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Swedish Firm Developing DNA Sequencing-Based Diagnostics Using Proprietary Sample Prep Technology


NEW YORK (GenomeWeb) – Swedish diagnostic company Devyser recently launched two next-generation sequencing-based assays that it expects will have CE marking for in vitro diagnostics in Europe by the end of the summer.

The tests, one for cystic fibrosis and one that analyzes the BRCA1 and BRCA2 genes, are the company's first entrants into the clinical NGS space. Previously, it had been developing molecular diagnostics based on PCR and capillary electrophoresis sequencing and launched a number of CE-IVD products using that technology. Now, however, it plans to develop NGS-based diagnostics in the fields of reproductive health, oncology, and genetic disease, Ulf Klangby, CEO of Devyser, told GenomeWeb.

Klangby founded Devyser in 2004, along with Anders Hedrum, head of R&D at Devyser, and Dan Hauzenberger, who chairs the company's medical advisory board and is medical director of transplantation immunology at the Karolinska Hospital in Stockholm. The three founders all previously worked at Sangtec Molecular Diagnostics, which has since been acquired by Cepheid.

Sangtec focused on infectious diseases, and Klangby said that the three had been developing PCR-based infectious disease molecular diagnostics. But they had ideas for developing rapid noninvasive prenatal diagnostics based on multiplex PCR, so they left Sangtec and founded Devyser.

The company, which now has 25 employees, is privately funded by both the founders and business angels, Klangby said.

The first product was a rapid prenatal aneuploidy diagnostic, Klangby said. The company now has four different prenatal diagnostic tests that analyze various chromosomal aneuploidies and boast turnaround times of five hours using quantitative fluorescence-PCR, which analyzes microsatellite sequences to determine chromosomal aneuploidy. The company describes the technology in a white paper on its website.

Also within the reproductive health space, the firm offers tests that analyze pregnancy loss and infertility, and tests for cystic fibrosis, hereditary hemochromatosis, uniparental disomy, thrombophilia, APOE genotyping, and a multiplexed PCR kit that analyzes eight genetic risk factors for cardiovascular disease.

"For the first couple of years, we focused on developing niche products," he said. But a few years ago, customers started expressing both interest in and frustration with NGS technology. "They were frustrated with the tedious protocols," he said, "so we started to look at more rapid, easier protocols for NGS library prep."

The company was able to apply its experience with multiplexed PCR and QF-PCR technology to the front end of sequencing workflows in order to streamline the protocols, he said.

Essentially, in order to use the technology for diagnostic purposes, it would be important to make it simple, reproducible, and less prone to user-generated errors, he said. One important facet was to be able to perform the sample prep steps in a single tube. Many research-based library prep protocols "require that you split primers into several different reactions," Klangby said. "But in our minds, that was not appropriate for routine diagnostics." Instead, the firm developed technology that could perform multiplexing in a single tube.

Klangby said the company has filed a patent application on the method, so he did not disclose details, but he said that it uses "hundreds of overlapping primers serially in a single tube to select amplicons that should be amplified."

The BRCA test and the CFTR test will be amenable to both Illumina's MiSeq and Thermo Fisher Scientific's Ion Torrent PGM and will be CE-IVD marked first on the MiSeq, followed by the PGM. Klangby said that Devyser validated the assays on Illumina's and Thermo Fisher's open platforms rather than their CE-marked systems because those are the platforms its customers operate.

The BRCA test sequences all BRCA1 and BRCA2 exons along with exon/intron junctions and the promoter regions. The cystic fibrosis assay also covers all exons of the CFTR gene, the exon/intron junctions, and promoters, but it also analyzes some known deep intronic sequences and structural deletions, a known variants within intron 9, and a specific TG repeat number.

Later this year, Devyser plans to launch two additional hereditary cancer gene panels, one that looks at genes involved in homologous recombination and another for hereditary nonpolyposis colorectal cancer, Klangby said. It also plans to launch additional NGS-based products in the reproductive health and hereditary disease spaces next year.

Devyser's primary customers are routine diagnostic laboratories, Klangby said, particularly laboratories that are just starting to use NGS routinely. The company currently ships its products to between 45 and 50 countries, the vast majority of which are in Europe, but it also has customers in Southeast Asia.

Klangby said that Devyser tries to distinguish itself from the competition by its focus on developing products that meet the needs of diagnostic laboratories. "Everything we do is done in close collaboration with the end user — the routine diagnostic lab," he said. Thus far, while there are a lot of researchers and companies focused on NGS technology, it is still in the early stages of moving from research labs to diagnostic labs, "and the requirements of routine diagnostics are very different," he said.

Devyser also plans to enter the US market, although Klangby did not have a timeline. When it does, however, he said the company would submit its BRCA and CFTR tests to the US Food and Drug Administration for premarket approval.

In addition, he said, the company plans to publish results of the validation studies of its assays in peer reviewed journals later this year.