Remember that genome book? The one that took an entire decade to read the first time? Genomics researchers worldwide generally analyze an entire genome in about 150 hours — a fantastic leap, certainly, but still unequal to the speed demanded by the COVID-19 pandemic. Even isolating and sequencing the bits that code for protein and propagate viruses—a handful of pages called exomes—usually takes at least 4 hours.
Now, BGI researchers can access HPC clusters optimized to assemble and analyze hundreds of whole genomes and thousands of exomes.
“With this donation, our hope is to extend the existing resources BGI researchers already have at their disposal so that the biomedical community can do more and get there faster,” Dr. Giraldo said. “I can’t think of a better example of using technology to tackle humanity’s greatest challenges than one where a multidisciplinary team of scientists, clinicians, and engineers have come together to pool their combined brain power to fight back the coronavirus global pandemic.”
I can’t think of a better example of using technology to tackle humanity’s greatest challenges than one where a multidisciplinary team of scientists, clinicians, and engineers have come together to pool their combined brain power to fight back the coronavirus global pandemic.
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Building on a powerful solution first developed by Intel, Lenovo developed an optimized hardware and system architecture to radically reduce those genome processing times. Lenovo’s solution for population-level genomics—the Genomics Optimization and Scalability Tool (GOAST)—leverages the Broad Institute’s open-source Genome Analysis Toolkit (GATK) software on an optimized hardware recipe. Identifying the right optimizations and hardware building blocks to accelerate genomics required testing hundreds of HPC configurations.
“The year-long process focused entirely on the real needs of scientists,” Giraldo said. “Researchers’ time is better spent by focusing on the science; not on the underlying hardware. So we performed a systematic permutation test of all the hardware building blocks available to us to find the right hardware recipe that reduced execution time. Our tests used the same software used by researchers in the lab to make this tool immediately deployable.”
The results? A whole human genome sequenced in five and a half hours, and exomes in just four minutes—up to a 40-fold speed-up. Supported by a dedicated supercomputing cluster, BGI researchers will soon be hard at work using GOAST to study COVID-19 on the long road to a vaccine.
In the short term, predicting virulence based on a patient’s dominant strains may also help hospitals more effectively triage patients—knowing who is at greatest risk as soon as they reach a clinic and what therapies may be effective. In the long term, even beyond a vaccine, the COVID-19 genome contains hints of its source. Knowing its genomic history and point of origin can help predict and prevent future outbreaks.
All in all, a staggeringly dense and high-stakes puzzle to solve.
“The equipment and technology will speed up the rapid identification of COVID-19 infected people and the study of virus genome characteristics, providing strong support for accurate diagnosis, treatment and epidemic prevention of COVID-19,” Jin said.