title: Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing.
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.
  
  
  RESULTS
  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
  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.
authors: Robarts Research Institute, London, Ontario, Canada.
authors: Piya
authors: P
authors: Lahiry
authors: Leo J
authors: LJ
authors: Lee
authors: Brendan J
authors: BJ
authors: Frey
authors: C Anthony
authors: CA
authors: Rupar
authors: Victoria M
authors: VM
authors: Siu
authors: Benjamin J
authors: BJ
authors: Blencowe
authors: Robert A
authors: RA
authors: Hegele
mesh_terms: D001848:Bone Diseases, Developmental / Q000235:genetics* / Q000473:pathology; D001927:Brain Diseases / Q000235:genetics* / Q000473:pathology; D002460:Cell Line; D049109:Cell Proliferation; D004700:Endocrine System Diseases / Q000235:genetics* / Q000473:pathology; D005347:Fibroblasts / Q000378:metabolism / Q000473:pathology; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*; D012867:Skin / Q000473:pathology