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NIPD Genetics Pursues Potential of Methylation Markers for Prenatal Testing, Other Applications

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NEW YORK (GenomeWeb) – NIPD Genetics of Cyprus has been advancing research into epigenetic markers to distinguish fetal from maternal DNA, which may eventually lead to new clinical tests for prenatal screening, cancer diagnostics, and other applications. In parallel, the company has been expanding sales and applications for its current Veracity noninvasive prenatal test and plans to offer microdeletion testing next year.

Last week, company researchers and their colleagues at the Cyprus Institute of Neurology and Genetics published a study in Genetics Research in which they used methylated DNA immunoprecipitation (MeDIP) and next-generation sequencing to identify differentially methylated regions (DMRs) between fetal and maternal DNA on a genome-wide basis. Combining MeDIP with in-solution enrichment and NGS, they then confirmed a subset of these markers in another set of samples.  

The new study builds on 10 years of research experience by the institute — which spun out NIPD Genetics in 2011 — in the field of epigenetics of maternal and fetal DNA, in particular methylation analysis. In fact, in 2011, the team published a proof-of-concept study in Nature Medicine showing it could use MeDIP, in combination with real-time quantitative PCR, to detect trisomy 21in maternal blood. Following two validation studies published in Prenatal Diagnosis in 2012 and 2013, the company had originally planned to develop this strategy into a commercial noninvasive prenatal test.

However, it later decided to go with a different approach that relies on targeted sequencing of cell-free plasma DNA and determines aneuploidy and fetal fraction with great accuracy. Based on this technology, a year ago the company launched the Veracity test, which can detect fetal trisomies 21, 18, and 13 and determine fetal sex. The launch was followed by the publication of a study in Clinical Chemistry earlier this year that showed the test detected all instances of fetal trisomies and identified fetal sex correctly in all cases, while not missing any aneuploidies.

The latest publication is a continuation of the group's previous efforts to identify and validate fetal-specific DNA methylation markers, this time using next-gen sequencing instead of qPCR, a "very powerful technology" that "leads us to a higher number of markers and a much better characterization of these markers," according to Philippos Patsalis, NIPD Genetics' CEO and the senior author of the study. 

For methylation markers, "we envision a lot of applications and opportunities for diagnostics in the field of noninvasive prenatal testing as well as other related fields," such as cancer, he told GenomeWeb.

The approach may ultimately lead to tests that are simpler, faster, and less expensive than current tests, while still providing high accuracy, he added.

For their study, the researchers initially applied MeDIP-NGS to three chorionic villus sampling (CVS) specimen — representing fetal DNA — as well as to three blood samples and two plasma samples from non-pregnant women. This yielded 1,453 DNA regions that were hypermethylated in the fetal samples and hypomethylated in the maternal samples. The scientists then selected a subset of 331 regions and analyzed them in DNA from eight normal CVS samples as well as eight blood and eight plasma samples from non-pregnant women. Overall, they found significant methylation differences between the three sample types in those regions, with more pronounced differences between CVS and blood samples than between CVS and plasma samples.

Patsalis said the team continues to characterize and optimize the methylation markers it found. "Epigenetic biomarkers exhibit inherent biological and inter-individual variability and need to be thoroughly validated and tested before they can be used in clinical practice," he said, and of thousands of differentially methylated markers, "we strongly believe that very few of them may have the characteristics that enable us to put them into clinical practice."

In parallel, the researchers are constructing detailed fetal and maternal epigenetic maps, a project that is supported with €2.5 million (about $2.7 million) in grant funding from the European Research Council.

Patsalis declined to speculate when a methylation-based NIPT might be ready for clinical use, stressing that the current work is still very much at the R&D stage. "The clinical and scientific community will always look for better tests — faster, simpler, cheaper, and of course much more accurate," he said.

However, the epigenetic approach might allow NIPD Genetics to branch into areas outside of prenatal testing that it did not envision in 2011. "Back then, we thought that we would focus only on noninvasive prenatal testing. But as researchers, we're always looking to solve problems and needs of the clinical world, and the field of noninvasive testing for cancer is a major area these days," Patsalis said.

In the meantime, the company is expanding its existing business. Veracity is now sold in 12 countries, he said, and is expected to be available in more than 30 countries next year.

The firm has also expanded the Veracity test to sex chromosomal aneuploidies and has validated it for twin pregnancies. Patsalis said the company recently completed a validation study in twin pregnancies, results of which will be published in the near future. A prospective part of the study involved 200 twin pregnancies and a retrospective part included samples from 100 twin pregnancies, the latter provided by the UK's Fetal Medicine Foundation. NIPD Genetics was able to pick up all five twin pregnancies that were discordant for one of the three trisomies and did not miss any cases.

In addition, NIPD Genetics is exploring a new approach that will allow it to detect fetal microdeletion and microduplication syndromes with high accuracy. Patsalis declined to provide further details on the method at this time but said the test is expected to be available in the first quarter of 2017.

Finally, the company is working on prenatal noninvasive tests for point mutations associated with single-gene disorders and has "very good preliminary results," he said.

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