Genome loaded onto a quantum computer in world first
Scientists have achieved a world first by loading a complete genome onto a quantum computer – a major step towards using quantum computing to tackle some of biology’s most complex bioinformatic challenges.
The breakthrough comes from a collaboration between the Wellcome Sanger Institute and the Universities of Oxford, Cambridge and Melbourne, with Kyiv Academic University as an additional partner. The genome was loaded onto an IBM quantum computer, powered by the company’s latest 156-qubit Heron processor.
The team successfully completed the milestone as part of the Quantum for Bio (Q4Bio) Challenge, a competitive and international research programme funded by Wellcome Leap. 1 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.
A pangenome is a collection of genome sequences from many individuals of the same species and they are particularly challenging to analyse using classical computing methods.2 Rather than representing a single reference genome, pangenomes capture the genetic diversity across many populations, which provides a more complete view of genetic variation. However, analysing multiple genomes at once dramatically increases computational complexity: as more genomes are incorporated into a pangenome, the burden on classical tools grows rapidly.
The Quantum Pangenomics team, led by the University of Oxford and the Sanger Institute, chose the Hepatitis D virus to load onto the quantum computer because it has a compact genome and is an important and clinically relevant pathogen. Hepatitis D virus can cause a severe, blood-borne liver infection and is spread through contact with infected blood, semen or bodily fluids.
‘Loading’ the Hepatitis D genome onto the quantum computer means encoding DNA sequences data into a format that quantum computers can handle, allowing the quantum algorithms to process and analyse the genetic information. The researchers developed efficient methods for creating quantum circuits to encode bio-sequences in a format first suggested by University of Melbourne collaborator Professor Lloyd Hollenberg at the beginning of the quantum bioinformatics story over 25 years ago. By successfully encoding the Hepatitis D viral genome, the researchers have demonstrated that quantum computers can now begin to handle suitably represented real-world genomic data and have proved that there is an alternative approach to using traditional computers in genomics.
The team now wants to take the findings of this project and transform it into a usable tool for the wider scientific community, not just quantum-enthusiasts. They want to be able to package these capabilities into a service where researchers can upload data, choose their preferred approach to solving a given computational challenge – either classical or quantum or potentially both, and receive back the desired results.
The work represents an early but important step towards a future where quantum computing accelerates biological discovery. Faster and more powerful genomic analysis could help enable rapid tracking of infectious disease, improved understanding of rare genetic disorders and more precise identification of disease-causing mutations.
“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 a 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.”
Dr Sergii Strelchuk, Associate Professor, Department of Computer Science at the University of Oxford
“In the 1970s, by sequencing the first complete DNA genome, Fred Sanger and his team marked a ‘hello world’ moment for classical genomics. Nearly fifty years later, through Wellcome Leap’s Q4Bio programme, the Oxford–Sanger team is laying the groundwork for a new ‘hello world’ moment by encoding and loading a complete genome into a computer – only this time, a quantum one.”
Dr Shihan Sajeed, Q4Bio Programme Director at Wellcome Leap
“This is a landmark moment for both genomics and quantum computing. By successfully loading the Hepatitis D genome on a quantum computer, we have set the stage for further quantum genomics research as we have shown that real data can be translated into a form that these high-powered machines can process.”
Dr James McCafferty, Chief Information Officer at the Wellcome Sanger Institute
More information
Notes to editors
- To discover more about Wellcome Leap Q4Bio programme goals and background, including the quantum computing context, visit https://wellcomeleap.org/q4bio/program/
- To read more about human pangenomes, see here: https://humanpangenome.org/. The Human Pangenome Reference Consortium (HPRC) is an NIH-funded project that aims to engage scientists and bioethicists in creating a human pangenome reference and resource that represents global human genomic variation.
Funding
This project is funded by the Wellcome Leap Q4Bio Supported Challenge Program.
