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Counsyl Developing Own NIPT; Converting Carrier Screening Test to NGS


NEW YORK (GenomeWeb) – Counsyl is developing a noninvasive prenatal test using technology the firm licensed from Illumina and Sequenom's joint patent pool, company officials told GenomeWeb this week.

The firm is also in the midst of converting its carrier screening test to use solely next-generation sequencing. Previously, it offered a genotyping version with the expanded NGS version as a reflex test. In addition, it has launched a 22-gene hereditary cancer panel.

Jim Goldberg, Counsyl's chief medical officer, told GenomeWeb that for about the last year, the firm had been ordering Illumina's Verifi test for customers while providing its own clinical report and genetic counseling. It decided to switch to running the test in house to have more control over it, he said.

Initially, Counsyl's NIPT, called the Informed Pregnancy Screen, will be nearly identical to Illumina's Verifi test in terms of the method it uses and the disorders for which it screens. "As the technology improves, that may change," Goldberg said, adding that the test could be expanded to screen for other disorders in the future.

Goldberg said that Counsyl would begin offering its in-house NIPT this year. One facet that sets it apart from other NIPT providers is that Counsyl reports a positive predictive value for each individual test it runs, Goldberg said.

Counsyl has included PPV in its reports from tests it orders from Illumina since February and will continue to do so for its own test, Goldberg said. He noted that PPV is a critical component of noninvasive prenatal tests because it takes into consideration not only the test's sensitivity and specificity, but also the individual patient's a priori risk factors, adding a bit of customization.

"Most [NIPTs] have close to 99 percent sensitivity for Down syndrome, but that doesn't really correlate to the individual patient's risk when they get back a positive result," Goldberg said. For instance, a positive result on an NIPT for a woman in her 20s may only correspond to a PPV of around 30 percent, Goldberg said.

Currently, few if any laboratories report PPV, but the American College of Obstetrics and Gynecology and Society for Maternal-Fetal Medicine recently recommended that labs do so. In their joint statement the organizations noted that the most common ways for labs to report NIPT results — either as a binary positive or negative, or reporting the chance of aneuploidy at greater than 99 percent or 1 in 10,000 for either high or low risk — are not as useful to obstetric providers and patients as a positive predictive value.

"People confuse sensitivity with PPV," Goldberg said, adding that "the initial marketing of NIPT led some to think of it as closer to a diagnostic test. But, it's really still a screening test."

Goldberg said that including PPV in the test result will help put the test into context, and will be particularly important as NIPT becomes more widely available to all women, and not just those at high risk. In their statement, ACOG and SMFM also said that NIPT should not be used to screen the general population, but Goldberg said that nevertheless more women at average risk are requesting the test and there is "fairly robust data available in the literature suggesting it is as effective in the average-risk population as in the high-risk population."

Over the last year, a number of studies showing that NIPT is comparable to standard first trimester screening for average-risk women have been presented at meetings and published in journals

Counsyl's NIPT will also help it further carve out a niche within the reproductive health market. Goldberg said that the market for NIPT and carrier screening overlaps. "The market segments are related in terms of offering tests for different stages in a woman's or a couple's life," he said. "And we're seeing that many providers prefer to use one lab" for carrier screening and NIPT.

Good Start Genetics is also developing a suite of tests for the reproductive health market. Initially launching an NGS-based carrier screening test in 2012, it now also has plans to launch NIPT and preimplantation genetic screening tests.

Counsyl initially began offering NGS-based expanded carrier screening as a reflex test to its standard genotyping test in 2013. The NGS version screens for the same disorders as the genotyping test, but assesses over 10,000 variants in those disorders, versus just 400 in the genotyping test.

The company is now in the midst of transitioning to make the NGS version its primary test. Goldberg said that for now it will continue to offer the genotyping test to customers who prefer it, but added that the two tests are now priced the same — around $349 for patients who are underinsured or have no insurance. For patients with insurance, the price varies depending on the specific plan, Goldberg said. The company is in network for most major providers, he said, and patients can determine the specific coverage policy and price on Counsyl's website.

The NGS carrier screening test now assesses just over 100 disorders with a two-week turnaround time, Goldberg said, and clinicians can customize their orders — choosing to screen for all disorders or just some.

Goldberg said that some 30 percent to 40 percent of the screening market is expanded screening, and that number is continuing to grow as physician demand increases.

Earlier this year, the American College of Medical Genetics and Genomics, the American College of Obstetricians and Gynecologists, the Maternal Society for Maternal-Fetal Medicine, the National Society for Genetic Counselors, and the Perinatal Quality Foundation issued a joint statement on the use of expanded carrier screening tests. While the statement stopped short of endorsing such tests, it was a first step in that direction and sought to provide clinicians and laboratories at least a bit of guidance on such tests, and their benefits and risks.

Counsyl also recently entered the hereditary cancer market. Last year, it launched a screening test for the BRCA1 and BRCA2 genes, and recently began a "soft launch" of a 22-gene hereditary cancer panel, with a full commercial launch planned for August, Goldberg said. Turnaround time for that test is about two weeks.

Goldberg said the hereditary cancer panel is essentially a continuum of its other services. "The primary customers that we're seeing are the same providers that are using our other tests," he said.

Similar to carrier screening and NIPT, evidence is converging that broader screening for hereditary cancer may be useful, Goldberg said. In addition, the ACOG Committee on Genetics recently published an opinion on assessing risk for hereditary cancer syndromes in Obstetrics and Gynecology.

While ACOG does not specifically endorse hereditary cancer panel testing, it does say that if an initial family history assessment suggests a risk of hereditary cancer, the patient should be referred for genetic counseling and potentially genetic testing.

"We feel that the panel provides much better detection" than just BRCA1 and BRCA2 testing, Goldberg said.

For instance, data presented by genetic testing company InVitae last year found that out of about a 1,000-patient cohort, 9 percent carried a BRCA1 or BRCA2 variant and 4 percent had a pathogenic variant in another cancer risk gene. In addition, a change in clinical management was indicated for 70 percent of patients with a non-BRCA risk variant — highlighting the importance of screening for such variants.

Goldberg said that it was still too early to say what percentage of Counsyl's patients would benefit from the expanded panel, but expected it to be on par with findings from other labs. As with other labs, the main challenge to screening for genes other than BRCA1 and 2 is that the test will yield a greater number of variants of unknown significance. Goldberg said that Counsyl has a large curation team that will seek to better understand these variants. The firm is also offering ordering physicians the option to either receive those VUS results or not.

In the future, Goldberg said that Counsyl will continue to expand its carrier screening test to include new disorders and said that the firm also plans to broaden its position in the cancer market. "There is the potential to increase the number of panels," Goldberg said, "and the whole area of liquid biopsy is exciting and something we're looking at," he said.