Show simple item record

dc.contributor.authorPipek, O.en_US
dc.contributor.authorRibli, D.en_US
dc.contributor.authorMolnár, J.en_US
dc.contributor.authorPóti, Á.en_US
dc.contributor.authorKrzystanek, M.en_US
dc.contributor.authorBodor, A.en_US
dc.contributor.authorTusnády, G. E.en_US
dc.contributor.authorSzallasi, Z.en_US
dc.contributor.authorCsabai, I.en_US
dc.contributor.authorSzüts, D.en_US
dc.date.accessioned2017-03-28T23:49:27Z
dc.date.issued2017en_US
dc.identifier.citationPipek, O., D. Ribli, J. Molnár, Á. Póti, M. Krzystanek, A. Bodor, G. E. Tusnády, Z. Szallasi, I. Csabai, and D. Szüts. 2017. “Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut.” BMC Bioinformatics 18 (1): 73. doi:10.1186/s12859-017-1492-4. http://dx.doi.org/10.1186/s12859-017-1492-4.en
dc.identifier.issnen
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:31731739
dc.description.abstractBackground: Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic processes. However, most of the routinely used mutation calling algorithms are not optimised for the simultaneous analysis of multiple samples, or for non-human experimental model systems with no reliable databases of common genetic variations. Most standard tools either require numerous in-house post filtering steps with scarce documentation or take an unpractically long time to run. To overcome these problems, we designed the streamlined IsoMut tool which can be readily adapted to experimental scenarios where the goal is the identification of experimentally induced mutations in multiple isogenic samples. Methods: Using 30 isogenic samples, reliable cohorts of validated mutations were created for testing purposes. Optimal values of the filtering parameters of IsoMut were determined in a thorough and strict optimization procedure based on these test sets. Results: We show that IsoMut, when tuned correctly, decreases the false positive rate compared to conventional tools in a 30 sample experimental setup; and detects not only single nucleotide variations, but short insertions and deletions as well. IsoMut can also be run more than a hundred times faster than the most precise state of art tool, due its straightforward and easily understandable filtering algorithm. Conclusions: IsoMut has already been successfully applied in multiple recent studies to find unique, treatment induced mutations in sets of isogenic samples with very low false positive rates. These types of studies provide an important contribution to determining the mutagenic effect of environmental agents or genetic defects, and IsoMut turned out to be an invaluable tool in the analysis of such data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1492-4) contains supplementary material, which is available to authorized users.en
dc.language.isoen_USen
dc.publisherBioMed Centralen
dc.relation.isversionofdoi:10.1186/s12859-017-1492-4en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282906/pdf/en
dash.licenseLAAen_US
dc.subjectNext generation sequencingen
dc.subjectMutagenesisen
dc.subjectSomatic mutation detectionen
dc.subjectMultiple isogenic samplesen
dc.subjectLow false positive rateen
dc.subjectDemonstrative algorithmen
dc.titleFast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMuten
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalBMC Bioinformaticsen
dc.date.available2017-03-28T23:49:27Z
dc.identifier.doi10.1186/s12859-017-1492-4*


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record