Sequenom, Cypher Genomics partner for NIPT

The companies will take advantage of Cypher's Mantis technology for analysis of sub-chromosomal variants in maternal blood

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SAN DIEGO—Genome informatics company Cypher Genomics Inc. and Sequenom Inc. have begun a development agreement to generate next-generation noninvasive prenatal tests (NIPT). Sequenom will apply Mantis, Cypher's genome interpretation technology, to advance the analysis of clinically relevant fetal sub-chromosomal variants detected in maternal blood. Though they are often not detected until after birth, these variants make up more than 50 percent of rare chromosomal abnormalities beyond the more common aneuploidies and are linked to significant risks of morbidity and mortality.
Dr. Dirk van den Boom, chief scientific and strategy officer of Sequenom, noted that, "In our continued effort to advance pregnancy care, next-generation NIPT offerings will expand the opportunity for physicians to provide parents with more comprehensive information to improve pediatric outcomes. We have been impressed with the performance of Cypher's industry-leading Mantis technology in our research validation studies, and we look forward to advancing our collaboration with Cypher Genomics as we develop a next-generation NIPT offering and expand into new areas outside of prenatal testing.”
While sequencing-based NIPT generally focus on whole chromosome events such as aneuploidies or trisomies, sub-chromosomal structural variations—such as microdeletions, microduplications or copy-number variations (CNV), which may occur de novo—represent a larger proportion of clinically relevant abnormalities, though they are harder to detect and classify. The physical boundaries of CNV associated with similar diseases can vary widely, which makes it difficult to accurately classify the pathogenicity of the variations for use in NIPT. The Mantis technology offers a solution to that challenge.
"We are excited to announce this development agreement with Sequenom, the pioneer of noninvasive prenatal testing," said Adam Simpson, president and chief operating officer of Cypher Genomics. "We have been working closely with Sequenom to validate our automated Mantis technology to classify clinically relevant sub-chromosomal genomic structural variations, such as copy-number variations, in circulating fetal DNA from maternal blood samples, which may have applications in the development of a new, more comprehensive NIPT offering."
This agreement is one of several steps Sequenom has taken lately to expand its footprint in the field of NIPT. In October 2014, the company announced that it had purchased NIPT intellectual property from Isis Innovation Ltd., the technology transfer company of the University of Oxford, for $14.55 million. That sum includes $3.2 million as the final royalty payment to Isis Innovation under a prior agreement as well as the waiver of $2.1 million in paid legal fees that Isis owed to Sequenom, with additional downstream payments contingent on revenues surpassing certain thresholds. Per the agreement, Sequenom is now the owner of global intellectual property for noninvasive prenatal genetic diagnostic testing on paternally inherited fetal nucleic acids derived from maternal plasma or serum. The company previously had exclusive rights to the intellectual property under a licensing agreement with Isis Innovation that began in 2005; under this purchase agreement, Isis has rights in certain fields of use.

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