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Genomics England to Sequence 8K Genomes for Two Pilots in 2014, Establish Sequencing Centers


Genomics England, a UK government-owned company that has been tasked with running the country's 100K Genomes Project, plans two pilot projects in the areas of rare genetic disorders and common cancers for 2014. It also aims to set up several sequencing centers, to be ready in 2015, as well as a centralized database.

The 100K Genomes Project, led by the UK's National Health Service, was announced almost a year ago by British Prime Minister David Cameron (GWDN 12/10/2012). Funded with £100 million ($159.5 million), the project aims to sequence the genomes of 100,000 patients, as well as several pathogen genomes, over five years and to train geneticists and the UK healthcare community in using genome-based medicine.

This summer, the UK Department of Health said that Genomics England will oversee the project, including managing contracts for sequencing and data analysis and organizing storage of the data (GWDN 7/5/2013).

The project will focus on rare inherited diseases, common cancers, and bacterial and viral pathogens. According to Mark Caulfield, chief scientist of Genomics England, two pilot projects are planned for 2014, which are "geared to allow us to understand the competitive landscape in sequencing provision as it exists from commercial providers, and also to improve our understanding of the optimal solution to handling the sequence."

Under one pilot project, announced by Cameron last month (GWDN 10/2/2013), Genomics England will collaborate with Cancer Research UK to sequence 6,000 genomes, of matched tumor/normal samples from 3,000 cancer patients. Caulfield said this project will focus on lung, colon, and breast cancer, all common cancers with high mortality rates.

The other pilot will sequence the genomes of 2,000 individuals from families with rare inherited diseases, spanning a range of genetic disorders, particularly those where little is known about the cause.

The goal is to complete both projects, return the data to the NHS, and make it available to clinicians and researchers from academia and industry by the end of 2014.

Also next year, Genomics England plans to establish a number of sequencing centers in England — the number has not been determined yet, but it will be more than one. Starting in 2015, these centers will produce whole-genome sequencing data for 30,000 genomes per year in the three focus areas of the project. The goal is to complete 100,000 genomes by the end of 2017.

While the buildings for the sequencing centers will be owned by Genomics England, they will be operated and outfitted with equipment by commercial sequencing providers, "because we are keen to encourage competitiveness in this marketplace as a route to bring the price down for everyone," as well as to encourage technological innovation, Caulfield said.

He said the company is considering "sequencing providers from anywhere in the world" and has talked to "all the major providers of sequencing worldwide."

Besides serving scientists participating in the 100K Genomes Project, the sequencing centers will be open on a fee-for-service basis to researchers working on inherited diseases, common cancers, or other disorders, as long as they agree to make the data available to the research community through Genomics England's database. The centers will also remain open following the completion of the project in 2017.

Genomics England plans to build a data center where individual-level data will be housed behind a firewall of the NHS. The data will also be linked to patients' electronic health records with the NHS. While the location of the data center has not been determined yet, it will likely be in geographic proximity to the sequencing centers.

In addition, the company will procure third-party IT solutions for data analysis, including annotation, data management, and clinical information systems.

Qualifying researchers in the UK and abroad who want to use the sequencing data can "bring their computational power inside our firewall," Caulfield explained, which is possible remotely, though no data will be stored in the cloud. "They can run any algorithm they want, providing it's within the terms of the informed consent for the patient. That will allow them to take the data away, but it will not be the individual patient data, it will be a summary analysis of what they have run on our data."

Genomics England will be responsible for generating the sequence data, and calling and annotating the variants. The data will then go to clinicians at the NHS, who will return the results to patients. Caulfield said the plan is to return "clearly actionable" results as well as variants of uncertain significance. Doctors may also inform patients of incidental findings, based on their clinical judgment. "I don't think there is an absolutely right answer of what to do with incidental findings," he said.

"This is not really a research project," Caulfield said. "It's actually designed to transform the way the National Health Service uses genomic medicine to help stratify patient care in cancer, understand more about rare inherited disease, and, if possible, identify new therapeutic targets or repurpose existing medicines, identify routes to understand bacterial and viral resistance to current therapies, and give a platform for industry or academia to develop new therapies."