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Abstract
The proteome holds great potential as an intermediate layer between the genome and phenome. Previous protein quantitative trait locus studies have focused mainly on describing the effects of common genetic variations on the proteome. Here, we assessed the impact of the common and rare genetic variations as well as the copy number variants (CNVs) on 326 plasma proteins measured in up to 500 individuals. We identified 184 cis and 94 trans signals for 157 protein traits, which were further fine-mapped to credible sets for 101 cis and 87 trans signals for 151 proteins. Rare genetic variation contributed to the levels of 7 proteins, with 5 cis and 14 trans associations. CNVs were associated with the levels of 11 proteins (7 cis and 5 trans), examples including a 3q12.1 deletion acting as a hub for multiple trans associations; and a CNV overlapping NAIP, a sensor component of the NAIP-NLRC4 inflammasome which is affecting pro-inflammatory cytokine interleukin 18 levels. In summary, this work presents a comprehensive resource of genetic variation affecting the plasma protein levels and provides the interpretation of identified effects.
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1 University of Tartu, Estonian Genome Centre, Institute of Genomics, Tartu, Estonia (GRID:grid.10939.32) (ISNI:0000 0001 0943 7661); University of Tartu, Institute of Molecular and Cell Biology, Tartu, Estonia (GRID:grid.10939.32) (ISNI:0000 0001 0943 7661)
2 University of Tartu, Estonian Genome Centre, Institute of Genomics, Tartu, Estonia (GRID:grid.10939.32) (ISNI:0000 0001 0943 7661); University of Lausanne, Department of Computational Biology, Lausanne, Switzerland (GRID:grid.9851.5) (ISNI:0000 0001 2165 4204); Swiss Institute of Bioinformatics, Lausanne, Switzerland (GRID:grid.419765.8) (ISNI:0000 0001 2223 3006); University Center for Primary Care and Public Health, Lausanne, Switzerland (GRID:grid.511931.e) (ISNI:0000 0004 8513 0292)
3 University of Tartu, Estonian Genome Centre, Institute of Genomics, Tartu, Estonia (GRID:grid.10939.32) (ISNI:0000 0001 0943 7661)
4 University of Tartu, Institute of Computer Science, Tartu, Estonia (GRID:grid.10939.32) (ISNI:0000 0001 0943 7661)