Friday, 5 July 2013

Genome England: 100,000 genomes here we come!

We've waited since Christmas to find out more and on the NHS’ 65th birthday we finally get to hear more about how the NHS is going to roll out clinical sequencing for patients in England. In December last year Prime Minister David Cameron announced the 100,000 genome project while visiting the CRUK Cambridge Research Institute. While here he visited my lab and started a MiSeq run, probably the only world-leader to sequence a genome so far.

 

Late last year Prime Minister David Cameron revealed that the personal DNA code (genome) of up to 100,000 patients or infections in patients will be sequenced over the next five years. You can find out more about the new "Genomics England" by emailing enquiries@genomicsengland.co.uk or by reading the Science Working Group report.


One of the aims of the project is to "train a new generation of British genetic scientists to develop life-saving new drugs, treatments and scientific breakthroughs". I am hopeful that this investment is going to push England to the top of the genomic-health tree. 

Genomics England is chaired by Sir John Chisholm, former head of the MRC and will manage the contracts for sequencing and analysis of 100,000 patients over the next five years. There is no clear indication of what sequencing platforms will be used or where the sequencing will happen. Although there are rumours of a new facility being prepared in England.They wil also "strictly manage secure storage of personal data ... designed to securely protect patient information" at least they aren't trying to suggest it will be anonymised anymore. 

Ethics working group: Michael Parker led a small group to "provide advice on how the Government might address the ethical issues associated with a recent commitment to deliver the whole genome sequencing of 100,000 NHS patient". The group suggest three key ethical issues that need to be considered; consent, data-access and feedback. 

Cancer working group: This is the disease most likely to yield real benefits to patients n the HNS from genome, exome or amplicon sequencing. The science working group report (prepared by Mark McCarthy with input from Gil McVean, Euan Ashley, Nazneen Rahman and Sian Ellard) point to the fact that while WGS costs remain high there is real potential in analysing panels of genes in all cancer patients.

They also make it clear that blood-based monitoring of cancer is going to be important. Pretty cool since we only published this as a useable technology two years ago!

Suggesting that multiple samples are going to be needed including the tuomor, patient normal and possibly additional samples "separated in either space or overtime during the course of the disease". The priorities look like they'll be Lung, Paediatric, rare familial cancers, and metastatic disease of unknown origin (see Nitzan Rosenfeld's work from his days at Rosetta).

I'm less convinced about the focus on lung cancer. Although it has a high mortality burden there is an effective treatment the government could focus on and that is getting people to stop. They missed a golden opportunity earlier this year in following Scotland's lead in plain packaging on fag packets. My wife and I watched a file the other night and in one scene people were smoking on a plane. My kids will hopefully think I'm pulling their legs when I say we had a choice of smoking or non-smoking when we went on our first holidays. The culture is changing and a ton of cash on lung cancer genomes might be better spent on a different disease. 

Rare diseases working group: ~6% of the population is affected by a "rare" disease but even with sequencing a significant challenge is that while in many cases we might identify a causal variant, there may be no possibility of treatment. The working group report suggests a transitional model where exomes are sequenced instead of genomes. This seems a sensible short-, and possibly even long-term solution. 

Infectious diseases working group: HIV, HepC and TB have been prioritised and their sequencing will help establich the infrastructure required for wider pathogen/microbial sequencing programs. Rather worryingly the working group report points out that HIV had a record number of new infections!

£100M was announced by David Cameron but this won't go far even at £1000 per genome. Once sample collection and analysis are included then perhaps only half of the money will be left for sequencing. So amplicons and exomes are going to be needed in the next few years. True £1000 genomes are on the way but I think we'll wait five, even ten, years before seeing this in the NHS.
Genomics England will provide the investment and leadership for the 100,000 genome project, which will hopefully build on the UK's track-record in medical science and genome-sequencing technology, keep the UK at the forefront of the genomics revolution and make us the place to develop better tests, drugs and ultimately treatments. The impact on our understanding of disease is likely to be significant and should improve patient outcomes.









2 comments:

  1. I agree. Always be better to be positive than worry about the sums!
    btw which genome did he sequence on a Miseq? Surely not a human, unless there some poetic licence here. I guess you didnt you trust him to press go on a Hiseq run!

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  2. It was Prince Philip's genome, part of the Nobility-genome project.
    ;-)

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