Clinical Interpretation

Impressions from Genomics England Clinical Interpretation Partnership Open Meeting


I had the privilege to attend the first Genomics England Clinical Interpretation Partnership (GeCIP) Open Meeting. The room was absolutely packed with VIPs. I almost was left out because I had not signed the EventBrite registration form for the event. Luckily I was allowed in last minute even though the event was oversubscribed.

Genomics England Representative Panel. From left to right: Dame Key Davies, Sir John Chisholm, Professor Mark Caulfield FMedSci,  Professor Tim Hubbard and Mr Nick Maltby.

Wellcome Trust’s Headquarters at Euston, London (5-Dec-14): Genomics England Representative Panel. From left to right: Professor Dame Kay Davies, Sir John Chisholm, Professor Mark Caulfield FMedSci, Professor Tim Hubbard and Mr Nick Maltby.

The purpose of this meeting was to engage with the clinical and academic community regarding the access and analysis of the wealth of data that Genomics England will be able to provide: i.e., 100,000 genomes. It was also an informative session on the current state of the project and how they plan to execute its objectives in the next coming years.

Lots of information was given. I hereby present 10 points that caught my attention. This is not a complete report but a summary of the things that were said that interested me.

1) The Chief Scientist, Professor Mark Caulfield, mentioned that many people would be envious of the privileged exclusive access that researchers based in England will have. Apparently, there is a 6 month exclusive access of the data for researchers who engage in the so called “Clinical Interpretation Partnership”. These Genomics England Clinical Interpretation Partnerships (GeCIP) must be led by England-based researchers and must have an National Health Service (NHS) based clinician in them. Those GeCIP that are approved will have exclusive access to the data for 6 months, giving them a competitive advantage.

2) The way data are going to be shared. No raw data will come out of the firewall. Only summary statistics will be allowed out. Relevant findings will be allowed to be deposited in public databases as usual. The access will be tightly regulated and monitored, to ensure that the data are used ethically. The access will be provided via virtual machines, in which operation of specific algorithms and tools will be permitted.

3) Genomics England is going to spend £25 Million, just on training alone and a Training Director is going to be appointed as well. It is expected that about 1,000 bioinformaticians will be required to do the analysis work, hence why it is so crucial to engage with the local scientific and clinical community as well as international collaborators.

4) Their consent form from patients allow researchers to contact patients up to four times a year.

5) Patients will own their genomes. They will be able to download their VCF and Bam files if they want to (these are the primary files that contain variant or sequencing information from which analyses will be derived). This is great news indeed for the personal genomics field, which hopefully will catalyse a) the number of public genomes available on the Internet and b) the citizen science efforts to understand personal genomes.

6) A new building is being constructed at a fast pace in the Genome Campus, Hinxton, Cambridgeshire. This building will house the sequencing done for Genomics England. The data will probably be stored in a data centre somewhere in London. At the beginning they are going to rent processing power and storage from the cloud.

7) The sequencing will be done by Illumina, which has signed a special agreement to develop their technology in this new sequencing facility. Engineers from Illumina will run it and the company will provide their latest technology as they develop it.

8) Genomics England will end in 2018. The preparatory phase is about to finish and the production phase will start in 2015. It is expected that at the peak of production, 100 genomes a day will be yielded.

9) Genomics England is not providing any funding. They see themselves as enablers of the science that will happen based on these data. Their objective is to provide a fair system which allows researchers locally and internationally to make use of the data to enhance the diagnostic capabilities and health care delivered by the NHS.

10) There are currently talks about what will happen to the samples and the data infrastructure created once the project is completed.

Overall, there was a lot of excitement in the air. Lots of professors and well known faces, a room completely packed and wine and peanuts to close the evening and start creating GeCIPs. The deadline for submission of expressions of interest to form introductory GeCIP domains is on January 26th 2015.

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