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Muver, a computational framework for accurately calling accumulated mutations

Overview of attention for article published in BMC Genomics, May 2018
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Title
Muver, a computational framework for accurately calling accumulated mutations
Published in
BMC Genomics, May 2018
DOI 10.1186/s12864-018-4753-3
Pubmed ID
Authors

Adam B. Burkholder, Scott A. Lujan, Christopher A. Lavender, Sara A. Grimm, Thomas A. Kunkel, David C. Fargo

Abstract

Identification 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. Muver 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. Benchmarking 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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 23 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 23 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 5 22%
Student > Ph. D. Student 4 17%
Student > Bachelor 3 13%
Student > Postgraduate 2 9%
Student > Master 2 9%
Other 4 17%
Unknown 3 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 5 22%
Biochemistry, Genetics and Molecular Biology 4 17%
Engineering 3 13%
Computer Science 2 9%
Psychology 1 4%
Other 4 17%
Unknown 4 17%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 14 May 2018.
All research outputs
#13,360,706
of 23,052,509 outputs
Outputs from BMC Genomics
#4,795
of 10,699 outputs
Outputs of similar age
#164,121
of 327,411 outputs
Outputs of similar age from BMC Genomics
#103
of 250 outputs
Altmetric has tracked 23,052,509 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,699 research outputs from this source. They receive a mean Attention Score of 4.7. This one has gotten more attention than average, scoring higher than 53% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 327,411 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 250 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 57% of its contemporaries.