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Sequenom in Discussions with FDA on Premarket Application for Sequencing-Based Trisomy 21 Test


By Monica Heger

This story was originally posted March 9.

Sequenom is on track to launch its sequencing-based prenatal diagnostic test for trisomy 21, called SensiGene T21, as a laboratory-developed test by the end of 2011 or early 2012 and plans to file for premarket approval of the test with the US Food and Drug Administration by late 2012 or early 2013.

In a conference call to discuss the company's fourth-quarter 2010 earnings last week, officials said the firm has begun meeting with the FDA about necessary preclinical and clinical studies required to gain premarket approval.

The company also said that as part of its clinical validation study, some principal investigators are also testing the feasibility of the same sequencing approach to detect trisomy 13 and trisomy 18.

CEO Harry Hixson said that the company had its first meeting with the FDA in January. While he could not comment on specifics of the meeting, in response to an investor question, he said that "it's safe to say that [the FDA] has not raised any concerns" about the trisomy 21 test.

The company plans to launch its test on the Illumina HiSeq 2000. In response to an investor question on whether the platform itself would be subject to certain design control processes by the FDA, Hixson said that the company discussed that issue with the agency and came to an understanding of a "pathway going forward to use the HiSeq 2000 in a PMA application," but did not elaborate.

The company also provided an update to its clinical validation study for the trisomy 21 test. It is currently validating its method at its CLIA-certified and CAP-accredited laboratory in 2,000 patient samples from the Women and Infants Hospital in Rhode Island. Of the 2,000 patient samples, 200 are positive for trisomy 21, with half of those samples obtained from the first trimester of pregnancy and half from the second trimester.

The company is using the same methodology in the study that it used in its sample study of 480 patients (IS 1/4/2011), except that the sequencing is being done on the Illumina HiSeq 2000 instead of the Genome Analyzer.

As part of the clinical validation study, some principal investigators will also test the methodology for its ability to diagnose trisomy 13 and trisomy 18. However, Ron Lindsay, Sequenom's vice president of research and development, said that those trisomies are "works in progress," and that there would not be enough samples in the current clinical validation study to give the methodology statistical significance.

"The sequencing methodology should apply to trisomy 13 and 18, and we are certainly looking at that," Lindsay said. "The issue with 13 and 18, at least in the short term, is to acquire sufficient samples where you can understand the precision of the test," he said.

The company expects its clinical validation study to be completed by the second quarter of 2011, with a laboratory-developed test being offered to physicians after publication of the study in late 2011 or early 2012.

Separately, in documents filed with the SEC, Sequenom expressed some concern about the intellectual property that underlies the test. While it holds a broad patent for the noninvasive detection of fetal DNA from maternal plasma for diagnoses, the patent is not specific to sequencing-based diagnostics.

In the 10-K filing, the company wrote that while it believes that the patent "provides us substantial rights with respect to prenatal diagnostic products independent of platform and we are also the licensee of a patent application that contains claims regarding the use of [massively parallel shotgun sequencing] in prenatal diagnostics, we are also aware of other patent applications that contain the same claims and similar claims are owned or controlled by a potential competitor."

For example, Sequenom cited a patent that was recently issued to Stanford University titled "Non-invasive Fetal Genetic Screening by Digital Analysis," which includes claims for methods to detect fetal aneuploidy. Stanford's Stephen Quake, the named inventor on the patent, has co-licensed his technology to Fluidigm and Artemis Health.

Sequenom said in the filing that any potential patent dispute could hinder its ability to bring its test to market.

Sequenom's total fourth-quarter revenue grew 28 percent to $13.8 million compared to $10.8 million for the same quarter in 2009. Its research and development expenses increased from $10 million to $10.5 million from the fourth quarter in 2009 due primarily to clinical sample acquisition costs associated with the trisomy 21 program.

At the end of 2010, the company had total cash, cash equivalents, and marketable securities of $135.5 million.

Have topics you'd like to see covered by Clinical Sequencing News? Contact the editor at mheger [at] genomeweb [.] com.