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Gene Logic to Help FDA, Industry Get ‘Comfortable’ with Genomic Data Subs

Findings from a recently announced collaboration between Gene Logic and the US Food and Drug Administration to share quality-control methods and metrics will eventually be made available for public debate, and may lead to industry-wide standards for genomic data assessment — which industry would welcome.
Gene Logic issued a statement last week announcing that it had entered into a collaboration with the agency in which Gene Logic will submit quality-control metrics and work with FDA officials across its divisions to improve the agency’s understanding of microarray-based genomic data that companies submit as part of regulatory submissions.
“What we are going to do with the FDA is share the quality-control metrics and work with some of the people at the FDA and help define which [types of data] are really needed and which ones may not be that informative anymore,” Donna Mendrick, scientific fellow and vice president of toxicogenomics at Gene Logic, told Pharmacogenomics Reporter this week.
The alliance is different from a collaboration Gene Logic and the FDA penned in 2006 in which the company agreed to share data and software to help the agency evaluate sponsors’ voluntary genomic data submissions. Under that program, only high-quality data were provided, whereas in this current agreement the company will provide the agency both “good data and bad data, or data that the company failed using its own quality metrics,” Mendrick said.
In this way, the FDA “can start looking at what made this data bad,” she said. Through this process Gene Logic hopes to try to help the agency identify the metrics that are important for the whole industry, she added.
According to Gene Logic, pharmaceutical companies are wary of turning over genomic data to the FDA for products undergoing regulatory approval if there are no federal or industry-wide standards for how to submit these data.
“There’s still a fair amount of concern on the pharmaceutical side in terms of how will [FDA] look at the data: ‘What will they do, what is it going to mean to me?’” Mendrick said.
By working with the FDA Gene Logic “can help the [agency] feel comfortable with genomic data and therefore make sponsors feel comfortable with genomic data.”
Also, “it certainly helps Gene Logic if pharmaceutical companies feel more comfortable supplying genomic data to the FDA,” since the company has collaborations with several companies to generate gene-expression data for their clinical trials and pre-clinical testing, she said.
The collaboration, under the aegis of the FDA’s Critical Path Initiative, is still in its infancy and doesn’t have a set timeline. Currently, Gene Logic is working out the details of the research plan with the agency.
“We don’t want it to take years by any means but we don’t have a firm timeline yet because it’s going to take effort on both sides to actually do the data analysis and comparisons,” Mendrick said.
Ultimately, at the end of the collaboration, Gene Logic and the FDA will make the findings publicly available by publishing them in a peer-reviewed journal.
“It’s not going to help anyone if the FDA tried to set up some kind of a private standard,” Mendrick said. “That’s not what they are trying to do, nor are we. We want these standards to be in the public domain. … The only way you get true standards accepted by the community at large is to make them public and everyone will argue and disagree and, hopefully, agree at the end of the day on what they should be.”
Although details of the collaboration have yet to be solidified, Gene Logic said it plans to work with multiple divisions with the FDA for this effort.
“One of the things we want to do is work with some of the people at the FDA on the diagnostics wing, because they may not get much microarray data but they are going to be getting genomic data as well,” Mendrik said. “We have also been talking with them about what it is they need to understand when they get submissions to that division. … So, we’re going to be working with multiple divisions at the FDA on this.”
Gene Logic’s experience lies with microarrays, and Mendrick noted that the agency is probably also studying submissions for genomic data from other platforms.
The FDA, which refused to comment for this article, has in the past openly acknowledged that its understanding of genomics and pharmacogenomics could be vastly improved.
Indeed, the agency this year rolled out several pharmacogenomics-related Continuing Medical Education courses for MDs, PhDs, and PharmDs after an internal review revealed that the FDA’s staff had limited knowledge about pharmacogenomics.
In 2004 the FDA identified a need to communicate effectively about PGx within its own corridors and created its own education programs. At that time it decided to develop the CME courses for health-care professionals [see PGx Reporter 01-03-2007].

By working with the FDA Gene Logic “can help the [agency] feel comfortable with genomic data and therefore make sponsors feel comfortable with genomic data.”

The agency has several efforts underway to help sharpen its understanding of genomics, among them the Voluntary Genomic Data Submissions program, which is focused on improving understanding of genomic data submissions, and the MicroArray Quality Control Project, which aims to improve the assessment of microarray platforms.
Unofficial Partners
According to Mendrick, Gene Logic has had an unofficial collaboration with the FDA for several years looking at data quality issues. The company, located in close proximity to the FDA in Gaithersburg, Md., touts one of the world’s largest toxicogenomic reference databases, has processed more than 200,000 Affymetrix microarrays, and has developed more than 40 quality metrics.
“We have the largest commercial shop in the world to generate data, not only for our internal projects but for companies that come to us and want us to generate gene-expression data for clinical trials, for pre-clinical testing,” Mendrick said.
She noted that with genomic data, sponsors need to maintain the biological quality of the sample, as well as the integrity of the processing steps. “The generation of genomic data can be a complicated process … and various things can go wrong,” Mendrick said, adding that its experience with Affy arrays, the reference database, and internal metrics sets it apart from others in the industry.
According to the company, the lack of federal or industry standards for genomic data submissions has been a deterrent for both industry and the FDA – making companies apprehensive about submitting such data and the agency unsure about reviewing these types of submissions.
“Because there are no universal standards of what makes genomic data deemed good or bad, [the FDA] can have difficulty if they get genomic data in if they think that the quality isn’t good enough, but they really have no way of determining that,” Mendrick observed. “What the FDA has said for several years is that the pharmaceutical companies want them to be experienced in analyzing genomic data, and yet the FDA by definition doesn’t have large databases of genomic data,”
In addition to the collaboration with Gene Logic, the FDA has an ongoing partnership with Iconix Pharmaceuticals for access to the company’s DrugMatrix toxicogenomics database, but this agreement does not cover data quality standards.
Pharmaceutical companies “would like to have some standard set that would discern if data is of good quality or of bad quality,” Mendrick said, noting that these firms “are concerned about submitting genomic data when they don’t know the quality of analysis of the other side.”
Felix Frueh, head of the FDA’s Interdisciplinary Pharmacogenomics Research Group, has said that in the second year of the VGDS program sponsors were more comfortable submitting complex data sets than they were in the first year of the initiative. Similarly, when the current Gene Logic/FDA collaboration wraps up and its findings are published, companies may feel even more at ease submitting genomic data.
Publishing the findings from this collaboration will at least set the groundwork for a discussion about setting federal standards for genomic data submissions, Mendrick hopes.
“We’re not trying to do something behind closed doors. It will be closed doors for a period of time but then we’re going to put it out in the public domain and let people fight about it,” she said.

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