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Sequenom, Collaborators Publish Study on Sequencing-Based Method to Detect Down Syndrome

NEW YORK (GenomeWeb News) – Sequenom and collaborators at the Chinese University of Hong Kong have published a study that validates the use of a sequencing-based method for noninvasive prenatal testing for Down syndrome, the company said today.
In a paper scheduled to be published in the Early Edition of the Proceedings of the National Academy of Sciences this week, the collaborators demonstrate that the method, based on massively parallel genomic sequencing, “accurately quantified maternal plasma DNA sequences for fetal Trisomy 21, or Down syndrome, based on samples taken from women in the first and second trimesters of pregnancy,” the company said.
While the approach is similar to one under development by Stephen Quake and colleagues at Stanford University that was published in October, Sequenom said that its study is the first to suggest that the approach can be effective in women who had not previously undergone invasive procedures.
Sequenom’s study used the Illumina Genome Analyzer to quantify maternal plasma DNA sequences in samples from 28 women in the first and second trimesters of pregnancy. All 14 Down syndrome fetuses and normal fetuses were correctly identified, the company said.
"This is the first study to show that this approach can be used for the detection of Down syndrome in both the first and second trimesters, based on a rigorously controlled clinical cohort in which the pregnant women with fetuses affected by Trisomy 21 and those with normal fetuses were matched in gestational age, and in which most of the studied subjects had not previously undergone an invasive procedure,” said Dennis Lo, a co-author of the study and a professor of medicine at the Chinese University of Hong Kong, in a statement.
“The latter point is important as it shows that the method would truly work in the noninvasive prenatal diagnostic scenario,” Lo added.
Lo said that the new method is likely “several years away as a commercially viable test,” but may offer “a complementary approach” to an RNA SNP allelic ratio approach that Sequenom and the university are developing for Trisomy 21 detection that is slated for launch next June.
“The two approaches have performance and cost profiles which would potentially be synergistic to one another," he said.
Sequenom has licensed the exclusive rights to the methods used in the current study from the university.
Harry Stylli, president and CEO of Sequenom, said in a statement that while the company continues to “evaluate other promising approaches” for noninvasive fetal diagnostics, “we believe massively parallel genomic sequencing is a promising approach to prenatal diagnostics that may offer a future extension to our SEQureDx prenatal diagnostics franchise.”
In addition to the IP developed at the Chinese University of Hong Kong, Sequenom also holds exclusive licenses to methods for noninvasive prenatal diagnostics developed at the University of Oxford. The company noted that because its rights to these methods are platform-independent, they provide “exclusivity (with the narrow exception in Europe for RT-PCR-based Rhesus D tests) for development and commercialization of noninvasive prenatal screens and tests on any platform and are not limited to the company's MassARRAY platform.”
This week’s study follows a paper that Sequenom and its collaborators published last week in PNAS that described a size-selection strategy to enrich for fetal DNA in maternal blood.
For that study, the researchers used Fluidigm’s Biomark system and Digital Arrays as part of a method called relative mutation dosage, or RMD, to compare the relative amounts of mutated and normal DNA sequence present in each sample.
A Sequenom official told GenomeWeb Daily News last week that other than the use of the Fluidigm products, Sequenom has exclusive rights to the technology described in that paper, and that “everything” described in the study “is proprietary, including the use of digital PCR for prenatal diagnostics."
Fluidigm today announced that it has licensed rights to IP developed at Stanford University for detecting fetal genetic characteristics in maternal plasma, including the use of digital PCR for that application.

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