Mutation saturation for fitness effects at human CpG sites
- Columbia University, United States
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.
Data availability
All source data are freely available to researchers, with sources provided in the manuscript. Data and code to generate the figures is available at https://github.com/agarwal-i/cpg_saturation.
Article and author information
Author details
Funding
National Institutes of Health (GM122975)
- Molly Przeworski
National Institutes of Health (GM121372)
- Molly Przeworski
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Jeffrey Ross-Ibarra, University of California, Davis, United States
Version history
- Received: June 22, 2021
- Accepted: November 21, 2021
- Accepted Manuscript published: November 22, 2021 (version 1)
- Version of Record published: December 17, 2021 (version 2)
- Version of Record updated: December 21, 2021 (version 3)
Copyright
© 2021, Agarwal & Przeworski
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Mutation saturation for fitness effects at human CpG sites
eLife 10:e71513.
https://doi.org/10.7554/eLife.71513
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