Provides rapid genomic pathogen sequencing analysis of COVID-19 data
BioInfoExperts LLC, a bioinformatics company located at UF Innovate | Accelerate at Sid Martin Biotech, has licensed FoxSeq®, a community cloud-based platform that integrates pathogen genetics with clinical data and contact tracing efforts in near-real-time, to Ochsner Health LSU Health Sciences Center New Orleans, and the New Orleans Department of Health. The oil and gas industry also has adopted FoxSeq for genomic pathogen sequencing analysis to better understand transmission in their vulnerable employee population.
“FoxSeq enables collaboration between these institutions in near real-time. This collective network of infection control practitioners, state contact tracers, and hospital physicians is exactly the kind of modernized infrastructure that defends communities against covert and high-risk outbreaks. This dynamic system, if multiplied across under-represented geographic areas, would have a substantial national impact,” said Susanna Lamers, CEO of BioInfoExperts.
Analyzes COVID-19 contact tracing data rapidly
BioInfoExperts is improving the ability of states to respond quickly to the most important COVID-19 cases: variants of concern, vaccine breakthroughs, and the rapid identification of outbreaks. Genomic sequencing is largely routine (i.e. gathering the data) but interpreting the data is labor-intensive and expensive, resulting in a bottleneck in making the data actionable. FoxSeq remedies this because it rapidly deciphers disordered data into web-based visualizations and reports that are immediately applicable to advancing surveillance efforts.
While select areas of the country have strong bioinformatics resources, the majority of the United States is currently underperforming when it comes to genomic surveillance at scale or speed. Infection rates in every state are largely consistent; however, sequencing efforts remain discordant, with 19 states sequencing less than 5% of their COVID-19 cases, often months after samples are collected. These under-represented regions require improved infrastructure to rapidly respond to emerging infection threats.
The FoxSeq platform is supported by the NSF Small Business Innovation Research program (SBIR). SBIR projects are peer-reviewed for innovation, technological feasibility, and commercial viability. The SBIR program validates technology through step-wise review involving a feasibility phase, an R&D phase, and several supplemental stages. FoxSeq technology has passed all of these milestones and was awarded every phase of funding with supplements, including an additional Phase I award targeting SARS-CoV-2.
BioInfoExperts’ funding track record and licensed customers demonstrate enthusiasm for implementing the FoxSeq software and its potential for revolutionizing the use of pathogen sequencing.
Eliminates guesswork, provides objective data on transmissions
“FoxSeq empowers my team to disseminate information to health department leadership, internal stakeholders, and contact tracers quickly, easily, and in a format that anyone can understand—not just scientists,” said Dr. Amy Feehan, Ph.D., Clinical Research Scientist, Department of Infectious Disease, at Ochsner Health System, Louisiana.
“Genomic sequence data eliminates guesswork by objectively identifying transmission events. We have already observed five instances of linked infections on three oil and gas platforms. These data demonstrate the importance of following the quarantine protocols in place by the industrial hygienists and can help them contain future outbreaks,” said Dr. Rebecca Rose, Chief Technology Officer at BioInfoExperts.
“For our high-throughput sequencing facility, FoxSeq automatically processes our raw sequence data and displays all of the results that I want to see on a private web browser. We can easily interpret, visualize and search our data for trends in a way that is significantly improved over other commercially available products,” said Judy S. Crabtree, Ph.D., Scientific, and Education Director, Precision Medicine Program and Director, School of Medicine Genomics Core at LSU Health Science Center, New Orleans.
As a resident at Sid Martin Biotech, BioInfoExperts demonstrates how the UF Innovate biotech program assists companies in reaching their goals to provide transformational, life-changing therapies and products.
“BioInfoExperts and the development of their FoxSeq® platform is a great example of how a public-private partnership can translate research into meaningful, life-changing products,” said Karl R. LaPan, director of UF Innovate | Accelerate.
About BioInfoExperts, LLC
BioInfoExperts collaborates with researchers, doctors, and health officials to understand and combat infectious disease transmission. Emerging antibiotic-resistant infections and the COVID-19 pandemic highlight the immediate need to improve the identification, tracking, and treatment of infections in hospitals. With >$1.4M in National Science Foundation funding, BioInfoExperts has developed a cloud-based platform that uses the latest advances in pathogen genomic analytics combined with patient data to effectively identify and mitigate infectious disease outbreaks. The platform, called FoxSeq®, is individualized for each working environment so that it can be integrated seamlessly into various workflows. FoxSeq is used by health systems, pharmaceutical companies, public health, and the oil and gas industry for improved diagnostics, identifying and tracking the emergence of pathogenic strains, and assisting in vaccine/drug discovery.
BioInfoExperts provides end-to-end customizable pathogen genomic analysis, including project and experimental design, laboratory services, cloud-based analytics, and interactive data visualizations.
Chief Executive Officer
About UF Innovate | Accelerate
UF Innovate | Accelerate is the overarching entrepreneurship support program that includes Sid Martin Biotech, the globally recognized biotechnology incubator headquartered in Alachua, Florida, at Progress Park, and The Hub, the award-winning mixed-used incubator in the Gainesville, Florida, Innovation District. The incubation facilities have been honored with nine national and international awards for incubator excellence and achievements in technology commercialization, funding access, job creation, and technology-based economic development. UF Innovate | Accelerate is dedicated to mentoring and accelerating the growth of innovative early-stage bioscience and technology companies and supporting the economic growth of the North Central Florida region. For more information, visit UF Innovate.
UF Innovate Contact:
UF Innovate | Accelerate
Karl R. LaPan