Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.

Kierczak M, Rafati N, Höglund J, Gourlé H, Lo Faro V, Schmitz D, Ek WE, Gyllensten U, Enroth S, Ekman D, Nystedt B, Karlsson T, Johansson Å

Nat Commun 13 (1) 2532 [2022-05-09; online 2022-05-09]

Despite the success of genome-wide association studies, much of the genetic contribution to complex traits remains unexplained. Here, we analyse high coverage whole-genome sequencing data, to evaluate the contribution of rare genetic variants to 414 plasma proteins. The frequency distribution of genetic variants is skewed towards the rare spectrum, and damaging variants are more often rare. We estimate that less than 4.3% of the narrow-sense heritability is expected to be explained by rare variants in our cohort. Using a gene-based approach, we identify Cis-associations for 237 of the proteins, which is slightly more compared to a GWAS (N = 213), and we identify 34 associated loci in Trans. Several associations are driven by rare variants, which have larger effects, on average. We therefore conclude that rare variants could be of importance for precision medicine applications, but have a more limited contribution to the missing heritability of complex diseases.

Bioinformatics Long-term Support WABI [Collaborative]

Bioinformatics Support and Infrastructure [Collaborative]

Bioinformatics Support for Computational Resources [Service]

Bioinformatics Support, Infrastructure and Training [Collaborative]

NGI Short read [Service]

NGI Stockholm (Genomics Production) [Service]

National Genomics Infrastructure [Service]

PubMed 35534486

DOI 10.1038/s41467-022-30208-8

Crossref 10.1038/s41467-022-30208-8

pmc: PMC9085767
pii: 10.1038/s41467-022-30208-8

Publications 9.5.0