ArticleProceedings. Biological sciences2010
Even small SNP clusters are non-randomly distributed: is this evidence of mutational non-independence?
Article in Proceedings. Biological sciences, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed, 95 citations in OpenAlex.
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- Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding.Royal Society open science · 2021Article
- Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana.BMC genomics · 2021Article
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- Application of Chaotic Laws to Improve Haplotype Assembly Using Chaos Game Representation.Scientific reports · 2019Article
- Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations.Genome research · 2019Article
- Linked Mutations at Adjacent Nucleotides Have Shaped Human Population Differentiation and Protein Evolution.Genome biology and evolution · 2019Article
- NGS sequencing reveals that many of the genetic variations in transgenic rice plants match the variations found in natural rice population.Genes & genomics · 2019Article
- Effect of Hybridization on Somatic Mutations and Genomic Rearrangements in Plants.International journal of molecular sciences · 2018Review
- An Unbiased Genome-Wide View of the Mutation Rate and Spectrum of the Endosymbiotic Bacterium Teredinibacter turnerae.Genome biology and evolution · 2018Article
- Direct Determination of the Mutation Rate in the Bumblebee Reveals Evidence for Weak Recombination-Associated Mutation and an Approximate Rate Constancy in Insects.Molecular biology and evolution · 2017Article
- Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Multi-nucleotide de novo Mutations in Humans.PLoS genetics · 2016Article
- Mutation rate analysis via parent-progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids.Proceedings. Biological sciences · 2016Article
- Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.BMC genomics · 2016Article
- Heterozygosity increases microsatellite mutation rate.Biology letters · 2016Article
- Article
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1 author at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide polymorphisms (SNPs) are distributed highly non-randomly in the human genome through a variety of processes from ascertainment biases (i.e. the preferential development of SNPs around interesting genes) to the action of mutation hotspots and natural selection. However, with more systematic SNP development, one might expect an increasing proportion of SNPs to be distributed more or less randomly. Here, I test this null hypothesis using stochastic simulations and compare this output with that of an alternative hypothesis that mutations are more likely to occur near existing SNPs, a possibility suggested both by molecular studies of meiotic mismatch repair in yeast and by data showing that SNPs cluster around heterozygous deletions. A purely Poisson process generates SNP clusters that differ from equivalent data from human chromosome 1 in both the frequency of different-sized clusters and the SNP density within each cluster, even for small clusters of just four or five SNPs, while clusters on the X chromosome differ from those on the autosomes. In contrast, modest levels of mutational non-independence generate a reasonable fit to the real data for both cluster frequency and density, and also exhibit the evolutionary transience noted for 'mutation hotspots'. Mutational non-independence therefore provides an interesting new hypothesis that appears capable of explaining the distribution of SNPs in the human genome.
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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.