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Perlegen to Debut Pre/Post-Diagnosis Breast Cancer Panel in First Half of '09


This article and its headline have been updated to reflect Perlegen's clarification of information presented at last week's conference.


Perlegen last week said it expects its new breast cancer diagnostic, slated to debut in the first half of 2009, to surpass the adoption rate of Myriad’s BRACAnalysis test on the strength of its lower price, easier follow-up measures, and commonality of genetic variants.

While Myriad’s genetic test for BRCA1 and BRCA2 breast and ovarian cancer mutations has a potential customer base of 250,000, Perlegen’s breast cancer test panel of eight SNPs could be used by 25 million women, Perlegen CEO Bryan Walser said last week at the UBS Global Life Sciences Conference in New York.
Following the conference, a company spokeswoman stressed that Myriad's test is focused on familial risk, while Perlegen test is targeting sporadic risk with its test, and that the firm views the two as "complementary" rather than competitive.
At the conference, Walser noted that a positive result from the BRACAnalysis Test may lead to “draconian measures,” such as the removal of breasts or ovaries. Comparatively, if Perlegen’s test detects an increased risk of breast cancer, doctors must decide on an MRI or a non-MRI follow up, or treatment with prophylactic tamoxifen or with raloxifene.
With more serious follow-up measures to consider and genetic variants indicative of familial genetic risk in 1 in 100 cancers and 1 in 1,000 breast cancer patients, the BRACAnalysis test costs around $3,000. In contrast, Walser said that with Medicare coverage, the price of Perlegen’s breast cancer test panel will range between $320 and $640. “So, it’s very accessible on an out-of-pocket basis,” Walser noted.
“The likelihood of adoption given that you have relatively benign follow-up measures have a hand in directing resources and a relatively lower price point, and we think we can help drive adoption of this test,” he added. “When you make the case to physicians that this is almost the reverse of the BRACAnalysis test, then the enthusiasm is pretty uniform across the board.”
Meanwhile, also at the UBS conference, Myriad CEO Peter Meldrum highlighted the strong position the company is in for its test, which has an annual market potential of $710 million.
Myriad’s molecular diagnostic revenues were $222.9 million for the year ended June 30, an increase of 53 percent over the prior fiscal year. The BRACAnalysis test is the company’s lead product and the BRCA1 and BRCA2 gene variants are covered by 23 patents in the US.

“When you make the case to physicians that this is almost the reverse of the BRACAnalysis test, then the enthusiasm is pretty uniform across the board.”

Meldrum noted that Myriad is in the process of building a sales force specifically to reach out to OB-GYNs at women’s health centers across the country. The company already has a 250-person sales force.
Myriad last year launched a television marketing and physician-education campaign for BRACAnalysis in several Northeastern states. This year, the company has focused its marketing efforts in the southern part of the country [see PGx Reporter 08-12-2007].
Perlegen developed its test, which contains eight SNPs, five of which are exclusive to the company, as part of a three-year collaboration with the University of Cambridge and Cancer Research UK.
The company intends to launch the laboratory test after acquiring a CLIA lab, said Walser. However, he said during a Q&A session at the conference that if Perlegen did not acquire a CLIA lab, then it would likely seek a lab partner, Pharmacogenomics Reporter sister publication GenomeWeb Daily News reported.
Walser did not discount the possibility of an alliance with Affymetrix Clinical Services Laboratory, the CLIA lab of Affy. Perlegen is a spin-out of Affymetrix, and Affy Chairman and CEO Steve Fodor also serves as chairman of the company.
Perlegen’s test is designed to stratify risk and help guide treatment selection. Thus, it will play in both the pre-diagnostic market, which includes Myriad’s risk-stratification test, as well as the post-diagnostic market, which includes therapy-guiding molecular diagnostics, such as Genomic Health’s Oncotype DX and the Molecular Profiling Institute’s MammoStrat.
Perlegen studied its test in 44,000 women across 22 clinical samples from the US, Japan, and the UK. Samples were validated at a greater-than-genome-wide significance, Walser noted. The eight alleles in the test panel are widespread in the populations.
“Each individual SNP has a low effect size,” Walser said. “So any one of these alleles is not particularly useful by itself, so it’s the aggregation of them that gets you a dynamic range.
“What [the test] does in sum is stratify your individual genetic risk and your background or clinical risk for folks who are at moderately elevated risk of non-familial, that is to say sporadic, cancer that is 85 percent of the cases of breast cancer, 90 percent in some populations,” he added.
Perlegen’s internal projections suggest the company will recoup the research and development costs for this test in two years. The firm did not disclose what those costs were.
This test is the first product to be launched in Perlegen’s women’s healthcare franchise. Other tests that will eventually be added to the franchise will include risk tests for endometrial and ovarian cancer, and for breast cancer risk in women on hormone replacement therapy.
Perlegen’s discovery efforts are bolstered by its partnership with an unidentified electronic medical records company that gives Perlegen access to a large patient medical database and potential candidates for samples. Perlegen has previously said it is also considering developing tests for cardiovascular disease risk, type II diabetes, and hepatitis C [see PGx Reporter 09-24-2008, 07-11-2007, 04-02-2008].
“By the time you add up all the markets we’re going after with the discovery engine in 2009 … we only have to hit on one or two of these to have a very good option at a second franchise while we build out our women’s health franchise,” Walser said.
At the conference, Walser mentioned that Perlegen is currently lining up investors for a Series E round of financing, but does not yet have a lead investor for the round. However, he noted that Pfizer and Affy — both previous investors — have expressed an interest in participating in the round. The firm hopes to raise between $20 million and $30 million.
Perlegen’s last round of private funding came in late 2005. In that round, Pfizer invested $50 million in the company in exchange for a 12 percent stake.

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