RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples

Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Maximo, Philippe Birembaut, Nhan Tran, Gunnar Dittmar, Laurent Vallar

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Background: RNA sequencing (RNA-seq) and microarrays are two transcriptomics techniques aimed at the quantification of transcribed genes and their isoforms. Here we compare the latest Affymetrix HTA 2.0 microarray with Illumina 2000 RNA-seq for the analysis of patient samples - normal lung epithelium tissue and squamous cell carcinoma lung tumours. Protein coding mRNAs and long non-coding RNAs (lncRNAs) were included in the study. Results: Both platforms performed equally well for protein-coding RNAs, however the stochastic variability was higher for the sequencing data than for microarrays. This reduced the number of differentially expressed genes and genes with predictive potential for RNA-seq compared to microarray data. Analysis of this variability revealed a lack of reads for short and low abundant genes; lncRNAs, being shorter and less abundant RNAs, were found especially susceptible to this issue. A major difference between the two platforms was uncovered by analysis of alternatively spliced genes. Investigation of differential exon abundance showed insufficient reads for many exons and exon junctions in RNA-seq while the detection on the array platform was more stable. Nevertheless, we identified 207 genes which undergo alternative splicing and were consistently detected by both techniques. Conclusions: Despite the fact that the results of gene expression analysis were highly consistent between Human Transcriptome Arrays and RNA-seq platforms, the analysis of alternative splicing produced discordant results. We concluded that modern microarrays can still outperform sequencing for standard analysis of gene expression in terms of reproducibility and cost.

Original languageEnglish (US)
Article number443
JournalBMC Genomics
Volume18
Issue number1
DOIs
StatePublished - Jun 6 2017

Fingerprint

RNA Sequence Analysis
Alternative Splicing
Gene Expression Profiling
Long Noncoding RNA
Exons
Genes
RNA
Gene Expression
Lung
Recombinant DNA
Transcriptome
Squamous Cell Carcinoma
Protein Isoforms
Proteins
Epithelium
Costs and Cost Analysis
Messenger RNA
Neoplasms

Keywords

  • Differential exon usage
  • Differential expression analysis
  • Microarrays
  • RNA sequencing
  • Splicing

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Nazarov, P. V., Muller, A., Kaoma, T., Nicot, N., Maximo, C., Birembaut, P., ... Vallar, L. (2017). RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples. BMC Genomics, 18(1), [443]. https://doi.org/10.1186/s12864-017-3819-y

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples. / Nazarov, Petr V.; Muller, Arnaud; Kaoma, Tony; Nicot, Nathalie; Maximo, Cristina; Birembaut, Philippe; Tran, Nhan; Dittmar, Gunnar; Vallar, Laurent.

In: BMC Genomics, Vol. 18, No. 1, 443, 06.06.2017.

Research output: Contribution to journalArticle

Nazarov, PV, Muller, A, Kaoma, T, Nicot, N, Maximo, C, Birembaut, P, Tran, N, Dittmar, G & Vallar, L 2017, 'RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples', BMC Genomics, vol. 18, no. 1, 443. https://doi.org/10.1186/s12864-017-3819-y
Nazarov, Petr V. ; Muller, Arnaud ; Kaoma, Tony ; Nicot, Nathalie ; Maximo, Cristina ; Birembaut, Philippe ; Tran, Nhan ; Dittmar, Gunnar ; Vallar, Laurent. / RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples. In: BMC Genomics. 2017 ; Vol. 18, No. 1.
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