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PLoS By Category | Recent PLoS Articles
Diabetes and Endocrinology - Neurological Disorders - Pediatrics and Child Health

Transcriptional Profiling of Endocrine Cerebro-Osteodysplasia Using Microarray and Next-Generation Sequencing
Published: Tuesday, September 27, 2011
Author: Piya Lahiry et al.

by Piya Lahiry, Leo J. Lee, Brendan J. Frey, C. Anthony Rupar, Victoria M. Siu, Benjamin J. Blencowe, Robert A. Hegele

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.

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