By Monica Heger
This story was originally published Oct. 17.
Sequenom said this week that it has launched its noninvasive lab-developed sequencing-based test for Down syndrome in 20 US metropolitan areas and has published a clinical validation study for the test in the journal Genetics in Medicine.
In the study, the Sequenom team demonstrated that the maternal plasma sequencing test, called MaterniT21, has 99.1 percent sensitivity and 99.9 percent specificity. Nearly 1,700 women from 27 sites around the world participated in the study, including 212 carrying fetuses positive for trisomy 21 and 1,484 controls. Around 100 cases were women in the first trimester at 10 weeks or later and 100 cases were women in the second trimester, up to 22 weeks.
The test initially identified 209 of the 212 cases of Down syndrome, with three false positives and three false negatives. After adjustments for GC content that are included in the commercial version of MaterniT21, the test correctly identified 210 of the 212 samples, with one false positive and two false negatives.
The company estimates that the false-positive rate for the test is 0.2 percent, compared to around 5 percent for currently available invasive screening methods.
The LDT has gone through the full range of "feasibility, optimization, verification, and validation" studies and is "available as of today in 20 major metropolitan regions across the United States when ordered by a physician," Sequenom CEO Harry Hixson said during a conference call to discuss the launch and results of the study.
As Sequenom previously stated, it will launch the test on the Illumina HiSeq, multiplexing four samples. The test will be run in Sequenom's CLIA-certified and CAP-accredited laboratory in San Diego. Additionally, Paul Maier, Sequenom's chief financial officer, said during the call that the company is "finalizing a CLIA lab in North Carolina, which should be operational by next year," that will provide additional capacity to run the test. The company also has a CLIA lab in Grand Rapids, Mich, but is not running its MaterniT21 tests out of that lab.
Right now, the company has a capacity of 100,000 patient samples per year using a 4-plex protocol and will have a turnaround time of eight to 10 business days. The test will be available initially in 20 metropolitan areas: Seattle, San Francisco, Los Angeles, San Diego, Phoenix, Denver/Salt Lake City, St. Louis, Dallas, Houston, Chicago, Indianapolis, Detroit, Pittsburgh, Nashville, Atlanta, Orlando, Charlotte, Baltimore, Philadelphia, and Boston.
The company has also submitted a licensing application for New York.
These cities represent around 3,000 maternal fetal medicine specialists and 2,000 OB/GYN offices, said Maier. Additionally, the company plans to expand to cover another 2,500 OB/GYN offices as the test develops.
Sequenom will initially offer the test as an out-of-network provider, said Maier. While the company is currently negotiating with payors about reimbursement, he said he expects insured patients to pay no more than $235 out of pocket. For uninsured patients, the test will cost around $1,900, he said.
For insured patients, the payor will be billed at the list price, and any outstanding amounts will be pursued from the payor, not the patient, on appeal, Maier said.
The test must be ordered by a physician, and results will be delivered directly to the physician, not the patient. Ron Lindsay, executive vice president of research and development said that in the case of a positive test, "it will be up to the physician and patient how to proceed," but at least initially, an amniocentesis or chorionic villus sampling will be ordered to confirm the result.
Conversely, if the result is negative, "we believe that with the high specificity and sensitivity of the test, the physician and patient may decide that the information is sufficient to make a risk assessment of what they wish to do, and potentially no further testing will be required," he said during the call.
The test will be aimed at high-risk pregnancies, of which there are around 750,000 annually in the US, as determined by the mother's age; an abnormal ultrasound or serum test; or a family history of trisomy 21. Eventually, the company expects the test to be effective on low-risk pregnancies and to diagnose trisomy 18 and 13, as well.
During the call, the company said that it is still on track to file a pre-market application with the US Food and Drug Administration to classify the test as an in vitro diagnostic in late 2012 or early 2013.
In response to an analyst question about whether the company is concerned that the FDA might look to regulate LDTs more closely, Lindsay said that because the company has "gone way beyond what is required by CLIA" for launching an LDT, the "general sense" is that the FDA would not move to restrict the MaterniT21 test.
Company officials have said previously that the FDA has not raised any concerns regarding the launch of the test as an LDT.
The clinical validation study was coordinated by the Woman and Infants Hospital in Providence, RI. Samples were collected from 27 different sites in the US, Canada, Europe, South America, and Australia. All pregnancies were high-risk pregnancies, and about half of the trisomy 21 cases were in the first trimester and half in the second trimester.
All the women were diagnosed by other validated means as well — typically either amniocentesis or CVS — but the results were blinded.
The Sequenom team performed the sequencing-based test in its San Diego CLIA lab using the same protocol of its 480-sample "locked-assay" test, published last year in the American Journal of Obstetrics and Gynecology, except that it used the HiSeq instead of the Genome Analyzer.
The researchers also incorporated additional bioinformatics analyses to correct for the GC bias inherent in Illumina sequencing, which is particularly problematic in maternal plasma sequencing, said Lindsay.
That change increased the test's sensitivity from 98.6 percent to 99.1 percent and its specificity from 98.9 percent to 99.8 percent. Additionally, the company was able to lower its "no result" rate from previous studies, where it was around 6.5 percent, to 0.8 percent, due to the fact that the team acquired two 10-ml blood draws from each patient instead of just one.
"These results reflect what we'll use in commercial practice," Lindsay said.
Additionally, said Lindsay, because of the supply agreement the company recently struck up with Illumina, it will have access to improved reagents, which it will incorporate as they become validated. For the Genetics in Medicine study, researchers used Illumina's version 1 chemistry. However, the version 3 chemistry should have a lower GC bias, which should further improve results, Lindsay said.
The University of California, Los Angeles, conducted an independent analysis on a subset of 605 samples, demonstrating high correlation between the two sites.
While the recent study focuses on identifying trisomy 21, Lindsay said that during the study a number of cases of trisomy 13 and 18 were also detected, and the results of that analysis would be included in a separate paper.
He said that while the MaterniT21 test has the capability to detect trisomy 13 and 18, because they are present in such a low percentage of the population, the researchers "haven't had sufficient samples to a statistically powered study."
However, "we're pretty confident that trisomy 13 and 18 will be detected," he said. If so, those results will be reported to the physician with the caveat that the detection cannot be validated.
While Sequenom is the first to launch a sequencing-based trisomy 21 test, the company will likely soon face competition from Verinata Health, which has said it will launch a sequencing-based test for Down syndrome either in the fourth quarter of this year or early next year.
Verinata also recently struck up a supply agreement with Illumina and has licensed a patent issued to Stanford University's Stephen Quake for the use of next-generation sequencing to diagnose fetal aneuploidies (CSN 9/7/2011).
However, Sequenom believes its patents, licensed from collaborator Dennis Lo of the Chinese University of Hong Kong, cover any sequencing-based trisomy 21 test, and Lindsay has previously said that if Verinata launches its test that it would be infringing on its patents.
Furthermore, Sequenom has already licensed its technology to would-be competitor GATC Biotech subsidiary LifeCodexx, which was planning to launch a sequencing-based test in Europe (CSN 8/17/2011). At the time, Sequenom said that the outlicense agreement demonstrates the validity of its patents.
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