Putting the tech in biotech
Albie Attias shines a light for the channel on the role of IT in genomic medicine
A year on from the government's announcement that 100,000 whole genomes from NHS patients will be sequenced by 2017, the medical community is preparing for a revolution in the way life-threatening illnesses, diseases and common conditions are detected, prevented and treated.
While this is a fascinating development for society as a whole, it is particularly interesting for the IT sector, which will be directly affected by the huge repercussions resulting from this shift in medicine.
Full genomic sequencing refers to the laboratory process of determining the order of every element of DNA within one person.
Billions of 'letters' form a person's DNA; every single one of these is read, recorded, then ordered to create a person's full DNA sequence.
This acts as a reference point for that individual, who can be re-sequenced an infinite number of times during his or her life, enabling medics to identify any changes to that person's DNA.
The amount of raw data that will be created, processed and stored through genomic sequencing is unprecedented. The pressure this places on servers and other infrastructure is vast, not to mention the security implications of dealing with this kind of data.
Medics and IT professionals are facing this challenge together, with a number of pioneering genomic projects already underway in the UK.
One such project is led by Dr Shahid Mian, who has partnered with the Universities of Cambridge and Nottingham to research breast cancer and lymphoma, using innovative genomic sequencing to analyse the genetic profile of patients.
Dr Mian says: "Our aim is to identify genes that are present in breast cancer sufferers, then explore how these change as the disease develops and as treatment is modified. We take a standard reference genome from a patient and compare this with subsequent DNA to understand how the person's genes have altered -- the more times we can do this the better. A few years ago the bottleneck for this process was simply how to generate the raw data, but with new high throughput DNA sequencers the issue has now moved to the problem of storing and analysing the data."
Cloud technology is an option for genomic researchers, but drawbacks include concerns over security and the ability to cope with the sheer volume of data being processed, analysed and uploaded on a daily basis.
Some research teams rely on portable hard drives which are used as a temporary storage and serve the purpose of recording and storing data. But this is a short-term answer to a problem that is only going to grow as the cost of genomic sequencing drops and the frequency rises.
The solution for Dr Mian is a high performance server equipped with a high number of processing cored for rapid, intensive data processing with 1.2TB of storage. This would enable ongoing research and constant analysis, as well as allow the team to maintain valuable records (so-called ‘cold data') that can be accessed long into the future.
Ethical and cost implications aside, if genetic sequencing from birth becomes commonplace, the need for hardware to process and record this data will grow exponentially.
With an ageing population placing a heavy burden on the NHS, genomic sequencing could provide an answer to treating - and indeed preventing - many of the conditions that affect the British public.
If the cost of genomic sequencing continues to drop, medics could introduce the process to more people and put them on preventative courses of action. The IT industry needs to act now in order to respond to this growing need for solid, powerful and secure technology that makes this potential medical revolution a reality.
King of Servers supplied Dr Mian's with a ML350p Gen8 tower server fitted with two 600Gb SAS drives, a 480GB solid state drive and 64GB of RAM.
Albie Attias is director of King of Servers