Open-source database enhances genomics research collaboration

Chloe Kent 4 November 2019 (Last Updated December 23rd, 2019 10:25)

An open-source database of genomic variants in health and disease has been developed by Australian and North American researchers to simplify the sharing of this information between academics.

Open-source database enhances genomics research collaboration
Until now, MAVE data from experiments has either been uploaded to journal websites or provided on request to other researchers. Credit: Walter and Eliza Hall Institute

An open-source database of genomic variants in health and disease has been developed by Australian and North American researchers to simplify the sharing of this information between academics.

The MaveDB database stores data from multiplex assays of variant effect (MAVE) experiments, which systematically measure the impact of thousands of individual sequence variants on a gene’s function. It was developed by researchers from the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia, as well as the University of Washington in the US and the University of Toronto in Canada.

MAVE experiments provide valuable information about how genetic proteins function, how genetic variants may contribute to disease, and how to engineer synthetic versions of naturally occurring proteins that are more effective than the original protein.

Until now, MAVE data from experiments has either been uploaded to journal websites or provided on request to other researchers. This has made it hard for clinicians to access the data of other groups, or even know if a particular MAVE experiment has been carried out elsewhere in the world, hindering both collaborations and the progress of genomics research.

Walter and Eliza Hall Institute bioinformatics researcher Dr Alan Rubin said: “MaveDB makes it easier for scientists to share their datasets in a single location, using a flexible format that is applicable to multiple research fields, and enables other scientists to easily access this data to enhance their research.

“We’ve also ensured MaveDB can ‘talk’ to other databases to add an extra level of collaborative capacity. For the growing field of MAVE research this database is an important step towards open science and reproducibility by ensuring data is made available.”

Alongside MaveDB the team developed a data visualisation platform called MaveVis, which makes it easier for researchers to understand and interpret the results of MAVE experiments.

Rubin said: “MaveVis provides an immediate and consistent display for MAVE data, including valuable annotations such as protein structure information, that will accelerate collaborative research.”

The research was funded by the Brotman Baty Institute for Precision Medicine, the US National Institutes of Health, the Canadian Institutes of Health, the Lorenzo and Pamela Galli Charitable Trust, the Australian National Health and Medical Research Council and the Victorian Government.