ArticleGenome biology and evolution2022
Hunting for Beneficial Mutations: Conditioning on SIFT Scores When Estimating the Distribution of Fitness Effect of New Mutations.
Article in Genome biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Translating functional molecular knowledge into crop-breeding success.Nature reviews. Genetics · 2026Review
- Gene-level complexity explains genome-wide variation in the distribution of fitness effects.Molecular biology and evolution · 2026Article
- A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them.Genome biology and evolution · 2026Article
- An Integrative Variant Scoring Function for Finding Novel Genes Associated with Ovarian and Thyroid Cancer.International journal of environmental research and public health · 2026Article
- In Silico Functional and Structural Analysis ofGenes · 2026Article
- In silico prediction of variant effects: promises and limitations for precision plant breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Estimating the proportion of beneficial mutations that are not adaptive in mammals.PLoS genetics · 2024Article
- Mutations in yeast are deleterious on average regardless of the degree of adaptation to the testing environment.Proceedings. Biological sciences · 2024Article
- Increased Positive Selection in Highly Recombining Genes Does not Necessarily Reflect an Evolutionary Advantage of Recombination.Molecular biology and evolution · 2024Article
- fastDFE: Fast and Flexible Inference of the Distribution of Fitness Effects.Molecular biology and evolution · 2024Article
- Gsw-fi: a GLM model incorporating shrinkage and double-weighted strategies for identifying cancer driver genes with functional impact.BMC bioinformatics · 2024Article
- Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Fitness Effects of Mutations: An Assessment of PROVEAN Predictions Using Mutation Accumulation Data.Genome biology and evolution · 2022Article
- A Novel NCSTN Mutation in a Three-Generation Chinese Family with Hidradenitis Suppurative.Journal of healthcare engineering · 2022Article
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Authors and funding
4 authors.
Funding
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Abstract
The distribution of fitness effects (DFE) of new mutations is a key parameter of molecular evolution. The DFE can in principle be estimated by comparing the site frequency spectra (SFS) of putatively neutral and functional polymorphisms. Unfortunately, the DFE is intrinsically hard to estimate, especially for beneficial mutations because these tend to be exceedingly rare. There is therefore a strong incentive to find out whether conditioning on properties of mutations that are independent of the SFS could provide additional information. In the present study, we developed a new measure based on SIFT scores. SIFT scores are assigned to nucleotide sites based on their level of conservation across a multispecies alignment: the more conserved a site, the more likely mutations occurring at this site are deleterious, and the lower the SIFT score. If one knows the ancestral state at a given site, one can assign a value to new mutations occurring at the site based on the change of SIFT score associated with the mutation. We called this new measure δ. We show that properties of the DFE as well as the flux of beneficial mutations across classes covary with δ and, hence, that SIFT scores are informative when estimating the fitness effect of new mutations. In particular, conditioning on SIFT scores can help to characterize beneficial mutations.
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