ArticleBMC genomics2018
Muver, a computational framework for accurately calling accumulated mutations.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Two distinct Okazaki fragment failure modes dominate mutagenesis in the absence of flap endonuclease 1.Nature communications · 2026Article
- Evidence that MutSβ repairs indels generated by mispair initiated template slippage.DNA repair · 2026Article
- Evidence that transient replication errors initiate nuclear genome mutations.Nucleic acids research · 2025Article
- Evidence that DNA polymerase δ proofreads errors made by DNA polymerase α across the Saccharomyces cerevisiae nuclear genome.DNA repair · 2024Article
- What can we infer about mutation calling by using time-series mutation accumulation data and a Bayesian Mutation Finder?Ecology and evolution · 2024Article
- High fidelity DNA ligation prevents single base insertions in the yeast genome.Nature communications · 2024Article
- Instability throughout the Saccharomyces cerevisiae genome resulting from Pms1 endonuclease deficiency.Nucleic acids research · 2024Article
- The rate of spontaneous mutations in yeast deficient for MutSβ function.G3 (Bethesda, Md.) · 2023Article
- Pif1 family helicases promote mutation avoidance during DNA replication.Nucleic acids research · 2022Article
- Article
- How asymmetric DNA replication achieves symmetrical fidelity.Nature structural & molecular biology · 2021Article
- The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe-S cluster in DNA polymerase δ.Nucleic acids research · 2021Article
- Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair.Cells · 2021Review
- Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging.Genome biology · 2020Article
- Loss of Heterozygosity and Base Mutation Rates Vary AmongG3 (Bethesda, Md.) · 2020Article
- Genome-wide mutagenesis resulting from topoisomerase 1-processing of unrepaired ribonucleotides in DNA.DNA repair · 2019Article
- Roles for DNA polymerase δ in initiating and terminating leading strand DNA replication.Nature communications · 2019Article
- GC content elevates mutation and recombination rates in the yeastProceedings of the National Academy of Sciences of the United States of America · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
backgroundIdentification of mutations from next-generation sequencing data typically requires a balance between sensitivity and accuracy. This is particularly true of DNA insertions and deletions (indels), that can impart significant phenotypic consequences on cells but are harder to call than substitution mutations from whole genome mutation accumulation experiments. To overcome these difficulties, we present muver, a computational framework that integrates established bioinformatics tools with novel analytical methods to generate mutation calls with the extremely low false positive rates and high sensitivity required for accurate mutation rate determination and comparison.
resultsMuver uses statistical comparison of ancestral and descendant allelic frequencies to identify variant loci and assigns genotypes with models that include per-sample assessments of sequencing errors by mutation type and repeat context. Muver identifies maximally parsimonious mutation pathways that connect these genotypes, differentiating potential allelic conversion events and delineating ambiguities in mutation location, type, and size. Benchmarking with a human gold standard father-son pair demonstrates muver's sensitivity and low false positive rates. In DNA mismatch repair (MMR) deficient Saccharomyces cerevisiae, muver detects multi-base deletions in homopolymers longer than the replicative polymerase footprint at rates greater than predicted for sequential single-base deletions, implying a novel multi-repeat-unit slippage mechanism.
conclusionsBenchmarking results demonstrate the high accuracy and sensitivity achieved with muver, particularly for indels, relative to available tools. Applied to an MMR-deficient Saccharomyces cerevisiae system, muver mutation calls facilitate mechanistic insights into DNA replication fidelity.
Indexed as
Identifiers
What OpenQuestion holds
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.