Information management and next-generation sequencing

In 2009, when the Queensland Centre for Medical Genomics (QCMG) received the two largest grants in Australian history for sequencing research, it knew it would have to get serious about managing data. It responded by implementing the GenoLogics LIMS, a system specifically designed to manage data associated with genomics, proteomics and next-generation sequencing.

A LIMS was a natural addition to QCMG, which runs a fleet of 10 SOLiD 4 Genome Sequencers, five 5500xL Next-Generation Sequencers and a suite of Ion Torrent PGMs. “We had built various informatics tentacles to support all of our lab activities, but we needed a centralised brain that could track everything and serve as a hub for us to monitor the work we were doing,” said Peter Wilson, Executive Officer at QCMG. “The LIMS serves as the brain.”

The LIMS has enabled QCMG to take control of previously unstructured data stored in scattered spreadsheets, enabling them to reduce pipeline stalling errors and measure lab progress to improve efficiency. David Miller, QCMG’s Sequencing Manager, noted that the system is particularly important given the necessary interaction between three groups of scientists at QCMG: sequencing, informatics and analysis.

“The time saved because of the LIMS is allowing our teams to look at the data in more depth, gain greater insight in the research and development experiments we run and spend less time on menial tasks like data entry and tracking and more on molecular biology,” he said.

The GenoLogics LIMS offered powerful functionality that provided the adaptability and flexibility QCMG demanded. “Even within the same platform, in two to three years we’re working with a totally different workflow,” said Conrad Leonard, Bioinformatics Engineer. “We need to be able to adapt and not have to send out for customisation or build out integrations ourselves. The GenoLogics LIMS offers the flexibility, through its Rapid Scripting API, to allow us to adopt the systems we need knowing that within the core LIMS we’ll be able to model pretty much any kind of workflow we need to use.”

Leonard described LIMS as an enabling technology. “Without a LIMS, there’s no way to automate anything; and with the amount of work we’re doing, it’s inconceivable to enter data at the command line, look up data scattered in half a dozen spreadsheets, and do this over and over for every single run,” he said.

Miller concurred. “Having worked in centres previously that lacked a true LIMS for next-gen sequencing, I can safely say that the benefits of this cannot be underestimated,” he said. “The sheer amounts of data, time and effort required to generate and analyse these datasets necessitate the use of a quality, well-maintained and well-utilised LIMS.”