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Perlegen Inks Deal With EMR Provider to Develop Dxs for Common Conditions

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Perlegen has formed a collaboration with an undisclosed electronic medical records provider and plans to mine its collection of clinical treatment and outcomes data to identify genetic markers and develop diagnostic tests that can help physicians personalize treatments for heart attack, breast cancer, hepatitis C, and nicotine addiction.
 
Perlegen announced last week that under the collaboration, it will have exclusive access to 4 million patient records, from which the company will identify subsets of records that meet inclusion and exclusion criteria for various discovery and replication studies to develop genetic tests.
 
Once these patient subsets are identified, Perlegen said it will work with their health care providers to obtain DNA samples from these patients “in a HIPAA-compliant, IRB-approved manner.”
 
The discovery of genetic markers that can help physicians personalize treatments “have been long delayed by the lack of appropriate DNA sample sets linked with rich clinical information,” Perlegen said in a statement. “But now, by collaborating to gain access to this dataset of long-term patient records integrated from multiple sources and mapped into a standardized, fully searchable data structure, Perlegen can quickly identify patients from whom properly consented, clinically meaningful DNA samples could rapidly be obtained.”
 
Under the terms of the deal, the EMR provider will earn subscription and program fees, as well as milestone payments upon the launch of new diagnostic tests resulting from the collaboration. In exchange, Perlegen will receive an ownership stake in the EMR upon the achievement of certain revenue levels.
 
“Right now the way medicine is practiced, it’s kind of like [cooking] spaghetti: You throw it up against the wall and see what sticks,” Perlegen CEO Bryan Walser told Pharmacogenomics Reporter last week. Instead, “if you could group people so that they responded to a given therapy and you could focus on places where there is a choice in therapies … then that would improve medicine for patients, payors, and for the entire system, because the right drug would get to the right patient at the right time.”
 
First Studies
 
Perlegen has already begun selecting patients and collecting DNA for its initial diagnostic programs. Additional sample collection programs are slated to begin in coming months.
 
“Most of the things that we’re interested in are to help physicians make decisions, so [the diagnostics being developed] are going to be aids to a physician facing an important decision; therefore [the tests] are likely to go through FDA and are likely not to go directly to [the] consumer,” Walser said.
 
With data from the EMR provider, Perlegen will gather DNA samples for a replication study for a diagnostic test the company is developing to gauge which patients will suffer edema and congestive heart failure following treatment with thiazolidinediones.
 
Last year, Perlegen announced it was in the process of collecting and analyzing DNA from diabetic patients treated with two popular insulin-sensitizing thiazolidinediones: GlaxoSmithKline’s Avandia and Takeda’s Actos [see PGx Reporter 07-11-2007].
 

“Right now the way medicine is practiced, it’s kind of like [cooking] spaghetti: You throw it up against the wall and see what sticks.”

After a study published in the New England Journal of Medicine by Cleveland Clinic cardiologist Steven Nissen found that Avandia was associated with an increased risk of myocardial infarction, the FDA in June requested that a black box warning about congestive heart failure be placed on Avandia and Actos’ label.
 
“Avandia and Actos are good medicines in the people where they don’t cause harm. So, if you could see people who weren’t at much risk for [congestive heart failure], you’d always want to monitor your patients carefully, but you’d be able to use that drug with more confidence,” Walser said, adding that the EMR will provide additional samples necessary to confirm the findings for this study.  
 
Perlegen has an additional portfolio of about eight drug-response indications that it is using to develop tests, and will use the resources of its EMR partner and those of other vendors with which it is in late-stage discussions.
 
Walser highlighted that Perlegen has so far validated and replicated markers for heart attack, breast cancer, and nicotine addiction. “We’re working with partners to commercialize those tests,” he added.
 
Finally, Perlegen and the SC Liver Research Consortium are looking at how patients with chronic hepatitis C infections respond to the standard-of-care treatment with interferon alfa and ribavirin. “Approximately 85 percent of patients with chronic hepatitis C infection don’t get treatment with interferon-alpha and ribavirin, which are the only treatments on the market that have been shown to be any good,” Walser said.
 
The cure rate for HCV patients treated with interferon alfa and ribavirin is roughly 50 percent, and many patients discontinue treatment due to serious side effects including fatigue, depression, fever, and anemia. “But if you could say … who had a greater likelihood of responding, then you would be able to really help direct patients to receive therapy that they might actually benefit from,” Walser said.
 
The platform for Perlegen’s diagnostics will depend on the structure of the human variation being identified, Walser added. For discovery, Perlegen is using Affymetrix’s GeneChip microarray platform with its own set of SNPs. For sequencing, Perlegen is using a Roche/454 Life Sciences platform. The commercial platform for its diagnostics will depend on the intended use of the tests, he said.
 
Privacy Concerns
 
With the Genetic Information Nondiscrimination Act still not passed in Congress, patients may be nervous about how industry and their health care providers use their medical, and particularly genetic, data.
 
To this end, Perlegen maintains that it will only have access to “de-identified patient records.” These records can only be re-identified by the healthcare institutions and must be done in a HIPAA-compliant, IRB-approved manner. The patients and physicians that agree to participate in Perlegen’s studies will receive compensation for providing DNA samples.
 
“We have RSA-enabled encryption to any external access. So, we have the highest level of external security. But any security is possible, theoretically, to breach,” Walser said. “But we’re absolutely incapable of providing a privacy breach because we don’t have any personally identifiable patient information that we use for these discovery purposes.”
 
The privacy concerns surrounding genetic data collection may be one reason Perlegen’s EMR partner has opted to remain anonymous.
 
“Folks really want to have an opportunity to explain in detail how they are making sure that there isn’t any data that’s going to be harmful, given that folks are sensitive about it,” Walser said. “I think that may have played a part in their decision that they would like to remain anonymous at the moment.”

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