Biomedical Engineering Reference
In-Depth Information
22.6 The Pistoia Alliance Sequence
Services Project
NGS has produced a boom in commercial opportunities; from companies
that build the robots to do the work, and reagents needed to fuel the
process, to high-tech sequencing centres with the capacity and expertise
to service the sequencing needs of many life science companies.
Consequently, a great deal of sequencing is outsourced to these centres.
Once the raw sequencing has been completed, the complex process of
assembling the DNA jigsaw starts, prior to the next level of analysis
where patterns in variation are identifi ed. These are correlated with other
observable traits (know as phenotypes to geneticists) such as how well
someone in a clinical trial responds to the treatment. Increasingly, it is
likely that some or all of this analysis may be done by specialist companies,
external experts or via research agreements with universities. All of this
work is done under complex legal contracts and conditions, which ensure
appropriately high ethical and security standards are always adhered to.
Managing these complex collaborations can produce a huge logistical
and security challenge for IT departments. The fi rst of these problems is
in shipping the data to where they are needed. As the data sets tend to be
very large, sending the data over the internet (usually a process known as
Secure File Transfer Protocol, or SFTP) can take a very long time. So
long, that it is often far faster to use what is jokingly called the 'sneaker
net', which in reality tends to be an overnight courier service transporting
encrypted hard drives. This then involves the complexity of getting the
decryption keys to the recipients of the hard drives, and therefore the
setting up of a key server infrastructure. Once the data have been
decrypted, they inevitably get moved onto a set of servers where they can
be assembled and analysed. Controlling who has access to the data, and
managing copies becomes hugely complex, and expensive to manage.
The past few years has seen a new phrase enter the IT professional's
vocabulary, 'cloud computing'. By 2011 almost every major IT company
offers its own cloud platform, and hundreds of analysts' reports
recommend that corporations leverage the cloud as part of their IT
infrastructure strategies. In theory, the cloud was the perfect platform to
answer the challenge of NGS data. The cloud is fantastically scalable, so
IT managers would not have to estimate data volumes at the beginning
of a budget cycle, then have spare capacity for most of the year, only to
have to scramble for more at the end of the cycle if use had been
underestimated. The cloud also has huge on-demand computational
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