Wellcome Leap Q4Bio
Quantum Leap in Genomics: Sanger Institute and Colleagues Use Quantum Computing to Address the Future of Biological Data
The Wellcome Sanger Institute, a preeminent genomic research institution, is leading a daring new frontier in genomics by collaborating with the world’s leading quantum computing company, Quantinuum, 25 years after the historic feat of decoding the human genome. Their bid in the Wellcome Leap Quantum for Bio (Q4Bio) project, which aims to use quantum computing to solve enduring computational constraints in genomics, heavily relies on this partnership. This revolutionary project seeks biological secrets that even the most powerful supercomputers cannot.
A “biological moonshot,” the 25-year-old Human Genome Project uncovered the full human blueprint, which includes over 3 billion base pairs. This momentous achievement led to medical advances, scientific advancements, and a deeper understanding of human biology. With the use of next-generation sequencers, a “reference genome,” and tremendous advances in algorithms and computing power, a procedure that formerly took 13 years and cost $2.7 billion may now be finished in less than 12 minutes for a few hundred dollars.
The capabilities of isolated classical computers are still being strained by some genomic difficulties, though, because they are so highly complicated. This involves analyzing pangenomes, which are collections of many genome sequences that show the genetic diversity within a population or species. In contrast to the original human reference genome’s linear shape, pangenome data are best processed and portrayed as a network or sequence graph that shows common genetic links. Finding the best paths across these graph nodes and mapping individual genomes to them both need enormous amounts of computing power. Pangenomes aim to bridge the gap between the current human reference genome, which is based on a small number of individuals, and human variety.
To overcome these obstacles, the Wellcome Leap Q4Bio challenge was created, providing money for studies of quantum algorithms that could advance computational genetics in the next three to five years. Under this program, the Wellcome Sanger Institute is working on two important projects:
- The Oxford-led Consortium for Complex Genomes: This consortium is focused on creating quantum algorithms to process the most complex and variable genomes. It is led by the University of Oxford and includes the Wellcome Sanger Institute, Quantinuum, and other esteemed academic partners like the Universities of Cambridge, Melbourne, and Kyiv Academic University. Their ambitious short-term objective is to use a quantum computer to encode and process the whole genome of the bacteriophage PhiX174. Given that Fred Sanger won his second Nobel Prize in Chemistry in 1980 for the sequencing of PhiX174, this undertaking has substantial symbolic significance. If this is accomplished, it would be the first time in history that quantum computing has been shown to be useful in biology and would be a significant indication that it is ready for practical use.
- The Cambridge/Sanger/EMBL-EBI Pangenomics Project: The Q4Bio challenge has given up to US $3.5 million to the Cambridge/Sanger/EMBL-EBI Pangenomics Project, which involves academics from the University of Cambridge, the Wellcome Sanger Institute, and EMBL’s European Bioinformatics Institute (EMBL-EBI). The difficult computational issues associated with creating, enhancing, and analyzing pangenomic databases for sizable population samples are the focus of this study. The team’s goal is to create quantum computing techniques that can greatly speed up the crucial steps of mapping data to graph nodes and figuring out effective paths through these intricate pangenome graphs.
The Sanger Institute chose Quantinuum, the largest quantum computing business in the world, as a technological partner because of its dominant position in commercially accessible quantum systems. With a current benchmark of 8,388,608 (2^23), its flagship quantum computer, System H2, continuously maintains the world record for Quantum Volume, a demanding test of a quantum computer’s performance on intricate circuits. Through this collaboration, the scientific research team will be able to take advantage of Quantinuum’s extensive technology stack, which includes software, hardware, and in-depth knowledge of developing quantum algorithms.
Compared to traditional computing, quantum computing functions on essentially different principles. Quantum bits, or qubits, can exist in numerous states simultaneously through quantum superposition, whereas classical bits retain information as binary 0s or 1s. This allows quantum computers to solve issues that are beyond the capabilities of classical machines, in conjunction with phenomena like 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 Rajeeb Hazra, President and CEO of Quantinuum, who expressed their honour in being selected.
Current quantum computer hardware has limitations due to its intrinsic sensitivity to noise and decoherence, which restricts its size and computational capacity despite its enormous potential. But in the next three to five years, major developments in quantum hardware are expected. The foundation of the Q4Bio Challenge is the belief that the best way to progress this novel computational approach in its early phases is to co-develop hardware, software, and applications.
Using actual genetic data, the method entails creating, modelling, and then putting into practice new quantum algorithms. In order to replicate the expected quantum computing hardware, these algorithms and techniques will first be evaluated and improved in robust, current High Performance Compute (HPC) environments. Small DNA sequences will be tested first, followed by comparatively small genomes like SARS-CoV-2, and finally the much larger human genome.
Dr. Sergii Strelchuk, Principal Investigator of the University of Cambridge-led initiative, emphasized that many difficult problems in pan genomics and computational genomics are well-suited for quantum computing speedups due to their structure. By comparing the early phases to “designing a rocket and training the astronauts,” David Holland, Principal Systems Administrator at the c Sanger Institute, recognized the innovative nature of displaying a pangenome in a quantum environment. While beginning from scratch, the initiative builds on “decades of systematically annotated genomic data generated by researchers worldwide,” as Dr. David Yuan, initiative Lead at EMBL-EBI, underlined, highlighting the significance of open data and collaborative science.
This work has enormous potential significance. Instead of using the current single reference genome, comparing individual human genomes to a human pangenome may yield superior insights for personalized medicine, allowing customised therapies based on genetic, environmental, and lifestyle factors. Quantum-powered approaches for bacterial and viral genomes might also help track and control pathogen outbreaks.
“Quantum computational biology has long inspired us at Quantinuum, as it has the potential to transform global health and empower people everywhere to lead longer, healthier, and more dignified lives,” said Ilyas Khan, the company’s founder and chief product officer. The Sanger Institute and Quantinuum‘s collaboration foreshadows a big advancement in human health research that could transform medicine and computational biology just as drastically as the original Human Genome Project did 25 years ago.
