Assessing differential expression measurements by highly parallel pyrosequencing and DNA microarrays: a comparative study

OMICS. 2013 Jan;17(1):53-9. doi: 10.1089/omi.2011.0065. Epub 2011 Sep 15.

Abstract

To explore the feasibility of pyrosequencing for quantitative differential gene expression analysis we have performed a comparative study of the results of the sequencing experiments to those obtained by a conventional DNA microarray platform. A conclusion from our analysis is that, over a threshold of 35 normalized reads per gene, the measurements of gene expression display a good correlation with the references. The observed concordance between pyrosequencing and DNA microarray platforms beyond the threshold was of 0.8, measured as a Pearson's correlation coefficient. In differential gene expression the initial aim is the quantification the differences among transcripts when comparing experimental conditions. Thus, even in a scenario of low coverage the concordance in the measurements is quite acceptable. On the other hand, the comparatively longer read size obtained by pyrosequencing allows detecting unconventional splicing forms.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Regulation*
  • Oligonucleotide Array Sequence Analysis*
  • RNA, Messenger / genetics

Substances

  • RNA, Messenger