DATA MANAGEMENT: BIOBANKING
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very much separated from the research data, Greenhalf says. Tissue is stored and used by the ECMC-GCLP facility, but the details of the patient are kept in the Liverpool Cancer Trials Unit or on-site in the hospital.
Next-generation biobanking
Biorepositories provide a resource for researchers to increase understanding of complex diseases. Studies such as the Lung Genomics Research Consortium (LGRC), a two-year project launched in October 2009, are going a step further than standard biobanking practices and characterising the samples with their molecular makeup. The molecular data can then be mined along with the clinical data. Led by National Jewish Health and funded
by the National Heart, Lung and Blood Institute, a division of the National Institutes of Health (NIH), the LGRC project consists of fi ve institutions, including Dana-Farber Cancer Institute. Collaborators in the project work with samples banked at the Lung Tissue Research Consortium (LTRC), which houses tissue samples and blood from lung disease sufferers, primarily chronic obstructive pulmonary disease (COPD), along with a rich set of clinical data from patients. The LGRC will take a subset of the LTRC’s
samples (around 500-1,000) and characterise their DNA, RNA and methylation profi les. All the sites involved in the project will generate molecular data that will be passed to Dana-Farber. The centre’s role is as a data coordinating facility to combine the clinical data captured by the LTRC with the molecular profi ling and make this available within the consortium and the scientifi c community at large. ‘One of the most valuable resources researchers have is well annotated tissue samples and in cancer research, scientists have been able to develop much more fi ne- grained characterisations of disease based on molecular profi les,’ remarks Mick Correll, associate director of the Center for Cancer Computational Biology at Dana-Farber. ‘We’re trying to do the same thing for lung diseases.’ IDBS’s ClinicalSense, a web-based clinical
cohort selection tool, was used to create an online, searchable data catalogue of all the clinical information in the LTRC to help initially with design of experiments. Using the software, the thousands of clinical attributes
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The laboratories at the Roy Castle Lung Cancer Foundation, University of Liverpool Cancer Research Centre.
were built into an ontology, which was made accessible through a web portal. This allowed collaborators to acquire summary information about the number of participants, the number of samples, and the type of samples that were available based on given criteria. ‘Ultimately, we want to move beyond just
capturing information and give clinicians and researchers a way to analyse the information that’s been collected,’ says Correll. ‘The information we’re working with is quite complex, it’s highly dimensional data, and in order to present this to a non-expert audience, visualisation is key.’ IDBS’s VisualSense software, a web-based data visualisation tool, means the data is presented in a meaningful way and allows researchers to fi nd elements they want and make selections between different assay data. One of the issues surrounding biobanking
that John Quackenbush, director of the Center for Cancer Computational Biology at Dana-Farber and one of the principal investigators (PIs) on the LGRC project, identifi es is how one collects and manages the clinical data associated with the samples, in terms of informed consent and dealing with ownership of data and samples. ‘There is a tremendous amount of clinical data available to the LGRC project from the LTRC,’ he comments. ‘However, once genomic data is generated, even though these are de- identifi ed samples, there are all sorts of issues surrounding how that data is made available to the community. There are concerns about privacy, because the genotype is a very precise way of identifying an individual.’ One of the solutions Quackenbush proposes to the privacy issue is to send the data to dbGaP, the database of Genotypes
SCIENTIFIC COMPUTING WORLD APRIL/MAY 2010
and Phenotypes maintained by the National Center for Biotechnology Information (NCBI), which has a structure in place for controlling and monitoring access. However, he states: ‘We believe that we can add signifi cant additional value to the data beyond what dbGAP can provide because of our ability to integrate the expression, variational, and clinical data that the LGRC will be generating. Elsewhere, the Canary Foundation, a non-
profi t organisation dedicated to early detection of cancer, in connection with the National Cancer Institute’s Early Detection Research Network (EDRN) has commissioned a translational research informatics platform to provide integrated translational research data (clinical and omics datasets). The cloud-based platform will be built by GenoLogics and NASA JPL and will aim to support research activities from discovery to biomarker validation to clinical results. Another challenge faced within the
LGRC project that Correll identifi es is how to catalogue the large amounts of molecular data generated in such a way as to make it useful, not only to the expert users – the biostatisticians – but to the researchers themselves. Dana-Farber’s contribution to the LGRC is trying to take all the genomics data and put it in an intuitive format for the broader community of users. ‘What’s going to describe whether our efforts in using biobanks to do genomic profi ling are successful, is whether or not this has any kind of clinical impact,’ says Quackenbush. ‘There are the ethical, social and legal problems, but there are also some serious technological problems for which we have to fi nd solutions,’ he added.
www.scientifi c-computing.com
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