SAN FRANCISCO (GenomeWeb) – Startup Arc Bio is the latest company that aims to tackle pathogen detection via next-generation sequencing.
Although the firm is entering an increasingly crowded space, it hopes to differentiate itself by combining techniques developed at Stanford University for analyzing trace amounts of degraded DNA with informatics technologies developed at Harvard University and by Australian company Spokade.
Arc Bio is headed up by CEO Todd Dickinson, who is also CEO of Dovetail Genomics and was previously vice president of commercial operations at BioNano Genomics. Dickinson has also held multiple roles at Illumina.
Dickinson had been working with Stanford and Harvard spinouts IdentifyGenomics and Big Data Bio, respectively, both of which were subsidiaries of EdenRoc Sciences. IdentifyGenomics had been spun out of Carlos Bustamante's lab at Stanford while Big Data Bio was spun out of David Sinclair's lab at Harvard, and both Bustamante and Sinclair are now on Arc Bio's scientific advisory board.
"It became clear that the two companies would be stronger together," Dickinson said. Arc Bio, now also an EdenRoc subsidiary, has 22 full time employees and offices in Menlo Park, California and Cambridge, Massachusetts.
In addition, the firm acquired technology from Sydney, Australia-based Spokade, which had been developing software tools and databases for antimicrobial resistance detection. Dickinson noted that Spokade's technology is a "critical component to our overall NGS pipeline that we are building" and is the basis of the ArcBio's first product, Galileo AMR, a cloud-based software tool for antimicrobial resistance profiling geared toward public health researchers.
Galileo AMR analyzes genomic data generated from any sequencing platform in order to identify antimicrobial resistance markers and mobile elements. Dickinson said that he anticipates initial customers will be public health researchers who use it to understand how resistance persists and how pathogens harness mobile elements and cassettes to spread resistance.
The IdentifyGenomics technology was originally developed in Bustamante's lab at Stanford to analyze ancient DNA, and Bustamante founded IdentifyGenomics to harness it for forensics. However, Dickinson said that when IdentifyGenomics and Big Data Bio merged to form Arc Bio, the team decided to instead focus on pathogen detection and infectious disease.
"We felt that there was a huge need in this area," Dickinson said.
Dickinson said that the ultimate goal is to develop an entire pipeline based on comprehensive next-generation sequencing and bioinformatics that will be clinically deployed. The Stanford technology, called WISC for "whole-genome in-solution capture," will play a key role in helping to parse microbial DNA from a high background of human DNA.
The Stanford researchers previously described the WISC technology for analyzing ancient DNA at several conferences and in a study published in the Proceedings of the National Academy of Sciences. Specifically, they described how it enabled them to sequence remains from a 17th century burial site on the Caribbean island St. Martin of three individuals who were likely victims of the transatlantic slave trade.
WISC involves using biotinylated RNA probes to grab human DNA from a sample while leaving out environmental DNA that has contaminated the sample. Although it was originally developed to sequence ancient DNA, the team modified it for forensics purposes, spinning out IdentifyGenomics. They also applied the technology to metagenomic sequencing, but have not published work on this application.
Dickinson declined to provide details of how it is being modified for metagenomic sequencing, but said that the firm and its collaborators would eventually publish such work in a peer-reviewed journal.
In current metagenomic sequencing approaches to identify pathogens in human blood, for instance, "much of the sequencing is wasted on host DNA," Dickinson said. "But, we've found a solution to that problem." Aside from enriching for the pathogen DNA, he said the researchers have also developed technology that depletes unwanted DNA.
Over the last several years, a number of companies have sprung up to use NGS for infectious disease diagnostics and antimicrobial resistance monitoring, and each has a slightly different approach. Fry Labs, for instance, is using targeted sequencing to diagnose common infections, while CosmosID focuses on metagenomic sequencing for applications such as water testing. Meanwhile, Curetis is harnessing an antibiotic-resistance database and developing complementary sequencing technology with BGI; while Karius is developing technology to analyze cell-free pathogen DNA in patients' blood. In addition, academic groups such as the University of California, San Francisco, are developing their own solutions.
It's not yet entirely clear how Arc Bio will differentiate itself from the growing array of competitors. However, Dickinson said that "it's exciting to see that there are a lot of different companies sprouting up to tackle this problem. It underscores the importance and dramatic need for new tools and technologies." He said that there is still a lot of room in the space and that Arc Bio is developing a "number of technologies that will position us in a unique way."
In addition, Dickinson said that although a few companies currently focus on genome-wide sequencing, most current pathogen-detection solutions involve either more traditional culture-based methods, targeted assays based on qPCR, or targeted sequencing panels. "These methods are all limited in their ability," he said. "We want to leverage the agnostic, genome-wide capability of NGS pipelines."
How exactly the technologies will be commercialized is something Arc Bio is still figuring out, Dickinson said, including whether it will sell various kits for the different components or an entire platform, or whether it will offer its technology through a service model.
Aside from the public health sector, Dickinson said that Arc Bio also plans to market to private companies developing therapeutics, which he thinks would be interested in both the Galileo AMR software product Arc Bio recently launched, as well as the broader range of the firm's products. Drug developers will need access to a "high-resolution diagnostic platform that can gauge the success and failures of therapies," he said.
Dickinson added that the company plans to solidify its strategy and commercialize additional products over the coming year.