This article was originally posted on January 8.
A number of customers of Panomics, the genomics firm Affymetrix paid $73 million to acquire at the end of 2008, believe the acquisition has not affected their relationship with either company.
When Affy announced its intention to acquire Panomics in November 2008, it said Panomics would give it a portfolio of assays to sell to customers involved in downstream research, particularly those involved in drug development, a market where Affy has seen sales of its GeneChips plateau in recent years (see BAN 11/18/2008).
Three Panomics customers interviewed by BioArray News in recent weeks said the acquisition has had little direct impact on their research. Given the variety of customers that use Panomics kits for low- to midplex profiling of nucleic acids, proteins, and cells, each has its own take on the buy.
While some say that they would like to take advantage of the acquisition to use other Affymetrix products, others say they are satisfied with the kits they are using.
One customer that is familiar with both Affymetrix and Panomics products is Paul Spellman, a computational scientist at Lawrence Berkeley National Laboratory. A former treasurer of the Microarray Gene Expression Data Society, Spellman is a longtime Affy customer. He and fellow researchers also use Panomics' QuantiGenePlex for gene expression signature in breast cancer research and clinical trials.
"The acquisition hasn't changed our relationship with either technology," said Spellman. "And like a lot of people, we are seeing the end of arrays as sequencing becomes cheaper. "We are finishing legacy projects on Affy, but we are moving to sequencing for new projects," he said.
"But I would not say anything has changed," he added. "Our business relationship is about the same."
Spellman began using Panomics kits about three years ago to perform gene-expression profiling assays of formalin-fixed, paraffin-embedded samples using sets of around 100 genes. He said that RT-PCR-based assays were evaluated as an alternative, but the fact that Panomics' assays don’t require users to purify RNA and instead use total cell lysates "sold it" for him. "From tumor sample to output it took us two weeks and the results were good," Spellman said.
While Spellman is looking to move more discovery projects over to second-generation sequencing platforms, he said that Affy's acquisition of Panomics "made sense" for the array firm.
Affy "really did not have a way to [look at] small gene sets in large sample sizes," Spellman said. "If you are willing to pay for an array, you can do as many [genes] as you want because the throughput on the array systems is basically infinite, but they did not have a cost-effective way of doing smaller gene sets or looking at FFPE samples. That is a big thing they were missing."
Spellman is also satisfied with the throughput of QuantiGene Plex, and said that he believes the platform could graduate to increased clinical use in the future. "We think of it as moving towards the clinic," he said. "The Panomics assay is very robust. We actually have a scheme of implementing that in clinical trials."
Elzbieta Izbicka and Rob Streeper are different kinds of Panomics customers. Co-owners of BTNS, a drug-development shop located in Marion, Texas, Izbicka and Streeper have used Panomics' Procarta cytokine profiling kits to explore the activity of HF1107, an investigational drug. Buruli ulcer disease, an ulcerative skin disease occurring primarily in Africa caused by Mycobacterium ulcerans, is one of the relevant diseases for this drug, according to the firm.
"We buy the kits and use them in our research," Streeper said. "Things haven't really changed. From our end as users, the service has always been very good. Everything has been very smooth and easily accomplished."
BU is the first target of BTNS' HF1107 drug, but Streeper said the anti-inflammatory drug, which the firm refers to as a membrane-acting immunomodulator, could be applied to a number of other indications, such as sepsis.
"Our position on the drug side is that we have first representative of a new class of drugs," he said. BTNS is therefore interested in characterizing HF1107 in as many ways as possible, which is one reason that the company is now considering taking advantage of Panomics' connection to Affymetrix.
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"For validating or cross-validating our results, there is a general interest in finding the relationship between gene expression and protein expression," Izbicka said. "We are interested in doing these kinds of projects in the future for a variety of applications. It may be useful for diagnostics purposes as well.
"Both methods together give your results more strength. We were considering using arrays before the acquisition," Izbicka added. "Technically, it’s a very valid point."
"The way we look at our project is that we started on the protein end of characterization of drug effects and we are looking to build a broader scientific picture of how the drug works," said Streeper. "We are headed up the genome looking to characterize the mechanism of the action of our drug.
"We think it would be best to fully characterize the response to the compound as best we can because, one, it's interesting science, and two, given the novelty of the concept we are advancing for this drug, we'll need that supporting data to convince people," he added.
Streeper characterized the firm's interaction with Affy so far as "extremely fruitful" because of the firm's access to Panomics' kits. "We laugh at the multimillions of dollars big drug companies spend getting to the point we get to on a tight budget, and it's all been facilitated by this technology," he said.
Unlike BTNS' Streeper and Izbicka, researchers at Worcester, Mass.-based RXi Pharmaceuticals said they are unlikely to move their projects onto an array platform soon, as they are focused on studying cells. Like other Panomics customers, RXi said that it has not been impacted by the acquisition.
According to Joanne Kamens, senior director of discovery research at RXi, the company has been using "a large number of Panomics QuantiGene kits to measure gene expression in RNAi-mediated gene silencing in cellular assays.
"We use quite a few QuantiGene kits to do almost all of our detection of expression of cellular assays," Kamens said. "We do a lot of message detection and examining of the remaining message after applying RNAi silencing reagents. We do a lot of samples per day and we use QuantiGene for that work."
William Stanney, a scientist at RXi, has actually helped Panomics develop QuantiGene viewRNA, a multiplex mRNA in situ assay for profiling cells. "We were some of the first users," Stanney said. "A lot of the feedback was being relayed to the scientists at Affymetrix and they made adjustments based on that. It started out with slide-based assay, and after about four or five months, they came out with the plate-based assay, which worked pretty well."
Kamens and Stanney said that Affy has kept them up to date with new product developments, from which they hope to benefit. "I know they are continuing to develop new technologies," said Kamens. "That's good for the customers."
Prior to using Panomics' kits, Kamens said that RXi was using TaqMan RT-PCR assays and some other platforms. "The Panomics QuantiGene and ViewRNA can give you advantages," Kamens said of the firm's choice to use Panomics' kits. "If you were validating results, you might want to go do the specific validation," she said. "A lot of times you'll have RNA and then you'll just go do PCR, but using pure RNA in QuantiGene kits gives good results as well."