laboratory informatics


team of Washington lawyers, while the technical work is being carried out by the German soſtware company Osthus.


Replacing old LIMS – transformational not incremental change Te pharmaceutical industry’s growing interest in data analytics discussed by Rachel Uphill had also been highlighted by Patrick Pijanowski in his keynote address, as one of the reasons that change was happening in the informatics industry now. But a second driver for change, he continued, is that existing mature laboratory informatics systems are being replaced because they have come to the end of their lives or because systems are no longer supported by the vendors. ‘LIMS is a ubiquitous common-core data


platform and represents a huge investment when it has to be replaced,’ he said. Companies will be unwilling the spend the money just to get an incremental upgrade, he believes; instead they will go for transformational, holistic change. Pijanowski’s thesis was exemplified in the


talk that immediately followed his presentation, when Christian Wolf described the FELD project (Future Environment Laboratory Domain) within Bayer Pharma. Wolf, who is head of IT Systems at Bayer’s Global Chemical and Pharmaceutical Development, explained that three of the major laboratory systems that the company had been using were no longer supported by the vendors. Indeed, one vendor was no longer in business. Faced with this situation, ‘we did not want to


replace but to have more time for science and spend less time on documentation,’ he said. Tey also wanted to use common IT platforms across three departments, which were geographically separate from each other. But in another theme common to many


presentations to the PLA, Wolf said that they wanted to harmonise laboratory processes as well as the informatics systems. Other objectives were to eliminate data redundancies and fragmentation, to have self-documenting processes, to connect up all the instruments in the laboratories, and to optimise data reporting. Te new system is expected to go live towards


the end of this year, with roll-out to the analytical laboratory early in 2016. Te optimistic scenario was, he said, that the resulting efficiencies would recoup the cost of the installation within two years. When pressed, he conceded that ‘there are no official pessimistic scenarios’.


Dead data and lost knowledge Although the Bayer Pharma project was intended to harmonise working practices across three disparate laboratories, it was not an outsourcing project – all three sites were part of Bayer. Te risks of outsourcing were highlighted by Ryan


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Sasaki of ACD/Labs in his talk to the Paperless Lab Academy. His talk picked up and further developed Pijanowski’s points about data analytics and data integrity in an externalised world. ‘Externalisation leads to lost knowledge,’ he warned. Te CROs to whom the pharma companies outsource operations will build up their own expertise and understanding of lab processes as a result and thus create knowledge that is not being captured by the pharma company itself. Sasaki pointed out that there is a difference


between small molecule and biologics in terms of where the intellectual property (IP) resides. It is usually the case that the IP for small molecules lies in the chemical structure – which the pharma company can capture for itself. However, oſten the IP for biologics lies in the process, not the product. Investing in laboratory informatics soſtware will therefore pay off relatively early in the case of small molecules – in the discovery or development lab – but it will be much later in the case of biologics. Te difficulty in capturing such knowledge is


all the greater because currently around 60 per cent of the data exchange between a CRO and the


MORE TIME FOR SCIENCE, LESS ON DOCUMENTATION


sponsoring company is being done by email and PDFs. ACD/Labs regards this as ‘dead data’, he told the meeting: ‘If the only way you’re receiving data from your CRO is via PDF, then you’re losing a lot of knowledge.’ Te inadequacies of such a method for


transferring scientific information also increase the risk that the ‘proof of identity’ of a sample might be lost in the transfer of materials between the contractor and its client – another form of lack of knowledge by the pharma company itself. As an example of just how serious the consequences can be, Sasaki cited the example of Bosutinib, a tyrosine kinase inhibitor that has received approval for the treatment of adult patients with some forms of chronic myelogenous leukemia (CML). However, as a selective kinase inhibitor, the compound is the subject of much more medical and basic research. Some three years ago, much of this was invalidated (including findings published in scientific literature) and had to be redone because researchers had unwittingly been using an isomer of Bosutinib instead of using the genuine compound. Te compounds had been synthesised by contractors and they had unwittingly produced biologically inactive isomers and this had not been detected by many of their customers. To combat some of these issues, he offered


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the ACD/Spectrus platform as one route to a ‘universal data language’ that could avoid the need to deal with ‘dead data’ in an externalised world and instead move to active data and knowledge generation. ACD/Labs was, he said later, a partner in the Allotrope initiative and saw that the work of Allotrope not only as complementary to ACD/ Labs own line but, by helping promote the concept of more usable data and metadata, as bringing about a wider realisation of the advantages of moving away from the dead data syndrome.


Disruptive technologies Te disparate threads of outsourcing, maintaining in-house knowledge and quality control, and disruptive technologies – both the cloud and big data – were brought together neatly in the presentation from Nicolas Goffard. He is bioinformatics platform manager for the French start-up biotechnology company Enterome Bioscience, which was spun out of Inria, the French public research agency dedicated to computational sciences, in 2012. Enterome Bioscience is looking for bacterial


genes specific to disease and is sorting through human faeces to find them. Te aim is to improve treatment of chronic metabolic, gastrointestinal, and autoimmune diseases. Although patients may have a genetic susceptibility, the conditions are also triggered by environmental factors including an imbalance in the intestinal bacterial ecosystem. A start-up, Enterome has to outsource its


sample collection and analysis, and has to send data out for biostatistics and bioinformatics analysis. According to Goffard, however, it is still vital, under whatever ‘virtualisation’ model might be adopted, to keep quality standards high even despite the pressures of trying to achieve results rapidly. Enterome reached for a cloud solution in the form of Core Informatics’ LIMS to manage the data collection, the data generation, and the results of the data analysis. Enterome outsources the process of collecting the stool samples and then processing them to extract material suitable for analysis; the DNA extraction and sequencing is the next step; and the final, added-value step is the application of bioinformatics and biostatistics methods to analyse the data. It opted for the Core LIMS web-based product, together with Pipeline Pilot, he said, because the system had to be highly configurable to support new workflows and new partners. ‘We didn’t have any trouble using the cloud’, Goffard said. ‘It’s secure.’ Te Paperless Lab Academy continues to


be possibly the most interesting and thought- provoking event dealing with laboratory informatics. By providing a synoptic overview of the informatics landscape and identifying trends and developments for the future, this year’s meeting of the PLA if anything surpassed the event in Amsterdam last year.l


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