NEW YORK and SAN FRANCISCO – Illumina and Genomics England announced Monday a new agreement to sequence up to 300,000 genomes over five years.
Under the terms of the agreement, Illumina will deliver up to 300,000 "whole genome equivalents," with an option to increase the number to 500,000. Initially, samples from NHS patients in England with known rare diseases and cancer types will be eligible for whole-genome sequencing (WGS) to support diagnosis and inform treatment.
The UK NHS Genomic Medicine Service will provide clinical samples, and Genomics England and the UK Life Sciences Strategy will provide samples for research purposes. Illumina Laboratory Services, based in Cambridge, UK, will perform sequencing using the NovaSeq 6000 sequencer.
"Population health is not about a one-time research program, but [about] all patients having access to sequencing as a standard of care," Illumina CEO Francis deSouza said Monday, while announcing the agreement at the JP Morgan Healthcare Conference in San Francisco. He added that the "UK is leading the adoption of genomics at population health level."
"Our 100,000 Genomes Project has already delivered life-changing results for many people, and this agreement between Genomics England and Illumina is another transformative step towards the NHS becoming a truly predictive, preventative, and personalized health service," UK Health Minister Nicola Blackwood said in a statement.
Illumina Chief Scientist David Bentley added, "The research component of this agreement is also incredibly important as, together, we will develop new approaches to unlocking the power of the genome and go on to identify more variants that underpin the full panoply of human diseases."
The agreement builds on the UK's 100,000 Genomes Project, announced in 2012 and completed in 2018; in 2014, Genomics England chose Illumina as its sequencing partner.
Illumina will put to use capabilities piloted during that project, an Illumina spokesperson said in an email.
Illumina's Cambridge lab can sequence 60,000 samples a year with an ISO accredited bioinformatics pipeline and with turnaround time of approximately 28 days for rare disease cases and 21 days for cancer cases. "We are currently the only company with capabilities to fit the bill," the spokesperson said.
The 100,000 Genomes Project took longer than initially thought, due to technical challenges, including generating high-quality cancer genomes and streamlining analysis.
Genomics England announced the WGS initiative in 2017, as it was wrapping up the 100,000 Genomes Project.
The sequencing service should go live in April, Illumina said, at which point NHS England consultants will be able to request whole-genome sequencing for conditions listed in the UK National Genomic Test Directory. One of the seven national NHS genomic medicine service labs will receive tissue or blood samples and extract DNA, before sending the samples to Illumina. Illumina will return the raw data file to Genomics England for processing and transfer to the commissioning genomic medicine service lab. Illumina said it will not store any patient samples or data. Illumina expects the number of indications beyond rare disease and cancer to increase over time.
"The UK is already leading the way, but this agreement builds on the strong foundations by demonstrating further the commitment of the UK life sciences sector to supporting the NHS's delivery of truly personalized care," Mark Caulfield, Genomics England CSO, said in a statement.
Ben Butkus contributed reporting from San Francisco.