Human variation in population-wide gene expression data predicts gene perturbation phenotype.

Bonaguro, Lorenzo; Aschenbrenner, Anna Christin; Arts, Peer; Gemünd, Ioanna; Reiz, Benedikt; Saglam, Adem; Mukherjee, Sach; Ulas, Thomas; Rahmouni, Souad; Schultze, Joachim L; Sun, Laura L; Hoischen, Alexander; Georges, Michel; Schulte-Schrepping, Jonas; Händler, Kristian; Netea, Mihai G; Carraro, Caterina; van de Veerdonk, Frank L; Joosten, Leo A B

doi:10.1016/j.isci.2022.105328

Journal Article

DZNE-2022-01665

Human variation in population-wide gene expression data predicts gene perturbation phenotype.

Bonaguro, L. (First author)DZNE* ; Schulte-Schrepping, J.DZNE* ; Carraro, C.DZNE* ; Sun, L. L. ; Reiz, B. ; Gemünd, I.DZNE* ; Saglam, A.DZNE* ; Rahmouni, S. ; Georges, M. ; Arts, P. ; Hoischen, A. ; Joosten, L. A. B. ; van de Veerdonk, F. L. ; Netea, M. G. ; Händler, K.DZNE* ; Mukherjee, S.DZNE* ; Ulas, T.DZNE* ; Schultze, J. L.DZNE* ; Aschenbrenner, A. C. (Last author)DZNE*

2022
Elsevier St. Louis

iScience 25(11), 105328 (2022) [10.1016/j.isci.2022.105328]

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Please use a persistent id in citations: doi:10.1016/j.isci.2022.105328

Abstract: Population-scale datasets of healthy individuals capture genetic and environmental factors influencing gene expression. The expression variance of a gene of interest (GOI) can be exploited to set up a quasi loss- or gain-of-function 'in population' experiment. We describe here an approach, huva (human variation), taking advantage of population-scale multi-layered data to infer gene function and relationships between phenotypes and expression. Within a reference dataset, huva derives two experimental groups with LOW or HIGH expression of the GOI, enabling the subsequent comparison of their transcriptional profile and functional parameters. We demonstrate that this approach robustly identifies the phenotypic relevance of a GOI allowing the stratification of genes according to biological functions, and we generalize this concept to almost 16,000 genes in the human transcriptome. Additionally, we describe how huva predicts monocytes to be the major cell type in the pathophysiology of STAT1 mutations, evidence validated in a clinical cohort.

Keyword(s): Clinical genetics ; Human genetics ; Pathophysiology

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ddc:050

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Appears in the scientific report 2022

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Medline

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Creative Commons Attribution-NonCommercial-NoDerivs CC BY-NC-ND 4.0

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