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UPDATE: Sequenom's Shares Soar on Study Results Publication

This article has been updated to include additional information from the journal article.

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Shares of Sequenom jumped as much as 15 percent in Thursday trade after the firm published results on its non-invasive fetal trisomy test in the online section of the American Journal of Obstetrics and Gynecology website.

Sequenom said the assay, which is based on massively parallel shotgun sequencing, was evaluated on a set of 480 plasma samples from pregnant women at high risk for fetal chromosomal aneuploidy. It said that using 449 samples, all 39 T21 samples were correctly identified, while one of the 410 euploid samples was misclassified as T21.

Sequenom said the overall classification showed 100 percent sensitivity and 99.7 percent specificity.

A total of 31 samples were removed due to insufficient quantity, breakage, or failing pre-specified quality-control criteria, the firm said.

"Compared to previously published studies, [three] important modifications were made to the sequencing protocol," corresponding author Dirk van den Boom, senior vice president of research and development for Sequenom, and co-authors wrote, explaining that the current study relied on custom purified enzymes for library generation, the latest Illumina GAIIx sequencing biochemistry and analysis tools, and the use of indexing primers during the amplification of DNA libraries to facilitate multiplexing of reactions.

Participants in the study had been classified as being at increased risk of Down syndrome pregnancies based on factors such as maternal age and family history.

The blood samples tested were collected prospectively before and stored with an independent firm, researchers explained, and the study was specifically designed to include at least 40 samples that were positive for trisomy 21 so sufficient data would be available for their statistical analyses.

The researchers processed plasma samples in five different batches, each containing 96 samples. The DNA extraction to sequencing steps took about 10 days per batch, they reported, and batches were processed in parallel with one another.

Although multiplexing was used, they noted, 10 samples were found to have low percentages of fetal DNA and were subsequently re-sequenced individually.

Given their findings so far, those involved in the study argue that the approach should be tested in an even broader clinical setting.

"Extending the scope of previous reports, this study demonstrates that plasma DNA sequencing is a viable method for non-invasive detection of fetal trisomy 21 and warrants clinical validation in a larger multi-center study," they wrote. "If the current results are confirmed in a larger multi-center trial, this method could have a substantial impact on future clinical practice."

The Sequenom Center for Molecular Medicine, Sequenom's CLIA-certified lab, initiated its pivotal clinical validation study of the SensiGene T21 Laboratory Developed Test in late December 2010. This validation study is designed to evaluate the clinical performance of the test for detecting an overabundance of chromosome 21 in maternal blood. Company officials said in September 2010 that the firm would develop the test to run on Illumina's HiSeq 2000 next-generation sequencing platform.

In Thursday trade on the Nasdaq, shares of Sequenom climbed as much as 15 percent to $7.74, before puling back to 7.29 in afternoon trade.

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