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Renamed Natera Opts for Sequencing over Arrays for Noninvasive Prenatal Dx

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By Molika Ashford

Prenatal testing company Natera recently closed a $20 million financing round that it will use to develop and commercialize a sequencing-based, non-invasive prenatal diagnostic for Down syndrome and other genetic disorders.

Natera, called Gene Security Network prior to raising the financing, had been developing a microarray-based noninvasive prenatal diagnostic but recently decided to move all of its prenatal, preimplantation, and paternity testing services to next-generation sequencing, co-founder and chief technology officer Jonathan Sheena told Clinical Sequencing News.

“With sequencing you have more flexibility,” Sheena said. “You can determine on the fly to measure with more depth on particular samples or types of samples, you can adjust assays easier, and with upcoming desktop sequencing machines, you can do things actually faster and cheaper than with arrays.”

Natera plans to use its latest funding round to support the development of its sequencing-based non-invasive prenatal diagnostic. These plans include the expansion of an ongoing clinical trial, called PreNATUS (Prenatal Non-invasive Aneuploidy Testing Using SNPs) led by Ronald Wapner at Columbia University Medical Center.

The company said it plans to begin marketing the test sometime this year, but did not provide further commercialization details.

“We're trying to provide an accurate non-invasive test that can be performed on free-floating DNA early in the pregnancy,” Sheena said. “What we are expecting … is that it's going to give parents another really viable option [beyond] current technology."

The opportunity for such a test is clear, but the company is entering a market that is growing increasingly crowded. First mover Sequenom launched its MaterniT21 sequencing-based trisomy 21 test last fall (CSN 10/19/2011), and a number of other firms, including Verinata Health, GATC Biotech subsidiary LifeCodexx in Germany, and newcomer Aria Diagnostics are looking to launch similar tests (see related story, this issue).

Sheena declined to detail the company's sequencing strategy, but said it relies on its proprietary "Parental Support" bioinformatics approach, which can identify fetal DNA via comparison to the mother's, or both parents', genomic information.

Parental Support takes "very clean measurements from mom and/or dad and combines those with data from the Human Genome Project to very accurately clean up the noisy measurements [you get] from minute amounts of DNA — whether that’s in a single cell from [in vitro fertilization preimplantation testing], or from free-floating DNA mixed up in maternal blood from normal pregnancy,” he said.

The prenatal diagnostic specifically looks at SNPs to identify aneuploidies. “Basically we are taking the same idea of Parental Support … which allows you to look at noisy data and come up with the only explanation for whether it’s trisomy or monosomy,” Sheena said.

“We’re not talking about details, but we think we'll be able to do much more over time than Sequenom [and others] can do because of the way we are approaching this problem,” he said.

Companies like Sequenom and Verinata "are taking a very quantitative approach,” he explained, “trying to look at the levels of how much [DNA] came from chromosome 21 and trying to compare against a reference genome.”

But, he said, “that [approach] has issues [because] when you get down to a low fraction of fetal DNA, the thresholds you set start to get fuzzy … Because of the way we do things, not only can we produce better results, we also can tell how confident we are in our results."

As a result, “we won’t be lulled to a false sense of security or fooled by low amounts of fetal DNA that tend to happen early in pregnancy and can happen all the time,” he said.

A lack of details on Natera's sequencing strategy leaves open the question of how the company will distinguish it's test the increasingly competitive noninvasive prenatal diagnosis space , but it's clear that it intends to stand its ground when it comes to the sector's intellectual property landscape.

Earlier this month, Natera filed a suit in the US District Court for the Northern District of California claiming that its noninvasive prenatal paternity test does not infringe a patent held by Sequenom on noninvasive prenatal diagnosis methods. The suit also claims that the patent in question — US Patent No. 6,258,540, entitled "Non-invasive prenatal diagnosis" — contains at least one invalid claim (CSN 1/11/2012).

Natera's legal move followed close on the heels of a similar suit by Aria Diagnostics, which is also developing a noninvasive prenatal test and filed a similar action against Sequenom in December. In its complaint, Aria similarly requested a declaration that its fetal aneuploidies test does not infringe the '540 patent, but unlike Natera, it did not argue any of the patent's claims were invalid (CSN 12/21/2011).

According to the suit, Aria believes that Sequenom has "misrepresented" the scope of its patent, with the goal of "deterring potential competitors from entering the market and deterring doctors and healthcare providers from using anyone other than Sequenom" (CSN 1/9/2012).

Natera officials declined to comment on the company’s suit but Sheena told CSN that the company does not believe its diagnostic infringes Sequenom's patent.


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

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