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Quantifying genetic effects on disease mediated by assayed gene expression levels

View ORCID ProfileDouglas W. Yao, Luke J. O’Connor, Alkes L. Price, Alexander Gusev
doi: https://doi.org/10.1101/730549
Douglas W. Yao
1Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA
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  • For correspondence: douglasyao@g.harvard.edu alexander_gusev@dfci.harvard.edu
Luke J. O’Connor
1Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA
2Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
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Alkes L. Price
2Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
3Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
4Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
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Alexander Gusev
5Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
6Division of Genetics, Brigham and Women’s Hospital, Boston, MA
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  • For correspondence: douglasyao@g.harvard.edu alexander_gusev@dfci.harvard.edu
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Abstract

Disease variants identified by genome-wide association studies (GWAS) tend to overlap with expression quantitative trait loci (eQTLs). However, it remains unclear whether this overlap is driven by mediation of genetic effects on disease by expression levels, or whether it primarily reflects pleiotropic relationships instead. Here we introduce a new method, mediated expression score regression (MESC), to estimate disease heritability mediated by the cis-genetic component of assayed steady-state gene expression levels, using summary association statistics from GWAS and eQTL studies. We show that MESC produces robust estimates of expression-mediated heritability across a wide range of simulations. We applied MESC to GWAS summary statistics for 42 diseases and complex traits (average N = 323K) and cis-eQTL data across 48 tissues from the GTEx consortium. We determined that a statistically significant but low proportion of disease heritability (mean estimate 11% with S.E. 2%) is mediated by the cis-genetic component of assayed gene expression levels, with substantial variation across diseases (point estimates from 0% to 38%). We further partitioned expression-mediated heritability across various gene sets. We observed an inverse relationship between cis-heritability of expression and disease heritability mediated by expression, suggesting that genes with weaker eQTLs have larger causal effects on disease. Moreover, we observed broad patterns of expression-mediated heritability enrichment across functional gene sets that implicate specific gene sets in disease, including loss-of-function intolerant genes and FDA-approved drug targets. Our results demonstrate that eQTLs estimated from steady-state expression levels in bulk tissues are informative of regulatory disease mechanisms, but that such eQTLs are insufficient to explain the majority of disease heritability. Instead, additional assays are necessary to more fully capture the regulatory effects of GWAS variants.

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Posted January 03, 2020.
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Quantifying genetic effects on disease mediated by assayed gene expression levels
Douglas W. Yao, Luke J. O’Connor, Alkes L. Price, Alexander Gusev
bioRxiv 730549; doi: https://doi.org/10.1101/730549
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Quantifying genetic effects on disease mediated by assayed gene expression levels
Douglas W. Yao, Luke J. O’Connor, Alkes L. Price, Alexander Gusev
bioRxiv 730549; doi: https://doi.org/10.1101/730549

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