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...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:RNA (Cambridge) Jg. 16; H. 5; S. 991
Hauptverfasser: Git, Anna, Dvinge, Heidi, Salmon-Divon, Mali, Osborne, Michelle, Kutter, Claudia, Hadfield, James, Bertone, Paul, Caldas, Carlos
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States 01.05.2010
Schlagworte:
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-Zugang:Weitere Angaben
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung: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.
Bibliographie: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