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At Piper Jaffray, More From Third Wave on HPV Test; Affy Talks Dx, Consumer Genetics

This story originally appeared in Biocommerce Week, a newsletter that has been discontinued.
Several BCW Index firms made presentations Tuesday at the Piper Jaffray Health Care Conference in New York with a focus on recently launched or soon-to-be introduced instruments.
Nearly all of Third Wave’s presentation focused on its human papillomavirus molecular test, which the firm said is on schedule for submission to the US Food and Drug Administration for clearance during the first quarter of 2008. Meanwhile, Affymetrix focused on its molecular diagnostic and consumer genetics efforts, and Applied Biosystems pitched investors on its genotyping collaboration with BioTrove.
Third Wave Targets FDA OK and Qiagen
Speaking at the Conference, CEO Kevin Conroy pitched investors and analysts on what he believes are the advantages of Third Wave’s test over the currently marketed test from Qiagen, which that firm gained through its $1.6 billion acquisition of Digene a few months ago (see BioCommerce Week 6/6/2007).
He said the first advantage is that Third Wave’s test provides a much lower false-positive rate than Qiagen’s HPV test, which he said has a false-positive rate of between 5 percent and 20 percent. “That’s an untenable situation for the long haul,” said Conroy.
He said comparative tests of the two technologies showed 86 percent agreement on results. But in that 14 percent of instances where the tests did not agree, resolution by sequencing showed Third Wave’s test was correct 79 percent of the time.
He said part of the problem with Qiagen’s test is that it lacks an internal control, which the Third Wave test has. In addition, he said the workflow environment for the Qiagen is test is too manual at the front end.
Qiagen officials were not available to comment by press time.
Conroy noted that two months ago the firm unveiled its fully automated HPV testing instrument, which the firm intends to launch next year.
Digene and Third Wave have been locked in a legal dispute since the beginning of the year over patents covering HPV testing. Digene sued Third Wave in the US District Court for the Western District of Wisconsin, alleging that Third Wave has infringed one or more claims of US Patent No. 5,643,715, entitled “Human Papillomavirus Type 52 DNA Sequences and Methods for Employing the Same.”
In a countersuit filed in March, Third Wave said its claims “are based on Digene’s repeated abuse of its substantial market power … and the direct and substantial antitrust injury to Third Wave and consumers resulting directly from Digene’s anti-competitive conduct.” (see BioCommerce Week 3/7/2007).
Even though a recent Markman ruling favored Third Wave’s claims in the case, Qiagen said that it would appeal the ruling and press forward with its claims against Third Wave (see BioCommerce Week 10/10/2007)
Despite the ongoing legal battle between the firms and Conroy’s insistence that Third Wave’s HPV test is a better product, he said, “Digene’s done a wonderful job creating this market.”
Conroy said that even though there is an HPV molecular diagnostic on the market, there is only 15 percent market penetration in the US. Since Qiagen owns the only FDA-cleared molecular test for HPV, it has a 90 percent market share, he said.
The market for molecular HPV tests has been pegged at anywhere from $200 million to $1 billion globally. This opportunity, combined with low penetration rates and limited competition, led Third Wave to place 80 percent of its efforts and resources two years ago into developing its HPV test, said Conroy.
He said the firm will submit its HPV test for FDA clearance in the first quarter of 2008 with clinical data on the test published soon thereafter.
Affymetrix Talks Up Dx, Consumer Genetics
Though it is the clear-cut market leader in the gene expression field and is battling Illumina for the top spot in the genotyping market, Affymetrix’s presentation at Piper Jaffray focused mostly on its emerging diagnostics efforts and its push into consumer genetics.
Doug Farrell, the firm’s vice president of investor relations, noted that Affymetrix now has 11 diagnostic partners and more than 20 tests in development based on its GeneChip technology. The tests target breast, colon, prostate, lung, brain, thyroid, and bone marrow cancer, as well as lymphoma and leukemia.
Oncology applications are the key focus in these partnerships because the array technology enables researchers to look at hundreds of genes, he said. Among Affymetrix’s diagnostic partners are Roche and Johnson & Johnson subsidiary Veridex.
Farrell also touched on the firm’s nascent efforts in the consumer genetics field. Affymetrix is providing the genotyping technologies used in Navigenics’ personal genetics service, which launched earlier this month but will not provide its services until early next year. That service will compete with similar services recently launched by Decode Genetics and 23andMe, the latter of which has announced it will use genotyping technology from Affymetrix rival Illumina (see BioCommerce Week 11/21/2007).
Farrell told conference attendees that he expects Affymetrix to work with additional partners in the consumer genomics field.
He said the firm was much more competitive on the genotyping front this past year, thanks in large part to the introduction of its Genome-Wide Human SNP Array 6.0, which contains more than 1.8 million markers and was launched in late May. According to Farrell, sales of the chip have been “very solid.” He cited the array’s unique copy number variation content, derived from Affymetrix’s collaboration with the Broad Institute, as a key selling point.
ABI Eyes Downstream Genotyping Market
Though much of the news surrounding Applied Biosystems recently has focused on its SOLiD next-generation DNA sequencer, the firm’s presentation was heavily weighted to its newly forged genotyping alliance with BioTrove (see BioCommerce Week 11/14/2007).
Peter Dansky, president of the Molecular and Cell Biology Consumables Division, said the pact would move the firm’s TaqMan chemistry into a new growth area and provide ABI and BioTrove with a new platform for downstream validation and screening applications. He said this provides a complementary offering to the firm’s SOLiD platform, which is used in the discovery phases of research.
Company officials also noted that the firm is developing an automated sample preparation system for the SOLiD. They admitted this has been an issue for users of the instrument, but stressed it has not been an obstacle to platform adoption.

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