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With Eye to Translational Research Market, Affy Launches WT Pico Target Prep Kit


NEW YORK (GenomeWeb) – With the launch of its GeneChip WT Pico Kit, Affymetrix is taking aim at a segment of the translational research market for which whole-transcriptome analysis is often a challenge due to the limited availability of samples.

It is becoming increasingly apparent that within a particular tissue or population of cells there are cellular subpopulations with a "large degree of heterogeneity," Christian Reese, an Affymetrix product manager, told GenomeWeb.

This is particularly true in cancer, where different mutations in small subpopulations of cells within a tumor have "noticeably different transcriptional profiles … that drive the fundamental biology and course" of the disease, he said.

At the same time, efforts to translate basic discoveries into clinical science — cancer-related or otherwise — often involves the use of hard-to-come-by biological samples. As a result, investigators are often "trying to use as little [material] as possible to preserve as much as possible for downstream experiments."

Similar issues exist for investigators studying expression patterns in naturally limited cell types, such as neurons, he noted.

To address this, Affymetrix developed the WT Pico Kit, which can prepare targets for use with the firm's GeneChip Whole-transcriptome arrays from as little as 100 picograms of total RNA input — approximately the equivalent of the transcriptomes of 10 cells, according to Reese.

Importantly for Affymetrix's interest in the translational research space, the kit works with various clinically relevant samples such as formalin-fixed paraffin-embedded specimens, as well as fresh and frozen tissue, cultured cells, and whole blood samples. It is also compatible with small sample isolation techniques including flow cytometry, laser capture microdissection, and fine-needle aspiration.

To develop the kit, Affymetrix had to make some adjustments to how it typically handles target amplification for its arrays, Chris Kubu, the director of reagent development in Affymetrix's gene expression unit, noted.

"We typically like to use in vitro transcription, a linear amplification method, for our arrays … in contrast to most of the RNA-seq methods that use a PCR step," he explained. "For this particular kit, we did have to use a few cycles of PCR in order to overcome … kinetic barriers [related to enzymes used in the kit] prior to the in vitro transcription step that we normally like to use for amplification."

"That was probably the key hurdle in the course of assay development for us," he said.

Reese declined to comment specifically on pricing for the WT Pico kit, but he did say that "there is a certain degree of value and complexity in the kit that prices it at somewhat of a premium toward our other products.

"But, in general, a customer is going to pay a similar amount to what they pay for their present Affymetrix target preparation products," he said.