Is there a niche for DNA microarrays in molecular diagnostics?

Abstract

DNA microarrays, 15 years after their appearance, have achieved presence in a number of medical settings. Several tests have been introduced and have obtained regulatory approval, mostly in the fields of bacterial identification, mutation detection and the global assessment of genome alterations, a particularly successful case being the whole-genome assay of copy-number variations. Gene-expression applications have been less successful because of technical issues (e.g., reproducibility, platform-to-platform consistency and statistical issues in data analysis) and difficulties in demonstrating the clinical utility of expression signatures. In their different applications, DNA arrays have faced competition from PCR-based assays for low and intermediate multiplicity. Now they have a new competitor, new-generation sequencing, that can provide a wealth of direct sequence information, or digital gene-expression data, at a constantly decreasing cost. In this article we evaluate the strengths and weaknesses of the DNA microarray approach to diagnostics, and highlight the fields in which it is most likely to achieve a durable presence.

Keywords::

• clinical utility
• diagnostics
• DNA arrays
• expression
• prediction
• prognostic
• regulation

Financial & competing interests disclosure

Bertrand R Jordan is an emeritus research director at the Centre National de la Recherche Scientifique (CNRS), France, and a co-founder and shareholder of Ipsogen (Marseille, France, a blood and breast cancer diagnostics company). He is also a consultant for PamGene (Hertogenbosch, The Netherlands, a biomarker company) and for Dr Chip (Hsinchu, Taiwan), a diagnostic microarray company. He has also been a consultant for Phalanx (Hsinchu, Taiwan) and Fujifilm (Tokyo, Japan) in the recent past. The author has no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.