A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

James R. Bradford, Yvonne Hey, Tim Yates, Yaoyong Li, Stuart D. Pepper, Crispin J. Miller

Research output: Contribution to journalArticlepeer-review

Abstract

Background: RNA-Seq exploits the rapid generation of gigabases of sequence data by Massively Parallel Nucleotide Sequencing, allowing for the mapping and digital quantification of whole transcriptomes. Whilst previous comparisons between RNA-Seq and microarrays have been performed at the level of gene expression, in this study we adopt a more fine-grained approach. Using RNA samples from a normal human breast epithelial cell line (MCF-10a) and a breast cancer cell line (MCF-7), we present a comprehensive comparison between RNA-Seq data generated on the Applied Biosystems SOLiD platform and data from Affymetrix Exon 1.0ST arrays. The use of Exon arrays makes it possible to assess the performance of RNA-Seq in two key areas: detection of expression at the granularity of individual exons, and discovery of transcription outside annotated loci.Results: We found a high degree of correspondence between the two platforms in terms of exon-level fold changes and detection. For example, over 80% of exons detected as expressed in RNA-Seq were also detected on the Exon array, and 91% of exons flagged as changing from Absent to Present on at least one platform had fold-changes in the same direction. The greatest detection correspondence was seen when the read count threshold at which to flag exons Absent in the SOLiD data was set to t
Original languageEnglish
Article number282
JournalBMC Genomics
Volume11
Issue number1
DOIs
Publication statusPublished - 5 May 2010

Research Beacons, Institutes and Platforms

  • Manchester Cancer Research Centre

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