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Following Clinical Trial, Sequoia Genetics Receives CE Mark for NGS-based Newborn Screening Dx

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Sequoia Genetics has received the European CE mark for its VariFind Neonatal assay for screening for cystic fibrosis and galactosemia in newborns. The assay runs on Life Technologies' Ion Torrent PGM and is approved for in vitro diagnostics in the European Economic Area.

The Russian molecular genetics company completed a clinical trial of its test in three European labs — the Institute of Molecular Pathology and Immunology of the University of Porto, Stab Vida in Portugal, and the Centre for Genomic Research at the University of Liverpool.

The firm originally developed the test to analyze cystic fibrosis, galactosemia, and phenylketonuria.

According to Sequoia CEO Alexander Pavlov, the test still assesses variants in the PAH gene for phenylketonuria, but in order to "reduce the time and complexity of certification," the company decided to exclude it from the Europe-oriented version of the assay. In Russia, the firm analyzes and reports back pathogenic variants for all three disorders. "Final results [for the version offered in Europe] do not include annotated variants from the PAH gene," Pavlov said. Although, clinicians could theoretically analyze the raw sequence data themselves to obtain information about phenylketonuria.

Screening for phenylketonuria will be included in the company's "next extended panel for neonatal diagnostics," he added.

The test targets 427 variants in the three genes, including 75 variants in the PAH gene for phenylketonuria, 318 variants in the CFTR gene, and 35 variants in the gene for galactosemia.

Illumina also recently launched an assay for cystic fibrosis that was cleared by the US Food and Drug Administration. Its screening assay assesses 139 pathogenic variants in the CFTR gene. However, it also has an FDA-cleared diagnostic assay that analyzes all the exons and exon/intron boundaries of the CFTR gene.

Pavlov said that Sequoia's screening test is validated not just for specific pathogenic variants in the CFTR gene, but also genomic regions, allowing the company to add new pathogenic mutations to its database as information becomes available.

"This feature is very important for highly genetically heterogeneous populations such as European, Russian, Brazilian, or African ones," he said.

In clinical trials of the test, the company demonstrated that it had an overall analytical sensitivity and specificity of 99.3 percent and 91.6 percent, respectively. Additionally, it had a diagnostic sensitivity and specificity of 99.6 percent and 100 percent, respectively. Pavlov said the test's analytical performance is "up to 47.7 percent higher than the performance of current PCR-based assays."

Pavlov said the company will make the test available both by partnering with sequencing service providers and also marketing directly to hospitals in Europe. He said some of the reference labs the company worked with during its clinical trial are already able to provide the test, and that the company is in discussions with the European CF Society about incorporating the assay in the newborn screening program.

Additionally, one region in Russia has been assessing the efficiency of incorporating the test in its screening protocol. "We hope to complete all feasibility studies in Russia by the end of this year, which will potentially make this NGS-based assay the first routinely used in clinics," he said.

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