Genomics England has today announced the four companies it has chosen to explore working with on the interpretation of the genomes of the first 8,000 patients participating in the 100,000 Genomes Project.
Genomics England continues to work with Illumina and are also expanding their partnership to explore a variety of bioinformatic challenges around sequencing and clinical interpretation.
Genomics England launched a ‘bake off’ for annotation and interpretation in the Spring of 2014 to determine the quality of offerings around the world. The ‘bake off’ attracted 28 participants, each of whom was sent the genomes of 15 rare disease trio samples and 10 cancer/normal samples and asked to interpret them. The submitted reports were then evaluated by a team within Genomics England.
A group of 10 companies passed this ‘bake off’ stage. These companies were then invited to take part in a tender to provide interpretation services in relation to the first 8,000 patients being treated within the 100,000 Genomes Project. The focus of the tender was whether the companies could provide an automated service with limited amounts of manual intervention in view of the establishment of the Genomics England Clinical Interpretation Partnership (GeCIP) which will provide the latter. Genomics England wished to appoint several providers so that it could learn from a variety of approaches in this fast moving area with the ideal being to appoint four providers to each provide reports on 2,500 patients, if this could be accommodated within the budget. For some patients interpretation reports will be provided by multiple providers to compare performance. It is expected that this phase of the project will be completed within 12 months.
Subject to passing a test phase and agreeing a contract, Genomics England will engage with Congenica and Omicia in rare disease, Nanthealth in cancer, and Wuxi Nextcode in both rare disease and cancer for this stage of the project. Lockheed Martin in partnership with Cypher Genomics has been appointed reserve bidder. Each of the successful suppliers will have to provide the services within the Genomics England data centre, thus ensuring that the data does not leave the data centre. It is expected that the services will commence from 1 August, 2015.
Genomics England intends to contract for its future requirements for clinical interpretation in early 2016 when it has learnt the lessons of the current pilot phase.
For more information on genome interpretation, Genomics Education Programme have a new blog, Finding needles in haystacks: making sense of genomic data.
This is an important milestone for the project. We are looking to provide high quality variant interpretation to assist clinicians within the NHS and these companies will enable us to deliver this service. We look forward to working with each of the successful companies over the next year.
Dr Augusto Rendon
Director of Bioinformatics at Genomics England