ArticleGenome research2013
The influence of genomic context on mutation patterns in the human genome inferred from rare variants.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed, 59 citations in OpenAlex.
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- Very Low Rates of Spontaneous Gene Deletions and Gene Duplications in Dictyostelium discoideum.Journal of molecular evolution · 2023Article
- Estimating the genome-wide mutation rate from thousands of unrelated individuals.American journal of human genetics · 2022Article
- Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations.G3 (Bethesda, Md.) · 2022Article
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- The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.Genome biology and evolution · 2021Article
- The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development.G3 (Bethesda, Md.) · 2020Article
- Mutational bias and the protein code shape the evolution of splicing enhancers.Nature communications · 2020Article
- Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The Interaction of Natural Selection and GC Skew May Drive the Fast Evolution of a Sand Rat Homeobox Gene.Molecular biology and evolution · 2019Article
- Significant Strain Variation in the Mutation Spectra of Inbred Laboratory Mice.Molecular biology and evolution · 2019Article
- Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans.Nature communications · 2018Article
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- Neutral Theory, Disease Mutations, and Personal Exomes.Molecular biology and evolution · 2018Article
- Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans.PLoS genetics · 2018Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
Abstract
Understanding patterns of spontaneous mutations is of fundamental interest in studies of human genome evolution and genetic disease. Here, we used extremely rare variants in humans to model the molecular spectrum of single-nucleotide mutations. Compared to common variants in humans and human-chimpanzee fixed differences (substitutions), rare variants, on average, arose more recently in the human lineage and are less affected by the potentially confounding effects of natural selection, population demographic history, and biased gene conversion. We analyzed variants obtained from a population-based sequencing study of 202 genes in >14,000 individuals. We observed considerable variability in the per-gene mutation rate, which was correlated with local GC content, but not recombination rate. Using >20,000 variants with a derived allele frequency ≤ 10(-4), we examined the effect of local GC content and recombination rate on individual variant subtypes and performed comparisons with common variants and substitutions. The influence of local GC content on rare variants differed from that on common variants or substitutions, and the differences varied by variant subtype. Furthermore, recombination rate and recombination hotspots have little effect on rare variants of any subtype, yet both have a relatively strong impact on multiple variant subtypes in common variants and substitutions. This observation is consistent with the effect of biased gene conversion or selection-dependent processes. Our results highlight the distinct biases inherent in the initial mutation patterns and subsequent evolutionary processes that affect segregating variants.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.