Homozygous loss-of-function variants in European cosmopolitan and isolate populations

Generation Scotland, UK10K, Vera B. Kaiser, Victoria Svinti, James G. Prendergast, You-Ying Chau, Archie Campbell, Inga Patarcic, Inês Barroso, Peter K. Joshi, Nicholas D. Hastie, Ana Miljkovic, Martin S. Taylor, Stefan Enroth, Yasin Memari, Anja Kolb-Kokocinski, Alan F. Wright, Ulf Gyllensten, Richard Durbin, Igor RudanHarry Campbell, Ozren Polašek, Åsa Johansson, Sascha Sauer, David J. Porteous, Ross M. Fraser, Camilla Drake, Veronique Vitart, Caroline Hayward, Colin A. Semple, James F. Wilson

Research output: Contribution to journalArticlepeer-review

Abstract

Homozygous Loss of Function (HLOF) variants provide a valuable window on gene function in humans, as well as an inventory of the human genes that are not essential for survival and reproduction. All humans carry at least a few HLOF variants, but the exact number of inactivated genes that can be tolerated is currently unknown - as are the phenotypic effects of losing function for most human genes. Here, we make use of 1,432 whole exome sequences from five European populations to expand the catalogue of known human HLOF mutations; after stringent filtering of variants in our dataset, we identify a total of 173 HLOF mutations, 76 (44%) of which have not been observed previously. We find that population isolates are particularly well suited to surveys of novel HLOF genes because individuals in such populations carry extensive runs of homozygosity, which we show are enriched for novel, rare HLOF variants. Further, we make use of extensive phenotypic data to show that most HLOFs, ascertained in population-based samples, appear to have little detectable effect on the phenotype. On the contrary, we document several genes directly implicated in disease that seem to tolerate HLOF variants. Overall HLOF genes are enriched for olfactory receptor function and are expressed in testes more often than expected, consistent with reduced purifying selection and incipient pseudogenisation.

Original languageEnglish
JournalHuman Molecular Genetics
DOIs
Publication statusPublished - 14 Jul 2015

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