Swiss bioinformatics company SmartGene has expanded its presence in the US market this week by licensing its Integrated Database Network System (IDNS) to Laboratory Corporation of America, which plans to use it to identify bacterial and fungal pathogens.
SmartGene this week also reinforced its foothold in Europe through an agreement with the Swiss Institute for Bioinformatics, which contracted the company to help develop a database on influenza viruses for the Global Initiative on Sharing Avian Influenza Data.
Both agreements are significant for the 10-year-old company, which so far “has been developing slowly and cautiously,” according to David Ellis, president of SmartGene Inc., the company’s US subsidiary, which was formed in Research Triangle Park, NC, last March.
LabCorp is SmartGene’s second US customer after a deal announced last summer with Associated Regional and University Pathologists Laboratories [BioInform 08-04-06].
Myla Lai-Goldman, executive vice president, chief scientific officer, and medical director for LabCorp, said in a statement that the updated information in IDNS creates “a helpful laboratory tool enabling more rapid and accurate identification of clinically relevant pathogens.”
In the GISAID project, meantime, SmartGene’s technology will serve as the “backbone” for a freely available database of sequence data from influenza isolates collected around the world.
Ellis said that the web-based architecture of the IDNS system makes it particularly well-suited for the multi-site project, since researchers can upload their own sequence data or access data from other sites regardless of where they are located.
Pharma Will Wait
SmartGene, located 10 miles from Lucerne in central Switzerland, has several customers in Europe, primarily academic research groups, “but we’re really quite new in North America, although the technology has been evolved and has gone through several iterations,” Ellis said.
Ellis said that SmartGene is targeting clinical labs like ARUP and LabCorp, as well as academic research centers and government epidemiology labs, for its web-based IDNS platform, which offers an integrated data-analysis workflow and reference genomic databases for a range of organisms, including bacteria, fungi, and viruses, including HIV, hepatitis C, and influenza.
Biopharma is another market that the company hopes to tackle, but that is a longer-term goal, Ellis said. “We’re confident that the technology would have those types of applications,” he said, “but we’re focused on what we need to do first. Once we see adoption in these initial markets, we’ll take it to others.”
While the firm has concentrated on microbial genomes so far, Ellis said that it is also developing modules of interest to human genetics and is currently prototyping a module for human leukocyte antigen in Europe.
Nevertheless, the company’s concentration on pathogens appears to answer an unmet need in the microbial research marketplace, where new genomes are being sequenced all the time and in-house bioinformatics teams have a hard time keeping up with vast amounts of public data.
IDNS offers an analysis interface that allows users to upload their own sequence trace files and then perform a string of tasks, such as proofreading, alignment, interpretation, and the creation of phylogenetic trees and reports, without leaving the application.
In addition, the platform provides a set of reference databases that are updated constantly with new data from GenBank that has been screened for quality using a series of proprietary algorithms.
The problem with unfiltered GenBank data, Ellis said, is that there is “no quality assurance.” Entries are often mislabeled or misidentified, and there is no mechanism in place to correct them, he said.
“We have algorithms that look at all the GenBank entries to see whether a reference is likely to be useful for the genetics of a sequence that’s been deposited,” he said. “Every time there’s a new release, it kicks off the extraction profiles, which look at every record to see what’s new or has been changed.”
“Our analysis of 300 clinical isolates illustrates that microbial identification improved with SmartGene compared with MicroSeq interrogations.”
The company’s reference databases are updated more frequently than curated reference databases, and also more likely to identify emerging pathogens and new organisms, Ellis said.
At least one customer agrees. Researchers from ARUP Labs published a paper in the December Journal of Clinical Microbiology that compared partial 16Sr RNA gene sequences in IDNS with those in Applied Biosystems’ MicroSeq sequence library.
“Our analysis of 300 clinical isolates illustrates that microbial identification improved with SmartGene compared with MicroSeq interrogations,” the authors wrote. Furthermore, IDNS provided “greater microbial diversity,” which increased the ability to accurately identify microorganisms, they noted.
“While MicroSeq potentially has higher-quality sequence data because it relies on type strains, we have demonstrated that the use of a single type strain to represent entire taxa is often inadequate,” they wrote. “The sequence heterogeneity of specific microorganisms within SmartGene is particularly valuable for identifying species, since many studies have demonstrated the existence of distinct interspecies and intraspecies variability.”
Ellis said the company expects the LabCorp and GISAID agreements to be the first of a series of high-profile deals it signs over the next six months to a year. “We hope to expand the number of contacts we have with market-leading institutions,” he said.
One particular goal is for customers to publish more studies in the scientific literature in order to increase visibility, he said.