Wednesday, 23 June 2010

Clinical Sequencing in the UK

It would appear that one of the first exome-sequencing projects run by the NHS is being launched at the Royal Brompton Hospital in London. Their aim appears to be to associate rare and common variants with cardiomyopathies and the results of MRI scans.

This is quite a leap forward for clinical sequencing, but I wonder whether they may be a little premature? The costs of sequencing have been plummeting for the last decade, but the current technologies have their own cons as well as pros. Sure they're faster and generally more high-throughput; but they also generate shorter read lengths and are thus more prone to sequencing errors which makes in depth sequencing a must for accurate data requisition. Then there is the computational analysis and storage requirements. Next-gen sequencers generate Gb of data and require specific bioinformatic tools to deal with sequence alignment because of the short read length, as well as the IT infrastructure to deal with the sudden explosion in data quantity; 10,000 exomes is a lot of information to handle and store. I can only assume they have these tools and expertise in place. What of the variants that are not known to be associated with cardiac defects, yet predispose to it nonetheless? Are they going to assess these as well. Their press release talks of tailoring each patients treatment to their genotype - that is premature!

The pros are just as numerous as the cons. Complete exome-sequencing will be able to uncover the rare variants that are most likely to have a high impact on disease risk and severity. They will be able to compare high resolution imaging directly with genotypic data, as well as other clinical and phenotypic information collected by the medical staff. This project may well set a precedent for clinical sequencing in the UK if the predicted results are as spectacular as they could be. Oh and they are looking for volunteers, preferably ones with a family history of cardiomyopathy. If it weren't all the way down in London I'd be tempted to give it a whirl, as long as I could get a copy of the data back for myself - cheaper than DTC testing!

I will be intrigued to see what comes of this project. I personally wouldn't have predicted routine clinical sequencing for another 20 years, perhaps the Royal Brompton Hospital researchers might be able to bump that forward a little.

Edit: Royal Brompton Hospital Press Release

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