, such as whole blood and tissue biopsies, which are likely to mask the cell type-context of the eQTL regulatory effects. Although this context can be investigated by generating transcriptional profiles from purified cell subpopulations, current methods to do this are labor-intensive and expensive. We introduce a new method, Decon2, as a framework for estimating cell proportions using expression profiles from bulk blood samples (Decon-cell) followed by deconvolution of cell type eQTLs (Decon-eQTL).

PMID: 32532224