Research carried out Barcelona Supercomputing Center (BSC) which reanalysed public genetic data using innovative computational methods has enabled the identification of new genetic markers associated with an increased risk to develop Type 2 Diabetes (T2D).
The study, published today in Nature Communications, represents a new way of exploiting preexisting genetic data to obtain new and relevant discoveries for genetics and biomedicine, highlighting the importance of data sharing initiatives and policies in science.
This study has generated and applied innovative approaches for GWAS analysis to publicly available genetic data for around 70,000 individuals. This method led to the identification of seven novel regions that are associated with increased risk for type 2 diabetes.
‘By re-analysing public genetic data in-house, we had the opportunity to deeply explore the role of genetic variation from the X chromosome, which is often neglected from genetic analysis. Our findings underscore that novel insights into disease biology have been missed for the mere fact of excluding this data’ commented Sílvia Bonàs-Guarch, first author of the study.
Although around 100 regions of the genome have been reported to be associated with increased T2D susceptibility, most of them modify the risk in the range of 5 to 30 per cent. One of the novel regions reported in this study corresponds to a rare genetic marker in the X chromosome that increases the risk for T2D by 200 per cent in males. This suggests that the identification of such marker prior the development of T2D could be useful to design and apply preventive strategies that delay or avoid the development of this disease. Furthermore, this study shed light on the potential mechanism behind this increased risk, pointing the gene AGTR2, as a potential target to develop effective treatments.
David Torrents, ICREA Research Professor and Computational Genomics group manager at BSC and Josep Mercader, collaborator at the same institution, have supervised the project. In addition, internal BSC efforts also included the activity of the Workflows and Distributed Computing group led by Rosa Badia.
‘The sharing of data in biomedicine allows its reanalysis using newer and more efficient approaches and to answer more ambitious questions regarding the basis of disease, as we have done in this study for type 2 diabetes’, added David Torrents.
The continuous increase of the production of data in biomedicine, mostly due to the advances in DNA and RNA sequencing technologies, allows the search of the genetic and molecular basis of disease at an unprecedented speed and resolution. This research and similar projects exploring the potential for genetic data are helping to pave the way for future studies into the use of precision medicine and could help to uncover new treatments or knowledge for serious conditions such as cancer or diabetes.
‘We honestly were surprised by the amount of additional information that can be obtained by reanalyzing the same data with novel computational and genetic resources’, said Josep Mercader, co-supervisor of this work.
Along with the BSC, other leading institutions around the world have contributed to this study, including the Institute for Research in Biomedicine (IRB, Barcelona), the Massachusetts General Hospital (Boston), the Imperial College (London), the Broad Institute of MIT and Harvard, and the University of Copenhagen, among others.
This work has been sponsored by the grant SEV-2011-00067 of Severo Ochoa Program, awarded by the Spanish Government. This work was supported by an EFSD/Lilly research fellowship.