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Startup Veracyte Presents Data, Prepares to Launch Thyroid MDx Test

By Tony Fong

NEW YORK (GenomeWeb News) – On the heels of data from a clinical validation study indicating its thyroid cancer test can classify fine needle aspirates as benign with high accuracy, Veracyte said this week it is on schedule to initiate commercialization of the test later this year.

At the International Thyroid Congress today, the South San Francisco molecular diagnostics firm presented initial data from its large-scale, prospective, multi-site validation study. In it, researchers found that in 66 fine needle aspirate samples, including 43 indeterminate samples, the company's test had a negative predictive value of more than 95 percent compared to histopathology reviews, the gold standard of care, meaning that with 95 percent accuracy, Veracyte's test could determine when a result was truly negative.

Based on those results and a study published last week that the company said validates the performance of its technology, Veracyte Co-founder and CEO Bonnie Anderson told GenomeWeb Daily News this week that the company will proceed to launch the test called Afirma initially in five to 10 academic sites with whom it has been partnering while the test was being developed and through the validation study process.

In early 2011, the company will broaden the commercialization effort by making Afirma available through a larger number of community sites "where those tests will really have a benefit," Anderson said.

The test will be available as a laboratory-developed test and its initial launch will be limited to the US, though Veractye is evaluating international opportunities.

Afirma, Anderson said, would address a $500 million market just in the US that continues to grow. While she could not say how much of that market the test could potentially capture, she said, "We think we can drive adoption through a significant percentage of that market."

Anderson said that a price for Afirma, which would be Veracytes' first product launch, had not yet been determined.

The academic centers that are participating in Afirma's first-stage launch were "very anxious" to become early adopters and Veractye wanted to support their enthusiasm, Anderson said. Additionally, choosing a limited and staggered launch allows the company to be "methodical" in its strategy.

"We want to make sure that [we have] all our processes for supporting high-quality services from our laboratory and make sure that we have the support mechanisms in place to properly service the accounts that we bring on board early," she said. "So we're going to manage it carefully in the early days and be ready to expand as the markets ready."

Product launches are a complex process with many moving parts, and while the company feels it has the support of its test-site partners who participated in the clinical trial, "the second part is making sure you have the doctors properly educated," she said.

As it ramps up its sales staff, the smaller launch also will allow Veracyte to properly train its personnel.

"If you hire 20 people at one time, that's sometimes harder to do than if you do it in groups of five," she said, adding that the firm is in negotiations with insurers and payors over reimbursement for the test.

Veracyte was launched in 2008, and this past June it announced that it raised $28 million in a Series B financing round.

The test combines machine-learning vectors and statistical models applied to a database containing more than 1 billion genomic measurements from hundreds of fine needle aspirate samples in order to identify genes that differentiate malignancy from benignity. A whole-genome analysis was performed to create the database.

Afrima is not a general screen for thyroid nodules, but instead is for use when results from thyroid nodule fine needle aspirates are inconclusive. Thyroid cancer has one of the higher survival rates among cancers, but it is also one of the fastest growing cancers in terms of diagnoses, Anderson said.

According to the American Cancer Society, an estimated 44,670 new cases of the disease will be diagnosed this year, more than double the number of diagnoses in 1990. And it is expected that thyroid cancer will kill around 1,690 people this year.

In addition to the number of new diagnoses, about 450,000 biopsies of suspected thyroid cancer are done each year by fine needle aspirate, Anderson said. The Achilles heel of fine needle aspirates is that the sample size tends to be very small and contains a cocktail of different cells and content, combining to make definitive diagnosis difficult.

As a result, about 20 to 30 percent of such cases have inconclusive diagnoses, Anderson said, with most of them leading to thyroidectomies. It turns out, however, that more than 70 percent of these patients who have all or part of their thyroids removed, in fact, have benign nodules.

According to the data presented at the International Thyroid Congress in Paris today, Afirma achieved 97 percent sensitivity, 64 percent specificity, and a negative predictive value of 98 percent among all 66 samples. In patients with indeterminate fine needle aspirate cytology, the test achieved 95 percent sensitivity, 63 percent specificity, and a negative predictive value of 96 percent.

"A test with this high negative predictive value will help doctors rule out malignancy and confidently monitor many patients with ambiguous thyroid nodules, enabling these patients to avoid unnecessary surgery," Bryan Haugen, the lead author on the study, said in a statement.

Haugen is a professor of medicine and pathology head, division of endocrinology, metabolism, and diabetes, at the University of Colorado.

The clinical trial is ongoing and results of the confirmatory performance study are anticipated to be published next year, Veracyte said.

Last week, a study describing the company's technology and the development of Afirma — which Anderson called "foundational" for Veracyte — was published online in the Journal of Clinical Endocrinology & Metabolism.

Using mRNA expression analysis, researchers including those from Veracyte, measured more than 247,186 transcripts in 315 thyroid nodules. The test achieved 96 percent negative predictive value and 84 percent specificity.

According to Anderson, the study offers proof that its approach to fine needle aspirates works, and will become the underpinning for future tests. Veracyte is performing early discovery work in lung cancer with the goal of developing a test for lung cancer fine needle aspirates, she said.

While fine needle aspirates are minimally invasive and are ideal for sample collection directly in a clinical environment, advances to their use have been limited, Anderson said. Because their diagnostic accuracy has been limited by microscopic methods, questions about their accuracy have pervaded.

"So one of the exciting aspects of the [JCEM] article is that it shows that we have addressed some of the challenges of working with fine needle aspirates which really lend itself to increasing the diagnostic accuracy of these very minimally invasive samples," she said.

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