Researchers last week encoded the complete genome of the hepatitis D virus into a quantum computer for the first time. This indicates that quantum computers could one day aid in genomics research.
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A team from the Wellcome Sanger Institute and partner universities Oxford, Cambridge, Melbourne and Kyiv Academic University encoded the viral genome using quantum circuits on IBM’s latest 156-qubit Heron processor. The researchers developed algorithms to compress DNA sequences and efficiently encode them into quantum states. Hepatitis D’s 1,700 RNA bases fit into just 117 qubits.
This could have an application in pangenomics. Pangenomes are collections of genome sequences from many individuals of the same species, capturing the genetic diversity across many populations. However, analyzing multiple genomes at once dramatically increases the computational complexity of the process. This work marks an early step toward using quantum computing to accelerate disease tracking, genetic research and mutation analysis.
The team wants to transform their findings into a usable tool for the wider scientific community, packaging the capabilities into a service where researchers can upload data, choose a classical, quantum or hybrid approach and receive results.
Funded challenge drives quantum genomics research
The team completed the milestone as part of the Quantum for Bio (Q4Bio) Challenge, a competitive international research program funded by Wellcome Leap. The challenge aims to accelerate the applications of quantum computing in human health, which may pave the way for faster tracking of infectious disease, deepen understanding of genetic disorders and more accurately identify disease-causing mutations.
The goal of the Quantum Pangenomics project within Q4Bio was to perform a range of genomic processing tasks for the most complex and variable genomes and sequences, a task that can go beyond the capabilities of current classical computers, including the use of artificial intelligence. These tasks include assembling genomes and pangenomes from DNA sequence data, as well as mapping DNA fragments into reference genomes, which is key for studying genetic variation.
Wellcome Leap’s Supported Challenge Program in Quantum for Bio is focused on identifying, developing and demonstrating biology and healthcare applications that will benefit from the quantum computers expected to emerge in the next 3 to 5 years. Up to $40 million in research funding will be awarded to multidisciplinary, multiorganizational teams and up to $10 million in challenge prizes will be available at the end of the program for successful proof-of-concept demonstrations on quantum devices with a clear path to scaling to large quantum computers.
“Our goal has always been to push the boundaries of what’s possible in genomics. When we work with pangenomes, the information is presented in the form of a tangled maze, but we are building quantum algorithms to help find the best path through this maze when regular tools, such as classic computers, just get hopelessly stuck. So, we’re aiming for a simple but game-changing idea by bringing quantum computing into the world of genomics,” said Sergii Strelchuk, associate professor in the Department of Computer Science at Oxford.
The researchers have posted a preprint describing the quantum algorithms that could be used to assemble pangenomic data.
It will likely be a long time until the 3.2 billion-base-pair human genome can be encoded onto a quantum computer, but this marks an important milestone towards that goal.
