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Users Staying with Arrays Due to Cost, Data Analysis


Some life-sciences tool vendors have pledged that digital gene expression applications performed on their second-generation sequencing platforms will eventually dominate the gene expression market at the expense of arrays. However, a variety of experts familiar with both technologies say cost, data analysis, and throughput issues are continuing to encourage researchers to choose arrays over DGE.

To date, Illumina has three DGE applications on its Genome Analyzer: mRNA-seq, to identify and quantify full-length poly-A transcript isoforms; tag profiling, to sequence short 3' end transcript fragments to quantify known and novel transcripts from any eukaryotic species; and small RNA discovery and analysis.

In 2007, Applied Biosystems, now Life Technologies, decided to shutter its expression array business, opting to push its customers to pursue gene expression studies on its SOLiD second-gen sequencing system. Last year, the company launched a gene expression profiling application on the SOLiD.

But while Illumina and ABI look to bite off a chunk of the expression array market, which Illumina has estimated is currently worth around $700 million, some users familiar with both array-based and sequencing-based expression profiling say the two applications are different and predict that arrays will continue to be a valuable platform for researchers, at least for the next few years.

Gary Hardiman, director of the Biomedical Genomics Microarray Facility at the University of California in San Diego, says that researchers may split in regards to what platform they use based on their different research projects. "I think that researchers just interested in which genes are altered with regards to expression in response to a biological phenomenon will stick with arrays for the time being — this analog information, the lists of genes that are altered, and the pathway and ontology analyses you can do with these lists, will continue to provide valuable insights into biological questions," Hardiman says.

Justin Petrone


$2 Billion
Value of the cytogenetics testing market as Estimated by Illumina CEO Jay Flatley.

Microarray Notes

With a four-year, $2.9 million grant from NIH, Boston University School of Medicine will use arrays made by Affymetrix and Invitrogen to study the genetics of chronic obstructive pulmonary disease.

The Children's Hospital of Eastern Ontario will use BioTrove's Open-Array platform to test its feasibility for identifying and quantifying more than 30 infectious respiratory viral and bacterial disease targets in children, such as influenza and MRSA.

Paris-based Biogemma has chosen to use Roche NimbleGen's sequence-capture technology to develop new technologies for its crop-breeding programs. The main goal is to design sequence capture arrays targeting unique genetic variations for wheat and rapeseed studies.

Funded Grants

$316,421/FY 2008
Bioinformatics for Protein Microarrays
Grantee: Richard Zangar, Pacific Northwest National Laboratory
Began: Feb. 1, 2007; Ends: Jan. 31, 2010

Zangar will use the grant funding to build ProMAT, software for analyzing protein antibody microarray data. He plans to establish novel protocols for the use of internal and external standards, develop the statistical foundation for evaluating data quality, and develop a sophisticated bioinformatics tool for rapid data analysis, including advanced quality control features. The end goal is to be able to use protein microarrays as a routine tool for clinical biomarker validation.

$371,080/FY 2008
Use of Microarrays to Understand Systemic Arthritis
Grantee: Virginia Pascual, Baylor Research Institute
Began: Sep. 22, 2003; Ends: May 31, 2013
Continuing her study of Systemic Onset Juvenile Idiopathic Arthritis, Pascual will start examining candidate genes for genetic and functional analyses. She will continue characterizing SoJIA-specific candidate gene signatures, study the cell types contributing to the signature, and characterize the role of infectious agents in the initial stage and flare-ups of patients with SoJIA. The end goal is to develop a diagnostic test and set the stage for future discovery of susceptibility genes.

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