Affymetrix's CEO Discusses Array Results vs RNA-Seq

Affymetrix CEO, Kevin King, remarked about the role microarrays continue to play despite the advancement of new sequencing technologies, such as RNA-Seq, during their recent Q1 2011 earnings call.

…a team led by Ron Davis at the Stanford Genome Technology Center, compared a custom Affy exon array to next-generation sequencing for understanding gene expression and Genome 1 identification of alternative splicing as well as infecting coding snips and non-coding transcripts. The performance of the array was examined and compared with miRNA sequencing, or RNA-Seq, over multiple independent replicate samples, and the results were published in February in the proceedings of the National Academy of Science.

To achieve comparable levels of sensitivity, the sequencing experienced cost 10x more than arrays and took much longer to complete. Even at that increased level of effort, the array had higher levels of sensitivity at the exon level. Even deeper sequencing will be required to address low abundance transcripts as well as the array did. The array has already been implemented in a multi-center clinical program involving thousands of samples, and as the author states, this platform is anticipated to have a wide range of applications and high throughput clinical studies. We believe the market for RNA arrays continues to be helping despite financial communities’ concerns over potential displacement by new sequencing technologies.

Affymetrix’s CEO Discusses Q1 2011 Results – Earnings Call Transcript

Q1 2011 Affymetrix Inc Earnings Conference Call
Wed, April 27, 2011 5:00 p.m. ET  Webcast Presentation

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