Tag Archives: Covid

McMaster University cracks genome sequencing to fight disease with HPE

Research Lab at leading Canadian university uses HPE technologies to collect and analyse vast amounts of genome data and accelerate the identification of how pathogens mutate and spread.

ONTARIO, Canada – July 27, 2022 – Hewlett Packard Enterprise (NYSE: HPE) today 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 to quickly ingest and process raw genomic data, unlock insights and help the world get ahead of virus mutations. The HPE solution was used effectively during the COVID-19 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 COVID-19 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 COVID-19 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, Ph.D., Professor in Biochemistry and Biomedical Sciences at McMaster University and member of the M.G. DeGroote Institute for Infectious Disease Research (IIDR) and Canada’s Global Nexus of Pandemics and Biological Threats. “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.” – Andrew McArthur, Ph.D., Professor in Biochemistry and Biomedical Sciences at McMaster University

In addition to the HPE Superdome Flex server, which provides the world’s most scalable and modular in-memory computing capabilities, McArthur Lab invested in other HPE solutions to store, compute and analyze a large volume of data. These solutions include:

  • HPE Nimble Storage HF20C to store vast amounts of raw genomic data coming in from sequencing teams.

  • HPE Apollo 6500 systems that are ideal for deep learning to develop AI algorithms to predict antibiotic failure based on bacterial genome sequence and to deploy machine learning to find new drugs.

“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.”

Long-term HPE authorized partners Arrow ESC Canada Ltd. and Compugen Inc. were instrumental in scoping and building the solution.

To learn more about McMaster Lab’s research leveraging HPE technologies, read the full story click here.