NEW YORK – Expansion plans are underway at Samplix as the Danish biotechnology firm rolls out its initial sequencing sample preparation offering. This week the firm introduced its Xdrop products for PCR-free target enrichment, claiming its approach can enrich genomic regions of around 100 kilobases from just a nanogram of genomic DNA. The company believes that Xdrop will find adopters in academia and clinical research, although diagnostics is on its radar.
"I can see the technology being used in more clinical applications, for instance, by pharmaceutical companies in clinical trials, and there will be diagnostic applications eventually, I have no doubt," said CEO Lars Kongsbak.
Kongsbak took the helm of Samplix, which is based in Herlev, a suburb of Copenhagen, in 2017, after leading expression analysis products firm Exiqon for 14 years until its acquisition by Qiagen.
When he joined Samplix, the six-year-old company still employed just a handful of people. Today, 30 work there as it scales up to support the launch of Xdrop, and by the end of next year, Kongsbak expects Samplix to employ around 60 people and have a US office in California.
"The new hires are primarily in sales and marketing, in our commercial organization," said Kongsbak. Some are former Exiqon colleagues, such as Hendrik Pfundheller, vice president of commercial operations, and Peter Mouritzen, vice president of application and market development.
"It's almost like getting together again," said Kongsbak. "Obviously, we had to team up with people with new competencies as well," he added. "We have managed to attract people from all over the world and we have recruited people from many competitors in the field and they have relocated to Denmark in that process."
According to Kongsbak, Samplix now has about 20 people involved in product development, a major focus for the company, and plans to "expand dramatically on the commercial side within the coming year," including adding an office in Silicon Valley.
"We will be present in the US with a substantial size as well," noted Kongsbak. "In this business, you need to be in the US. If you are not, then you are not a part of the game."
Xdrop's origins are thoroughly Danish, though, and Samplix's core technology has its roots in a team of inventors that previously worked at BioGasol and Estibio, Copenhagen-area firms involved in the manufacture of bioethanol. Marie Mikkelsen, who helped develop the technology while at those firms, co-founded Samplix in 2013 and serves as its CTO.
The company's approach relies on microfluidics to partition millions of DNA molecules into droplets so they can subsequently be sequenced using a variety of instruments. Customers can use Xdrop to isolate long fragments from small amounts of input DNA for which only a small sequence is known.
"It's really a high-quality, high-fidelity way to do enrichment of targeted long fragments for DNA sequencing," noted Kongsbak. While Xdrop might complement long-read sequencing applications run on Pacific Biosciences and Oxford Nanopore instruments, Kongsbak said the system works "just as well" for Illumina instruments. "It doesn't have to be a long-read sequencing instrument," he said. Illumina users might use Samplix to enrich for rare or low-abundance targets or in cases where they couldn't get sufficient sequencing depth without enrichment, he noted.
Samplix's sample preparation process involves first designing primers using the company's design tool, followed by amplifying a region of about 150 base pairs within or adjacent to the target region, which can stretch in size from 15 kb to 100 kb. The amplified product is then partitioned into millions of droplets using microfluidics. Primers then anneal and amplify a small PCR-product for detection of positive droplets containing the target region. Only droplets containing the region of interest are fluorescent, according to the firm.
These are sorted using flow cytometry and the droplets are broken, releasing the target DNA, which is then mixed with proprietary reagents for the following amplification step. The DNA target molecules are then partitioned into thousands of independent single-emulsion droplets and amplified using droplet-based multiple displacement amplification (dMDA). The amplified target DNA is then released from the droplets and can be analyzed by next-generation sequencing instruments, as well as other tools, such as microarrays.
Samplix is able to conduct these protocols using microfluidics cartridges. Its new offering includes the Xdrop instrument for cartridge control, which is priced at €33,000 ($36,000); different microfluidics cartridges, and consumables that support the use of the cartridges. The turnaround time for the entire process is around 24 hours, Kongsbak said, and costs roughly €140 per sample. Samplix cartridges can support the processing of eight samples at a time.
"What we do is sample preparation," said Kongsbak. "We isolate long fragments, maintaining the integrity of targets," he said. "If you have a rare target, it could be a mutation or other variants in your soup of DNA, we can do that."
The Xdrop system is now shipping, but the company has already placed it with some first adopters. One of those, Adam Ameur, a bioinformatician at the Uppsala Genome Center at Uppsala University in Sweden, previously discussed his use of the system at the Advances in Genome Biology and Technology meeting in Orlando, Florida, last year.
Ameur said this week that the Uppsala Genome Center has been a long-term PacBio sequencing site and has had a lot of interest in trying to enrich long DNA fragments, explaining its interest in trying Samplix's Xdrop system. He said that the new system "fills a niche that is not possible to [fill] with other technologies."
For example, he and fellow colleagues have been looking at virus integration sites in the genome. He noted that by using just a small piece of sequence — the integrated virus, for instance — the technology can support long reads stretching into the rest of the genome, so the researchers can see where the integration sites are located and how the genome is organized.
While target enrichment offerings have almost been around as long as next-generation sequencing itself, with a bevy of products to try, Ameur said there exists a market for Samplix's technology.
"There is still room for innovation in long-read sequencing technology," he said. "The market is quite mature when it comes to short reads and target enrichment, because we have good methods, either using PCR or hybridization-based approaches, but the problem with long reads is that the conventional PCR methods are not perfect, at least if you want to look at targets that are longer than 10 kilobases or something."
Ameur said he hopes Samplix will continue to innovate on its platform, such as by permitting enrichment of specific transcripts for RNA sequencing, something that Kongsbak acknowledged the firm is working on. Ameur is also interested in applying the technology in single-cell experiments.
"If you are interested in a specific gene, you could use a single-cell barcode and perform a kind of enrichment to get the isoforms for specific targets at single-cell resolution," said Ameur. "That would be really interesting."
Kongsbak noted that the company has other product development programs in place, including those for enrichment for single cells.
"This is similar to any other tool provider, in that you have the technology, you have the platform ready, and you have a limited menu," he said. "What we want to do right now is to expand the menu, so we will invest significantly into our applications and work with many different parties out there on applications where there may be a commercial opportunity going forward," he said. "The essence here is that we need to expand the applicability of the products so that our customers will have an easier workflow, but still using the same instrument," Kongsbak added.
To support its expansion and product development, Samplix will also seek additional investment from venture capital firms, he said. The European Commission awarded the company €1.9 million ($2.1 million) earlier this year through its Horizon 2020 – SME Instrument program to support the development of Xdrop. In total, Kongsbak said that Samplix has raised around €10 million to date.