ArticleBMC cancer2019
Nonsynonymous, synonymous and nonsense mutations in human cancer-related genes undergo stronger purifying selections than expectation.
Article in BMC cancer, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64 citing papers in PubMed, 111 citations in OpenAlex.
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- Synonymous mutations in essential genes infrequently produce fitness effects in human cell lines.Nucleic acids research · 2026Article
- Identification of the MYH6 c.804G>C Synonymous Variant Causing Exon Skipping in a Hypertrophic Cardiomyopathy Family.Molecular genetics & genomic medicine · 2026Article
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- Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.Genomics, proteomics & bioinformatics · 2025Review
- The genetic landscape of CYP24A1 polymorphisms in cancer risk: evidence from a systematic review.Discover oncology · 2025Review
- DNA-based immunotherapy for cancer: In vivo approaches for recalcitrant targets.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- RNA-sequencing Analysis of Hybrid Females Reveals a Dominance of Expression of Alleles From Outcrossing Species Over Those From Selfing Species.Genome biology and evolution · 2025Article
- Genome-Wide Selection Scans in Mexican Indigenous Populations Reveal Recent Signatures of Pathogen and Diet Adaptation.Genome biology and evolution · 2025Article
- Single nucleotide polymorphisms on Cholecystokinin B Receptor gene as a candidate gene for crowing in Pelung chickens.Journal of advanced veterinary and animal research · 2025Article
- Spotlight on amino acid changing mutations in the JAK-STAT pathway: from disease-specific mutation to general mutation databases.Scientific reports · 2025Article
- Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and coculture.The ISME journal · 2025Article
- The theory of massively repeated evolution and full identifications of cancer-driving nucleotides (CDNs).eLife · 2024Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundNonsynonymous mutations change the protein sequences and are frequently subjected to natural selection. The same goes for nonsense mutations that introduce pre-mature stop codons into CDSs (coding sequences). Synonymous mutations, however, are intuitively thought to be functionally silent and evolutionarily neutral. Now researchers know that the optimized synonymous codon usage is advantageous in the speedy mRNA translation process. With the advent of NGS technique, the explosion of NGS data generated from the tumor tissues help researchers identify driver mutations in cancer-related genes, but relatively less attention is paid to the SNP data in healthy human populations when studying cancer.
methodsHere, we analyzed the publically available human SNPs. We classified these SNPs according to their functional and evolutionary categories. By simply dividing the human genes into cancer-related genes and other genes, we compared the features of nonsynonymous, synonymous and nonsense mutations in these two gene sets from multiple aspects.
resultsWe provided lines of evidence that the nonsynonymous, synonymous and nonsense mutations in cancer-related genes undergo stronger purifying selection when compared to the expected pattern in other genes. The lower nonsynonymous to synonymous ratio observed in cancer-related genes suggests the suppression of amino acid substitutions in these genes. The synonymous SNPs, after excluding those in splicing regions, exhibit preferred changes in codon usage and higher codon frequencies in cancer-related genes compared to other genes, indicating the constraint exerted on these mutations. Nonsense mutations are less frequent and located closer to stop codons in cancer-related genes than in other genes, which putatively minimize their deleterious effects.
conclusionOur study demonstrated the evolutionary constraint on mutations in CDS of cancer-related genes without the requirement of data from cancer tissues or patients. Our work provides novel perspectives on interpreting the constraint on mutations in cancer-related genes. We reveal extra constraint on synonymous mutations in cancer-related genes which is related to codon usage bias and is in addition to the splicing effect.
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