ArticleBMC bioinformatics2011
New words in human mutagenesis.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- Corrigendum to "Comparative Analysis of Context-Dependent Mutagenesis Using Human and Mouse Models".BioMed research international · 2020Article
- Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans.Nature communications · 2018Article
- An expanded sequence context model broadly explains variability in polymorphism levels across the human genome.Nature genetics · 2016Article
- Preservation of methylated CpG dinucleotides in human CpG islands.Biology direct · 2016Article
- The somatic autosomal mutation matrix in cancer genomes.Human genetics · 2015Article
- Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog.International journal of molecular sciences · 2014Article
- Interaction-based evolution: how natural selection and nonrandom mutation work together.Biology direct · 2013Article
- Comparative analysis of context-dependent mutagenesis in humans and fruit flies.International journal of genomics · 2013Article
- Comparative analysis of context-dependent mutagenesis using human and mouse models.BioMed research international · 2013Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe substitution rates within different nucleotide contexts are subject to varying levels of bias. The most well known example of such bias is the excess of C to T (C > T) mutations in CpG (CG) dinucleotides. The molecular mechanisms underlying this bias are important factors in human genome evolution and cancer development. The discovery of other nucleotide contexts that have profound effects on substitution rates can improve our understanding of how mutations are acquired, and why mutation hotspots exist.
resultsWe compared rates of inherited mutations in 1-4 bp nucleotide contexts using reconstructed ancestral states of human single nucleotide polymorphisms (SNPs) from intergenic regions. Chimp and orangutan genomic sequences were used as outgroups. We uncovered 3.5 and 3.3-fold excesses of T > C mutations in the second position of ATTG and ATAG words, respectively, and a 3.4-fold excess of A > C mutations in the first position of the ACAA word.
conclusionsAlthough all the observed biases are less pronounced than the 5.1-fold excess of C > T mutations in CG dinucleotides, the three 4 bp mutation contexts mentioned above (and their complementary contexts) are well distinguished from all other mutation contexts. This provides a challenge to discover the underlying mechanisms responsible for the observed excesses of mutations.
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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.