Q4Bio

Quantum Leap in Genomics: Sanger Institute and Colleagues Face Biological Data Future with Quantum Computing

Twenty-five years after decoding the human genome, the Wellcome Sanger Institute is spearheading a bold new genomics frontier by cooperating with Quantinuum, the world's foremost quantum computing startup. They depend on this relationship to compete in the Wellcome Leap Quantum for Bio (Q4Bio) project, which uses quantum computing to tackle genomics' computational restrictions. Supercomputers cannot search for biological secrets like this new project.

A “biological moonshot,” the 25-year-old Human Genome Project discovered the whole human blueprint, including over 3 billion base pairs. This groundbreaking discovery advanced medicine, science, and human biology. Next-generation sequencers, a "reference genome," and breakthroughs in algorithms and computer power can complete a 13-year, $2.7-billion process in 12 minutes for a few hundred dollars.

Due to their complexity, genomic problems still limit standalone conventional computers. Pangenomes—collections of genome sequences that reveal genetic variety in a population or species—are analysed. Pangenome data are best processed and displayed as a network or sequence graph showing common genetic linkages, unlike the linear human reference genomic. Mapping genomes to network nodes and finding the optimum paths across them need massive computational power. Pangenomes strive to connect human variability to the standard human reference genome, which is based on a few individuals.

To tackle these limitations, the Wellcome Leap Q4Bio competition funded quantum algorithm experiments that might revolutionise computational genetics in three to five years. The Wellcome Sanger Institute is pursuing two major initiatives under this program:

The Oxford-led Consortium for Complex Genomes seeks quantum algorithms to process the most complex and changeable genomes. Oxford leads it, together with the Wellcome Sanger Institute, Quantinuum, Cambridge, Melbourne, and Kyiv Academic University. They want to encode and process the PhiX174 genome using a quantum computer in the near future. This project is symbolic since Fred Sanger won his second Nobel Prize in Chemistry in 1980 for sequencing PhiX174. This would be the first time quantum computing has been proved to be effective in biology and indicate its readiness for practical deployment.

The Cambridge/Sanger/EMBL-EBI Pangenomics Project: The Q4Bio challenge awarded up to US $3.5 million to the project, which involves Cambridge, Wellcome Sanger, and EMBL-EBI academics. This paper addresses the computational challenges of developing, improving, and analysing pangenomic databases for large population samples. The team wants to develop quantum computing methods to speed up mapping data to graph nodes and finding efficient paths through complex pangenome graphs.

The Sanger Institute chose Quantinuum, the world's largest quantum computer company, as a technological partner because of its dominance in commercial quantum systems. System H2, its flagship quantum computer, still holds the world record for Quantum Volume, a test of performance on complex circuits, with a current benchmark of 8,388,608 (2^23). The scientific research team will benefit from Quantinuum's software, hardware, and quantum algorithm development expertise through this collaboration.

Quantum computing works differently from regular computing. Qubits can exist in multiple states concurrently through quantum superposition, unlike classical bits that store information as binary 0s or 1s. Quantum computers can solve problems that classical machines cannot due to entanglement and interference. By bringing the world's highest performing quantum computers to this collaboration, we will help the team push the limits of genomics research with quantum algorithms and open new possibilities for health and medical science', said Quantinuum President and CEO Rajeeb Hazra, who was honoured to be chosen.

Although quantum computer hardware offers huge promise, its fundamental susceptibility to noise and decoherence limits its size and computing power. Quantum hardware is projected to advance in three to five years. In its early stages, co-developing hardware, software, and applications is the ideal method to advance this unique computational approach, according to the Q4Bio Challenge.

Using genetic data, new quantum algorithms are created, modelled, and implemented. These algorithms and methods will be tested and enhanced in robust HPC environments before being used to simulate quantum computing hardware. Small DNA sequences will be checked initially, then SARS-CoV-2, and lastly the human genome.

Dr. Sergii Strelchuk, Principal Investigator of the University of Cambridge-led program, noted that quantum computing speedups can solve many tough pan genomics and computational genomics problems due to their structure. By comparing the early stages to “designing a rocket and training the astronauts,” c Sanger Institute Principal Systems Administrator David Holland recognised the innovation of showing a pangenome in a quantum context. While starting from scratch, the program builds on “decades of systematically annotated genomic data generated by researchers worldwide,” Dr. David Yuan, EMBL-EBI initiative Lead, stressed the importance of open data and collaborative science.

This work has great promise. Personalised treatment based on genetic, environmental, and lifestyle factors may benefit by comparing individual human genomes to a human pangenome instead of the existing single reference genome. Quantum-powered bacterial and viral genome methods may help track and control infection outbreaks.