Flush with $23.6 million from a new Series A financing round, optical mapping company OpGen is making a fresh start, focusing on developing an instrument for identifying bacteria in clinical microbiology labs instead of providing optical mapping services, according to a company official.
“We consider this a restart of the company,” Colin Dykes, OpGen’s chief scientific officer, told In Sequence last week.
As part of the reorganization, OpGen has been phasing out its optical mapping services over the last six months, serving only existing customers. The company has yet to decide whether to provide optical mapping to the research market. A decision is expected shortly. “For commercial reasons, we are focusing on clinical [microbiology] first,” Dykes said.
A number of research groups have found OpGen’s optical maps useful at helping them assemble tricky microbial genomes.
“I have been a real supporter of the technology,” Barry Goldman, a researcher in biotechnology prospecting at Monsanto, told In Sequence last week. Over the last three years, his company has obtained optical maps for a handful of bacterial genomes that Monsanto sequenced in collaboration with academic groups.
Some of these bacteria contained several repeat regions, and the optical maps allowed the researchers to get them in the right order. In other cases, the optical map just cut down the time for sequencing the genome. “It saves a huge amount of time,” Goldman said.
In addition, he said, optical maps allow bench scientists to close gaps in a genome sequence on their own, without having to turn to a highly specialized finishing center like TIGR — now the Craig Venter Institute — the Joint Genome Institute, or Monsanto.
Earlier this month, a team of researchers led by German scientists published a paper in Public Library of Science Biology (PLoS Biol 5(9): e230 doi:10.1371/journal.pbio.0050230 ) in which they combined whole-genome amplification, 454 sequencing, and optical mapping to analyze the genomes of large sulfur bacteria from single filaments, which contain a few hundred cells.
Riding the Storm Out
A year ago, researchers from TIGR and the Advanced Center for Genome
Technology at the University of Oklahoma told GenomeWeb Daily News, In Sequence’s sister publication, that OpGen’s optical mapping services had been useful in bacterial and fungal genome sequencing projects. However, both scientists agreed that they only required optical maps for a small number of projects that could not be solved by sequencing alone, and that they could justify the high cost of such a map only in special cases.
At the time, OpGen said it charged between $5,000 and $7,000 for a bacterial optical map and between $20,000 and $50,000 for a fungal map.
Since then, the company, which was founded in 2003 to commercialize optical mapping technology developed by David Schwartz, a professor at the University of Wisconsin, has weathered some tough times. Initially, the company provided optical mapping as a service and raised a total of about $10 million, Dykes said.
Last year, OpGen changed its business plan to develop a commercial instrument but was unable to raise the necessary funding quickly enough. CEO Joe Shaw left OpGen late last year, and after running low on cash, the company had to cut its staff by two-thirds in March.
“We consider this a restart of the company.”
After “recruiting heavily” over the last two months, following the recent funding round, OpGen’s headcount is now up to approximately 20 again, more than before the layoffs, according to Dykes. The search for a new CEO is ongoing.
Following the advice of the new investors, which include CHL Medical Partners, Highland Capital Partners, and Versant Ventures, the company, which changed its name from OpGen Technologies to simply OpGen, is now focusing on developing an instrument for identifying bacteria in clinical microbiology labs.
“There is a huge unmet need in clinical microbiology currently, “ Dykes said. While a number of quick PCR-based tests screen for specific pathogens, most microbial identification methods take several days and sometimes do not come up with precise results. “The technologies currently used in the clinical micro[biology] lab are still based on culturing on differential media. It’s technology that comes from the last century,” Dykes said.
OpGen, on the other hand, promises to identify microbes within a few hours without having to culture them. The plan right now is to commercialize an instrument within two years. Most of the new funding will be spent “on taking our breadboard instrumentation that we currently use for our optical mapping service, and converting that into a robust standalone highly automated system that can be run by a technician,” Dykes said.
However, optical mapping for research projects is not completely off the table. “The company is currently addressing how to make optical mapping available to the research community,” Dykes said.