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UK Biobank: Out on a LIMS

May 15, 2007 | Last month, David Sanders, LIMS manager for the UK Biobank, managed the live deployment of the Thermo Scientific Nautilus LIMS.  The Biobank’s task is enormous: the UK Biobank is recruiting 500,000 volunteers from across the United Kingdom. In addition to answering some 200 lifestyle and medical questions using automated touch screen technology, participants will donate blood and urine for a total of up to 15 million individual aliquots. All that must be tracked without a glitch by the LIMS.

Prior to joining UK Biobank last year, Sanders had seven years of experience with Nautilus in various industries including pharma, so was happy with the selection.

Among the factors in the decision, Sanders says, was his colleagues’ past experience with Nautilus. “Other factors include location of Thermo’s service and support team [based near UK Biobank’s headquarters in Manchester], the experience and background of Thermo as a LIMS supplier, and the flexibility of the software itself with the option to build ‘extensions’ in order to interface to other systems.”

LabVantage’s LIMS, Sapphire, “was very much a consideration during the tender process,” says Sanders. “However, when two products satisfy your requirements, you have to look beyond the software and look more closely into what the company can provide in terms of service and support.”

LIMS Tracker
Nautilus has a massive job. Once volunteers’ blood and urine samples have been collected, they are couriered to the Biobank central laboratory, and fractionated by the state-of-the-art robotics systems into 30 aliquots per person.

Blood is separated into constituent parts, red blood cells, white blood cells, plasma, and serum, and samples are frozen at both —80˚ C and in liquid nitrogen (the latter stored at an external site.)

The aliquots are specially bar-coded in a way that works at very low temperatures. “The bar code is the key to tracking samples, aliquots, and data within the lab and it’s important that we don’t encounter duplicate barcode IDs throughout the lifetime of the project,” says Sanders.

The fractionation robots scan the bar codes from each 1-ml tube and rack, with output files recording the links between each. “Once the run is finished, the files are sent to the LIMS and a customized extension parses the files and enters the data within the LIMS in a hierarchical manner,” says Sanders.

Following fractionation, the sample racks are transported to frozen storage. The liquid nitrogen tanks contain towers and each compartment within the tower is bar-coded. “We use a PDA bar code scanner with bespoke software installed to take the bar code of the plate, its compartment position and the tower position. This information is then uploaded to the LIMS once all the plates for that day have been stored using instrument integration,” Sanders says.

The 15 million aliquots aren’t the end of it. “From a LIMS perspective, for each aliquot, we will be storing its parent (original 10-ml vacutainer barcode ID), it’s grandparent (anonymous participant ID), rack barcode ID, position on rack, location of rack in our store, aliquot contents, etc. In all we are looking at obtaining several hundred million data points within the [underlying] Oracle database.”

Looking further, it is possible that analytical results in addition to the raw data will also be stored within Nautilus once enough samples have been collected. “We’ll be making that decision closer to the time,” Sanders says.

Kasner says that the Sapphire biobanking module wasn’t ready when UK Biobank made its selection. He adds that the UK’s new national cancer tissue bank, OnCore UK looked very closely at the UK Biobank’s LIMS selection, and still ended up choosing Sapphire. -- K.D.

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    In the June 2007 issue, "Bio-IT World" issued a correction to this article as it had used the name "Out on a LIMS" not realizing it was the name of another publication, "Out on a LIMS: The Newsletter For People Who Risk Life and LIMS on a Daily Basis." Although this was a mistake on the part of "Bio-IT World," it was quick with its correction regarding this error.

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