VOL. 132 | NO. 135 | Monday, July 10, 2017
Memphis Researchers Planning Big Upgrades to Online Genetics Database
By Andy Meek
A pair of scientists in Memphis is using almost $2 million in grant money to make improvements to an online database and open-source software system called GeneNetwork, used by researchers to study genetic differences and evaluate disease risk.
Drs. Robert Williams and Saunak Sen, both part of the faculty at the University of Tennessee Health Science Center, won a grant from the National Institutes of Health for the project. GeneNetwork was launched in 2001 as part of a NIH Human Brain Project grant to UTHSC and was one of the first websites designed for gene mapping.
Williams, who chairs the Department of Genetics, Genomics and Informatics at UTHSC, said the grant money will be used to support major upgrades for the software infrastructure for gene mapping and analysis for the system. One of the system’s main uses, he said, is being able to predict more accurate health outcomes from genetic and environmental data.
The system itself is like a combination of Microsoft’s popular Excel spreadsheet software paired with large amounts of financial data. Except in this case, it’s biological rather than financial data, combined with a sophisticated spreadsheet that allows users to perform their analyses.
Those users include undergraduate, graduate and postdoctoral students. The biggest slice of users is scientists, Williams said, who are interested in understanding the relationship between genetic differences and health status.
“The grant has four major aims that will be stretched out over four years,” Williams said. “The first is to make this more useful to a larger community of users. Getting data in and out of GeneNetwork is quite a bit of work, so we’re going to be building some software that allows easier data entry into GeneNetwork.”
The team at UTHSC – which is where the GeneNetwork hub exists – also wants to make some statistical improvements to the system. They’ll also be developing new analytical methods as well as tools so that the system is accessible not only to students and scientists but also professional statisticians, computer scientists and users at big pharmaceutical companies who Williams said need a different type of interface than what exists now.
The team supporting GeneNetwork actually extends beyond Memphis, spanning the globe, in fact. Other key members include Dr. Pjotr Prins, a computer programmer based in the Netherlands who’s responsible for the software architecture. Dr. Karl Broman, a statistical geneticist from the University of Wisconsin-Madison, is also contributing to the project. And at UTHSC, Dr. Yan Cui, a computational biologist in the Department of Microbiology, Immunology and Biochemistry, is also working on the project.
According to Dr. Sen, GeneNetwork will facilitate “reproducible research” because of the way it gives researchers open access to both the data and the software code used to process it. “Reproducibility,” he said, “is essential to the scientific method, and we’re proud to be part of the open science movement.”
The second generation of the service, called GeneNetwork 2, can be accessed at http://gn2.genenetwork.org/.
“There are exponentially growing databases on humans and mice and rats and plants,” Williams said. “And it’s really difficult to handle all those huge data sets. So what we need are online tools for analyzing and integrating those data sets, and GeneNetwork is a tool for doing just that.
“It provides access to a lot of data sets and the genotypes of subjects, and it allows you to analyze what the relationship is between genetic differences and outcome measurements. Like, how much do you weigh, are you likely to have diabetes, how long will you live, things like that.”