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PLoS One. 2011;6(9):e25400. doi: 10.1371/journal.pone.0025400. Epub 2011 Sep 27.

Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing.

Author information

1
Robarts Research Institute, London, Ontario, Canada.

Abstract

BACKGROUND:

Transcriptome profiling of patterns of RNA expression is a powerful approach to identify networks of genes that play a role in disease. To date, most mRNA profiling of tissues has been accomplished using microarrays, but next-generation sequencing can offer a richer and more comprehensive picture.

METHODOLOGY/PRINCIPAL FINDINGS:

ECO is a rare multi-system developmental disorder caused by a homozygous mutation in ICK encoding intestinal cell kinase. We performed gene expression profiling using both cDNA microarrays and next-generation mRNA sequencing (mRNA-seq) of skin fibroblasts from ECO-affected subjects. We then validated a subset of differentially expressed transcripts identified by each method using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Finally, we used gene ontology (GO) to identify critical pathways and processes that were abnormal according to each technical platform. Methodologically, mRNA-seq identifies a much larger number of differentially expressed genes with much better correlation to qRT-PCR results than the microarray (r² = 0.794 and 0.137, respectively). Biologically, cDNA microarray identified functional pathways focused on anatomical structure and development, while the mRNA-seq platform identified a higher proportion of genes involved in cell division and DNA replication pathways.

CONCLUSIONS/SIGNIFICANCE:

Transcriptome profiling with mRNA-seq had greater sensitivity, range and accuracy than the microarray. The two platforms generated different but complementary hypotheses for further evaluation.

PMID:
21980446
PMCID:
PMC3181319
DOI:
10.1371/journal.pone.0025400
[Indexed for MEDLINE]
Free PMC Article

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