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

Joaquín Ariño, Antonio Casamayor, Julián Perez Pérez, Laia Pedrola, Miguel Álvarez-Tejado, Martina Marbà, Javier Santoyo, Joaquín Dopazo

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

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. © Copyright 2013, Mary Ann Liebert, Inc. 2013.
Original languageEnglish
Pages (from-to)53-59
JournalOMICS A Journal of Integrative Biology
Volume17
DOIs
Publication statusPublished - 1 Jan 2013

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