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

ABSTRACT: 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.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.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.

SUBMITTER: Lahiry P

PROVIDER: S-EPMC3181319 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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

Lahiry Piya P Lee Leo J LJ Frey Brendan J BJ Rupar C Anthony CA Siu Victoria M VM Blencowe Benjamin J BJ Hegele Robert A RA

PloS one 20110927 9

<h4>Background</h4>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.<h4>Methodology/principal findings</h4>ECO is a rare multi-system developmental disorder caused by a homozygous mutation in ICK encoding intestinal cell kinase. We performed gene expr ...[more]

PMID: 21980446

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Dataset Information

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

Publications

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

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