LABORATORY INFORMATICS
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format – to be stored in a variant database, OpenCB is a high-performance solution for indexing and analysing many hundreds of thousands of samples, he believes. Medina, who has been Head of the Computational Biology lab on the HPC team at the University of Cambridge since 2015, conceptualised and founded the OpenCB project while working in Spain during 2012. Within a few years, the platform was gaining the attention of some major genomics research initiatives. ‘At first, it was just a prototype – very small – but this was enough to raise the attention of EBI, the University of Cambridge and Genomics England in 2015, which adopted and contributed significantly to its development,’ he says. During this period, Medina remained the platform’s architect and has led the design and development of OpenCB. ‘Today, OpenCB also includes a metadata and clinical database, fine- grained security management and a knowledge database, representing a complete genome data interpretation platform,’ Medina notes. As an open-source platform, OpenCB
is accessible and free-of-charge for any organisation looking to manage and analyse genomics data in a non- regulated setting. In 2019, Medina spun Zetta Genomics out of Genomics England
22 Scientific Computing World Summer 2022
and the University of Cambridge to commercialise the OpenCB technology as XetaBase – a regulated, clinically validated and technically supported data architecture and software solution that is applicable for clinical genomics data management and evaluation at large scale. ‘Zetta Genomics is, effectively, the
commercial venture established to extend the scope of OpenCB, and XetaBase – OpenCB’s commercial name – was created and launched in 2020,’ says Medina. ‘XetaBase is now becoming a certified platform that meets the regulatory requirements for data in clinical settings, while also addressing the need for customer support and implementation skills ‘built-in’. It’s offered as a software and through a service model, so we provide updates, fixes and training, along with ongoing support.’ Medina remains the CTO of Zetta Genomics, which is now also the main
“Regulatory and security issues aside, clinical labs face particular challenges with respect to how you deal with patients”
contributor to OpenCB. In June 2021, Zetta won £2.5 million in VC seed- funding. This investment is being focused on growth, improving performance, stability and implementing new analysis. Some is also enhancing the company’s partnership network while it expands from the UK to open both Spanish and US offices. Resource is also being focused on talent; securing additional team members with software, development and commercialisation expertise. Importantly, the OpenCB and XetaBase data architecture supports regulatory governance for clinical and genomic data management, including NHS digital security and privacy policies. ‘Regulatory and security issues aside,
clinical labs face particular challenges with respect to how you deal with patients’ genotyping test data,’ Medina explains. These challenges relate to the sheer numbers of tests that are performed and the volumes of data generated but, also, the almost inevitable shortfall in human resources to analyse all the data for each patient in the hunt for a gene variant that might be the pathogenic cause of a disease. Another challenge that the OpenCB
platform and XetaBase address is one of data sharing between scientists. Typically, if a clinician identifies a new disease-
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