ArticleGenome biology and evolution2010
The genomic distribution and local context of coincident SNPs in human and chimpanzee.
Article in Genome biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 30 citations in OpenAlex.
- Article
- Article
- Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features.Science (New York, N.Y.) · 2019Article
- A new heterozygous compound mutation in theHuman genome variation · 2019Article
- Purifying selection shapes the coincident SNP distribution of primate coding sequences.Scientific reports · 2016Article
- Article
- SNP Formation Bias in the Murine Genome Provides Evidence for Parallel Evolution.Genome biology and evolution · 2015Article
- Genome-wide inference of ancestral recombination graphs.PLoS genetics · 2014Article
- Longevity and plasticity of CFTR provide an argument for noncanonical SNP organization in hominid DNA.PloS one · 2014Article
- Interaction-based evolution: how natural selection and nonrandom mutation work together.Biology direct · 2013Article
- Galactosialidosis: review and analysis of CTSA gene mutations.Orphanet journal of rare diseases · 2013Review
- Origins of shared genetic variation in African cichlids.Molecular biology and evolution · 2013Article
- Nonhuman primate models in the genomic era: a paradigm shift.ILAR journal · 2013Review
- Lack of genomic imprinting of DNA primase, polypeptide 2 (PRIM2) in human term placenta and white blood cells.Epigenetics · 2012Article
- Long-term balancing selection at the antiviral gene OAS1 in Central African chimpanzees.Molecular biology and evolution · 2012Article
- Paternal age effect mutations and selfish spermatogonial selection: causes and consequences for human disease.American journal of human genetics · 2012Review
- Variation in the mutation rate across mammalian genomes.Nature reviews. Genetics · 2011Review
- Mutation rate distribution inferred from coincident SNPs and coincident substitutions.Genome biology and evolution · 2011Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
We have previously shown that there is an excess of sites that are polymorphic at orthologous positions in humans and chimpanzees and that this is most likely due to cryptic variation in the mutation rate. We showed that this might be a consequence of complex context effects since we found significant heterogeneity in triplet frequencies around coincident single nucleotide polymorphism (SNP) sites. Here, we show that the heterogeneity in triplet frequencies is not specifically associated with coincident SNPs but is instead driven by base composition bias around CpG dinucleotides. As a result, we suggest that cryptic variation in the mutation rate is truly cryptic, in the sense that the mutation rate does not appear to depend on any specific primary sequence context. Furthermore, we propose that the patterns around CpG dinucleotides are driven by the mutability of CpG dinucleotides in different DNA contexts. We also show that the genomic distribution of coincident SNPs is nonuniform and that there are some subtle differences between the distributions of single and coincident SNPs. Furthermore, we identify regions that contain high numbers of coincident SNPs and suggest that one in particular, a region containing the gene PRIM2, may be under balancing selection.
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Registered trials
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.