This story has been updated to clarify that Asuragen is offering a service, and not a diagnostic assay.
Looking to attract researchers involved in biomarker discovery using formalin-fixed, paraffin-embedded sample material, Asuragen next month will roll out a service that it claims can mitigate the factors that often lead scientists not to fully trust data derived from FFPE sample experiments.
According to Scott Hunicke-Smith, the firm’s vice president and general manager, Asuragen plans to launch the service, called Encompass, at the annual meeting of the American Association for Cancer Research in San Diego next month. Hunicke-Smith said that Encompass is a “whole package” for gene-expression profiling from the submission of FFPE sample material through data analysis.
Asuragen, a successor company to Ambion, last year launched an miRNA-profiling service based on a custom Affymetrix chip called DiscovArray (see BAN 8/7/2007
). While Asuragen serves as a resource for pharmaceutical and biotechnology companies’ R&D projects, Hunicke-Smith told BioArray News
last week that the Encompass service can be valuable for any researcher involved in biomarker discovery.
“You could say [this service plays] well to biopharma accounts, but there are some very good research oncologists with access to outstanding tumor banks doing the same work,” he said. “The real keys to industrial accounts are quality, control, communication, reasonable price, and turn-around time. That’s true for any of our services.”
Hunicke-Smith touted the firm’s “extensive experience with FFPE from a wide range of tissue types, blocks, slices, and even slides,” and said that the Encompass assay will give users the “ability to profile whole-transcript (not just whole genome) data, with results that are robust to degradation.”
The cost for the basic service will be about the same as doing a standard Affymetrix profile from frozen tissues or cell culture, Hunicke-Smith said, but instead of using Affy’s U133 Plus 2.0 gene-expression arrays, the company has decided to use the newer Affy Gene 1.0 ST arrays or exon arrays as an option. Hunicke-Smith said that, “depending on the type of institution, [the Affy option] can be significantly less expensive than the standard.”
Asuragen isn’t the only company that has developed tools to perform expression profiling on FFPE samples. Large array vendors like Illumina and Agilent have also introduced kits and streamlined their assays to work with the material, while life-science companies like Genisphere have introduced kits to help researchers amplify DNA collected from FFPE samples.
According to Hunicke-Smith, Asuragen’s strength could lie in tying its Encompass service to other services on its menu, especially its miRNA-profiling services, which are offered both on DiscovArray as well as Applied Biosystems’ RT-PCR-based TaqMan platform.
“There is this ingrained perception that FFPE is not useful for comprehensive gene-expression studies, because the RNA is so degraded and there may have been some early processing that may alter the gene expression profile.”
“This makes for a very economical gene-expression profile overall and of course our prep methods are also miRNA compatible, so you could also get an miRNA profile on ABI TaqMan, an Agilent array, or DiscovArray from the same sample prep, subject to material available,” Hunicke-Smith said.
Casting a Broad Net
According to Mike Wilson, a senior scientist and array R&D manager at Asuragen, the firm has been encouraging its customers to look at both gene-expression profiles and miRNA-expression profiles to make their studies more comprehensive.
“The idea here is that if you are in a biomarker-discovery program, this allows you to cast the broadest possible net for RNA analysis,” he told BioArray News recently. “That is an advantage for someone on the discovery side of a pharmaceutical company who is looking for biomarkers that might stratify diseases and so on.”
Both Hunicke-Smith and Wilson declined to discuss the specific features of the Encompass service that make it able to deal with possibly degraded FFPE sample material. However, Wilson said that the service had been optimized at all steps, “from the time when the FFPE sample is taken, through isolation, labeling of the RNA, putting it on the array, and analyzing it.”
He said that Asuragen is using a “completely non-biased labeling technique” that acts as an “equal opportunity labeler in terms of labeling all the fragments of the RNA.” He said that the non-biased labeling approach, coupled with Affymetrix’s high-density arrays offered a “perfect combination” to get a “more accurate picture of the transcript.”
Wilson said that Asuragen has also done some work upstream on the RNA isolation step to optimize its yield and to optimize the purity of the RNA that it gets from the FFPE Block.
The main issue, Wilson added, will be convincing customers that it can be done.
“There is this ingrained perception that FFPE is not useful for comprehensive gene-expression studies, because the RNA is so degraded and there may have been some early processing that may alter the gene-expression profile,” he said.
“But I think that as we develop these automated tools that can get a good, comprehensive look at the RNA profile, that perception will change,” said Wilson. “People will become more aware that FFPE is actually a good resource for getting a robust gene-expression profile.”
Despite the concerns some may have about using FFPE in gene-expression profiling experiments, Wilson said that the reality is that FFPE is still the most common method of storing patient biopsy material.
He also pointed out that it is easier to get access to FFPE samples than frozen tissue samples.
Therefore, “for a discovery effort, FFPE is ideal because it is loaded with clinical background information, patient information, and it is easiest to get access to,” he said.