Mutation saturation for fitness effects at human CpG sites

Abstract

Whole exome sequences have now been collected for millions of humans, with the related goals of identifying pathogenic mutations in patients and establishing reference repositories of data from unaffected individuals. As a result, we are approaching an important limit, in which datasets are large enough that, in the absence of natural selection, every highly mutable site will have experienced at least one mutation in the genealogical history of the sample. Here, we focus on CpG sites that are methylated in the germline and experience mutations to T at an elevated rate of ~10-7 per site per generation; considering synonymous mutations in a sample of 390,000 individuals, ~99% of such CpG sites harbor a C/T polymorphism. Methylated CpG sites provide a natural mutation saturation experiment for fitness effects: as we show, at current sample sizes, not seeing a non-synonymous polymorphism is indicative of strong selection against that mutation. We rely on this idea in order to directly identify a subset of CpG transitions that are likely to be highly deleterious, including ~27% of possible loss-of-function mutations, and up to 20% of possible missense mutations, depending on the type of functional site in which they occur. Unlike methylated CpGs, most mutation types, with rates on the order of 10-8 or 10-9, remain very far from saturation. We discuss what these findings imply for interpreting the potential clinical relevance of mutations from their presence or absence in reference databases and for inferences about the fitness effects of new mutations.

The sequences of 150,119 genomes in the UK Biobank

“…1c ). Synonymous mutations are often assumed to be unaffected by selection (neutral) 29 ; however, we found that synonymous CpG>TpG mutations are less saturated (85.7%) than those that are intergenic (89.9%), supporting the hypothesis that human codon usage is constrained 30 .…”

“…The extensive saturation of CpG>TpG variants at methylated CpGs in large WES cohorts has been used to identify genomic annotation or loci where their absence could be indicative of negative selection 21 , 29 . In line with previous reports 21 , we saw less saturation of stop-gain CpG>TpG variants than those that are synonymous (Fig.…”

The sequences of 150,119 genomes in the UK biobank

“…1c). Synonymous mutations are often assumed to be unaffected by selection (neutral) 37 however we find that synonymous CpG>TpG mutations are less saturated (85.7%) than those that are intergenic (89.9%), supporting the hypothesis that human codon usage is constrained 38 .…”

“…The extensive saturation of CpG>TpG variants at methylated CpGs in large WES cohorts has been used to identify genomic annotation or loci where their absence could be indicative of negative selection 11, 37 . In line with previous reports 11 we see less saturation of stop-gain CpG>TpG variants than those that are synonymous (Fig.…”

Quantifying the fraction of new mutations that are recessive lethal

“…Here again, the extent to which sites depleted of genetic variation reflects the presence of lethal mutations is not entirely clear. Demonstrating this, Agarwal and Przeworski (2021) used a similar approach by examining invariant methylated CpG sites in a sample of 390,000 human genomes, concluding that an additive mutation with a selection coefficient as small as s = 1 e − 3 is sufficient to result in a lack of variation even in the large sample sizes they used. Thus, approaches for detecting lethal mutations based on genetic variation data may have inherent limitations not only in disentangling s from h , but also in separating lethal mutations from mutations that are strongly deleterious though far from lethal ( s on the order of -0.001 to -0.1).…”