Boosting Bioinformatics
February 16, 2022
The Michigan Department of Health and Human Services is enlisting experts and resources at Michigan State University to bolster the state’s fight against COVID. With grants totaling more than $5 million, MSU and health care partners will help build up Michigan’s capacity to respond to the current pandemic and future pathogens. MDHHS created what it calls the Michigan Sequencing Academic Partnership for Public Health Innovation and Response, or MI-SAPPHIRE, with federal funding from the U.S. Centers for Disease Control and Prevention.
Detecting and sequencing more viruses is just one part of surveilling the SARS-CoV-2 pandemic and trying to stay a step ahead of its variants. The state will also need the ability to analyze, understand and disseminate all of the data it’s gathering. In the context of health and biological sciences, solving these big data problems is referred to as bioinformatics.
Bioinformatics is a core component of another MI-SAPPHIRE grant, worth a total of $2.5 million, that has MSU working with Spectrum Health. Part of this investment will bring Spectrum Health West Michigan’s array of sequencing tools to bear in the fight against COVID. Another part, about $600,000 of the grant, will have Spartans leading an effort to ensure the state has the computational resources it needs to make the most of the data it collects.
“Our project is critical as we are unique in focusing on developing new computer tools for this pandemic and other viruses,” said Jeremy Prokop, an assistant professor in the College of Human Medicine who was recruited to MSU in 2018 as part of the Global Impact Initiative. “We want to launch new tools that can be used by everyone to quickly take sequence data of a viral genome and know if the differences correlate to strains of the virus, like omicron, or if new variants will alter the function of the virus and could be of major concern.”
These new tools will not only help detect, track and better understand future variants, but help prepare for future viruses and pathogens, said Prokop, who works in the Department of Pediatrics and Human Development and Department of Pharmacology and Toxicology.
“As we get past COVID, our goal is to also build these tools for other pathogens that could one day be pandemic,” he said.
Through the grant, Prokop’s team will also train undergraduates across the state in bioinformatics skills needed to develop and implement such tools. In preparing for the future, the state isn’t just focused on new tools and technologies, it knows it will need a workforce who knows how to use them.
This feature highlights the common thread between MI-SAPPHIRE projects. Michigan is tapping into the expertise it has in-state to build up infrastructure that will help serve and protect its residents now and into the future. Another key component of that, Prokop said, is building bridges between the state’s experts in health care, government and state research institutions.
“The projects are about bringing state, academic and medical resources together. The pandemic has highlighted the challenges of communication,” Prokop said. He and his team are a natural choice to help facilitate those connections, having published over 30 scientific papers with Spectrum Health since joining MSU.
The MI-SAPPHIRE grant will ultimately result in better care for patients, which the teams are working to demonstrate with its grant. “Just like with the human genome, understanding genetic details of the virus can transform our care for each patient,” Prokop said.