Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression

RNA abundance and DNA copy number are routinely measured in high-throughput using microarray and next-generation sequencing (NGS) technologies, and the attributes of different platforms have been extensively analyzed. Recently, the application of both microarrays and NGS has expanded to include micr...

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Bibliographic Details
Published in:	RNA (Cambridge) Vol. 16; no. 5; p. 991
Main Authors:	Git, Anna, Dvinge, Heidi, Salmon-Divon, Mali, Osborne, Michelle, Kutter, Claudia, Hadfield, James, Bertone, Paul, Caldas, Carlos
Format:	Journal Article
Language:	English
Published:	United States 01.05.2010
Subjects:	Algorithms Base Sequence Breast - metabolism Breast Neoplasms - genetics Breast Neoplasms - metabolism Cell Line, Tumor False Negative Reactions False Positive Reactions Female Gene Expression Gene Expression Profiling - methods Gene Expression Profiling - statistics & numerical data Humans MicroRNAs - genetics MicroRNAs - metabolism Oligonucleotide Array Sequence Analysis - methods Oligonucleotide Array Sequence Analysis - statistics & numerical data Reverse Transcriptase Polymerase Chain Reaction - methods Reverse Transcriptase Polymerase Chain Reaction - statistics & numerical data RNA, Neoplasm - genetics RNA, Neoplasm - metabolism Sequence Analysis, RNA - methods Sequence Analysis, RNA - statistics & numerical data
ISSN:	1469-9001, 1469-9001
Online Access:	Get more information
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Summary:	RNA abundance and DNA copy number are routinely measured in high-throughput using microarray and next-generation sequencing (NGS) technologies, and the attributes of different platforms have been extensively analyzed. Recently, the application of both microarrays and NGS has expanded to include microRNAs (miRNAs), but the relative performance of these methods has not been rigorously characterized. We analyzed three biological samples across six miRNA microarray platforms and compared their hybridization performance. We examined the utility of these platforms, as well as NGS, for the detection of differentially expressed miRNAs. We then validated the results for 89 miRNAs by real-time RT-PCR and challenged the use of this assay as a "gold standard." Finally, we implemented a novel method to evaluate false-positive and false-negative rates for all methods in the absence of a reference method.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Undefined-3
ISSN:	1469-9001 1469-9001
DOI:	10.1261/rna.1947110