Asuragen, a spin-off of Ambion, has begun to offer microarray analysis services for microRNA and mRNA profiling to its customers. Its transcriptional expertise is derived from a number of former Ambion employees who make up the current scientific staff.
Asuragen uses an RNA sample and target preparation chemistry first developed by Ambion. However, the company has spent significant amounts of time optimizing that protocol for FFPE by understanding the variables that affect yield and quality of RNA out of fixed tissues, including the effects of age of block, type of tissue and fixation parameters. They are now applying those findings to generate quality expression microarray data from FPPE samples.

“With the investment we’ve now made, we have a lot more to offer than simply executing a protocol which pretty much anybody could do from a purchased kit,” said Scott Hunicke-Smith, VP and General Manager, Asuragen Services. “When we look at concordance values of fixed versus freshly frozen from the same exact tissue, we get linear R2 values well north of 90 percent—even up to a year old—with microRNA profiles.”

Asuragen also expects to offer mRNA microarray profiling services from FFPE, and plans to use the Affymetrix Human Exon Array and Whole Transcript Assay, which uses a random primed targetpreparation protocol.

“Going forward, it’s going to be critical to profile not only microRNAs, but also mRNAs jointly out of the samples,” said Hunicke-Smith. “We are looking at the Affymetrix exon platform as something we think might give good data for mRNA off of FFPE samples.

get linear R2 values well north of 90 percent—even up to a year old—with microRNA profiles.

We are optimistic about some of the exon array profiling that we’ve seen. The Affymetrix exon platform has the potential to maintain quality data despite the degradation that you see in fixed tissue. If you are looking at differential detection with the exon platform, your results would be much more concordant with the fresh tissue than the conventional 3’ bias arrays. That’s largely because you are doing a random primed assay so your transcripts are fragmented at random locations.

SERVICES OFFERED
Broudy: What range of services do you offer for RNA profiling of FFPE samples?

Hunicke-Smith: We can take a sample and give the customer the total RNA with the microRNA content included, or we can do any of the downstream molecular profiling of microRNA now, and next with mRNA from the exon array.

To take it further, we can also do the