McMaster University Cracks Genome Sequencing to Fight COVID-19
HPE announced that McMaster University’s McArthur Lab developed one of the fastest and most accurate software packages for determining COVID-19 variants, using the HPE Superdome Flex server. The HPE solution was used effectively during the pandemic to help monitor variants and support researchers investigating COVID-19 infections by significantly reducing the time to collect and analyze data to sequence positive cases from typically nine to 10 hours to under an hour.
With researchers working to sequence raw genomic data, the team at McArthur Lab partnered with virologists at Ontario’s Sunnybrook Health Sciences Center to determine which viruses infect patients, and how pathogens evolve into new variants and spread between people. By working together at the start of the pandemic, these two teams were the first in Canada to isolate the SARS-CoV-2 virus in January 2020 to study it. The information was shared with public health agencies and pharmaceutical companies to help develop vaccines and drugs.
“Like all other infectious disease labs, we looked at what was happening in Wuhan, China. And in the first two weeks after scientists there sequenced the genome of SARS-CoV-2, we redesigned our entire pipeline and built a platform to prepare for capturing the virus’s genes,” says Andrew McArthur, Professor in Biochemistry and Biomedical Sciences at McMaster University. “You’ve got to have one-thousand-fold redundancy to figure out what’s infecting one patient when you’re doing genome assembly. So when you’ve got one hundred patients at a time, you’re rapidly approaching terabytes of information to compile, and you want it done in under an hour because the clinicians are calling to find out. The HPE solution reduced the time to collect and analyze data to sequence positive COVID-19 cases and accelerate decision-making.”
“In genomics, technology plays a key role in DNA research to help predict, diagnose and treat diseases by providing researchers with high-performing computing to process large quantities of data at scale,” said Justin Hotard, executive vice president, and general manager, HPC & AI, at HPE. “The impactful research that McMaster Lab contributed to the public is a tremendous example of how they used the computing capability of the HPE Superdome Flex to analyze massive data sets in real-time and provide timely answers to critical questions about COVID-19.”