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Dutch Group Adapts Non-Invasive Prenatal Trisomy Sequencing for SOLiD; Plans Clinical Use across Netherlands

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Researchers from Radboud University Nijmegen Medical Center have published a method of non-invasive prenatal diagnosis using massively parallel sequencing-by-ligation on the Life Technologies SOLiD 4 platform.

The team is now trying to validate the technique with the aim of implementing it as a screening test available across the Netherlands, though this will likely not be achieved for several years, according to Joris Veltman, an advisor to the researchers and a colleague at Nijmegen's Department of Human Genetics.

In a paper published online this month in the journal Expert Opinion on Biological Therapy, the group, led by Brigitte Faas, showed that fetal aneuploidies, including trisomies 21, 18 and 13, could be reliably detected in maternal plasma using a multiplex sequencing approach on the SOLiD system.

In their report, the authors wrote that almost all previous studies of non-invasive prenatal aneuploidy sequencing have used sequencing-by-synthesis methods on the Illumina GA and HiSeq platforms. Indeed, all the commercial efforts to develop sequencing-based trisomy tests — including those underway at Sequenom, Ariosa Diagnostics, Verinata, and Natera — are using the Illumina platform.

The Nijmegen researchers wrote that they routinely use ligation sequencing on the SOLiD 4 for postnatal diagnostics and in research settings, so they wanted to establish whether they could perform prenatal diagnosis using circulating cell-free fetal DNA methods reported by other groups on a ligation platform with comparable and robust results.

In the study, the Dutch group used a system of scoring samples initially reported by a group led by Dennis Lo of the Chinese University of Hong Kong, published in the Proceedings of the National Academy of Sciences in 2008.

Lo licensed his team's method for non-invasive prenatal diagnosis to Sequenom, which has recently sued Ariosa, Verinata, and Natera for infringing the patent at the heart of its MaterniT21 test (CSN 1/25/2012). Clinical Sequencing News could not reach Faas by publication time for comment on how the Nijmegen team plans to negotiate any potential legal issues.

In their study using the SOLiD, the Nijmegen researchers evaluated samples from 52 pregnant women and reported they were able to sequence up to 16 samples simultaneously and to calculate "Z-scores" according to Lo's team's algorithms to indicate the presence of fetal aneuploidies. The group reported it could predict all aneuploidies in the samples, including trisomies 13, 18, and 21, with no false positive or negative results.

The authors wrote that the results showed the platform could be applied "for the robust and reproducible detection of fetal aneuploidies with ccffDNA from plasma of pregnant women."

Moreover, the group suggested that use of the SOLiD system may have overcome some weak points of the diagnosis technique when applied to sequencing-by-synthesis methods.

The authors wrote that while previous research has suggested that separate algorithms using GC-correction are necessary for calculating Z-scores to diagnose trisomy 13 and trisomy 18, in its study the Nijmegen team was able to correctly predict aneuploidies in all cases using an un-GC-corrected algorithm. This result may have been biased, however, by the relatively small sample size, the researchers wrote. Of the 52 patient samples, only two represented trisomy 13 and only four showed trisomy 18.

The team also reported that to be comparable to sequencing-by-synthesis methods, the ligation sequencing method would have to be improved to a "threefold higher multiplexing sequencing rate" than presented in the study to reduce costs.

According to the paper, the group is currently working on studies along such lines.

Though Veltman was not directly involved in the project, he said he was connected to the work, and is mentioned as an advisor in the paper. He told Clinical Sequencing News in an e-mail that the team is "trying to move this work from the technological validation in one laboratory to the clinical validation and implementation as a national screening test offered to all pregnant women by different laboratories in the Netherlands."

This will require not only validating the method, but also efforts to establish guidelines and provide evidence to support reimbursement for the test from insurance companies, according to Veltman.

"In other words, technologically it may be feasible and the advantages of this test, because of its noninvasiveness nature, are clear, but practical implementation is still quite some years down the line," he said.

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