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dc.contributor.authorZaranek, Alexander Wait
dc.contributor.authorLevanon, Erez Y.
dc.contributor.authorZecharia, Tomer
dc.contributor.authorClegg, Tom
dc.contributor.authorChurch, George McDonald
dc.date.accessioned2013-01-30T15:18:25Z
dc.date.issued2010
dc.identifier.citationZaranek, Alexander Wait, Erez Y. Levanon, Tomer Zecharia, Tom Clegg, and George McDonald Church. 2010. A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing. PLoS Genetics 6(5): e1000954.en_US
dc.identifier.issn1553-7390en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:10246808
dc.description.abstractWhile it is widely held that an organism's genomic information should remain constant, several protein families are known to modify it. Members of the AID/APOBEC protein family can deaminate DNA. Similarly, members of the ADAR family can deaminate RNA. Characterizing the scope of these events is challenging. Here we use large genomic data sets, such as the two billion sequences in the NCBI Trace Archive, to look for clusters of mismatches of the same type, which are a hallmark of editing events caused by APOBEC3 and ADAR. We align 603,249,815 traces from the NCBI trace archive to their reference genomes. In clusters of mismatches of increasing size, at least one systematic sequencing error dominates the results (G-to-A). It is still present in mismatches with 99% accuracy and only vanishes in mismatches at 99.99% accuracy or higher. The error appears to have entered into about 1% of the HapMap, possibly affecting other users that rely on this resource. Further investigation, using stringent quality thresholds, uncovers thousands of mismatch clusters with no apparent defects in their chromatograms. These traces provide the first reported candidates of endogenous DNA editing in human, further elucidating RNA editing in human and mouse and also revealing, for the first time, extensive RNA editing in Xenopus tropicalis. We show that the NCBI Trace Archive provides a valuable resource for the investigation of the phenomena of DNA and RNA editing, as well as setting the stage for a comprehensive mapping of editing events in large-scale genomic datasets.en_US
dc.language.isoen_USen_US
dc.publisherPublic Library of Scienceen_US
dc.relation.isversionofdoi:10.1371/journal.pgen.1000954en_US
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873906/pdf/en_US
dash.licenseLAA
dc.titleA Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editingen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalPLoS Geneticsen_US
dash.depositing.authorZaranek, Alexander Wait
dc.date.available2013-01-30T15:18:25Z
dash.affiliation.otherHMS^Geneticsen_US
dash.affiliation.otherHMS^Health Sciences and Technologyen_US
dash.affiliation.otherHMS^Geneticsen_US
dc.identifier.doi10.1371/journal.pgen.1000954*
dash.contributor.affiliatedWait, Alexander
dash.contributor.affiliatedChurch, George


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