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PMID: 23598527 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants.

RNA (New York, N.Y.) ·Vol. 19 ·No. 6 ·2013-06-00 ·Pages 725-32

Lee JH, Ang JK, Xiao X

Abstract

RNA-sequencing (RNA-Seq) technologies hold enormous promise for novel discoveries in genomics and transcriptomics. In the past year, a surge of reports has analyzed RNA-Seq data to gain a global view of the RNA editome. Opposing results have been presented, giving rise to extensive debate surrounding one of the first such studies in which a daunting list of all 12 types of RNA-DNA differences (RDDs) were identified. Although a consensus is forming that some of the initial "paradigm-shifting" results of this study may be questionable, recent reports on this topic differed in terms of the number and relative abundance of each type of RDD. Many outstanding issues exist, most importantly, the choice of bioinformatic approaches. Here we discuss the critical data analysis and experimental design issues of such studies to enable improved systematic investigation of the largely unexplored frontier of single-nucleotide variants in RNA.

Keywords
RNA editing RNA-Seq RNA–DNA difference mapping error read mapping
MeSH Terms
Alleles Base Sequence Databases, Nucleic Acid Gene Expression Profiling/methods Humans Molecular Sequence Annotation Polymorphism, Single Nucleotide RNA Editing RNA Splice Sites Reproducibility of Results Research Design Sensitivity and Specificity Sequence Alignment Sequence Analysis, RNA/methods
Chemicals
RNA Splice Sites
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Lee Jae-Hyung
Department of Integrative Biology and Physiology, Bioinformatics Interdepartmental Program, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, USA.
Ang Jason K
Xiao Xinshu
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Article Info
Journal
RNA (New York, N.Y.)
Abbr.
RNA
ISSN
1469-9001
DOI
10.1261/rna.037903.112
Published
2013-06-00
Epub
2013-00-18
Pages
725-32
Language
English
Region
United States
NLM ID
9509184
PMCID
PMC3683905
Subset
IM
Grants
NHGRI NIH HHS · R01 HG006264 · United States
NHGRI NIH HHS · U01 HG007013 · United States
NHGRI NIH HHS · R01HG006264 · United States
External Links
PubMed source DOI: 10.1261/rna.037903.112 PMC Full Text View journal details
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