A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.

While 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 i...

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Autores principales:	Alexander Wait Zaranek, Erez Y Levanon, Tomer Zecharia, Tom Clegg, George M Church
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/a85d2d4d5e13428f9f52c85eb9e27268
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spelling	oai:doaj.org-article:a85d2d4d5e13428f9f52c85eb9e272682021-12-02T20:03:41ZA survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.1553-73901553-740410.1371/journal.pgen.1000954https://doaj.org/article/a85d2d4d5e13428f9f52c85eb9e272682010-05-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20531933/pdf/?tool=EBIhttps://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404While 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.Alexander Wait ZaranekErez Y LevanonTomer ZechariaTom CleggGeorge M ChurchPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 6, Iss 5, p e1000954 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Alexander Wait Zaranek Erez Y Levanon Tomer Zecharia Tom Clegg George M Church A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.
description	While 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.
format	article
author	Alexander Wait Zaranek Erez Y Levanon Tomer Zecharia Tom Clegg George M Church
author_facet	Alexander Wait Zaranek Erez Y Levanon Tomer Zecharia Tom Clegg George M Church
author_sort	Alexander Wait Zaranek
title	A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.
title_short	A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.
title_full	A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.
title_fullStr	A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.
title_full_unstemmed	A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.
title_sort	survey of genomic traces reveals a common sequencing error, rna editing, and dna editing.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/a85d2d4d5e13428f9f52c85eb9e27268
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A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing.

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