Massive Parkinson Disease Database Adding RNA Sequencing Data

AUGUST 23, 2019
Kenny Walter
Arthur Toga, PhD

Arthur Toga, PhD

A massive new dataset of RNA sequencing data is now included in the Parkinson’s Progression Markers Initiative (PPMI), a database which involves collecting clinical, biological, and imaging data from 1400 individuals over at least 5 years.

The new sequencing data was analyzed by the University of Southern California’s (USC) Institute of Translational Genomics and are being stored and shared by the Laboratory of Neuro Imaging, part of USC’s Mark and Mary Stevens Neuroimaging and Informatics Institute.

Arthur W. Toga, PhD, director of USC's Mark and Mary Stevens Neuroimaging and Informatics Institute, explained in an interview with MD Magazine® the database gives researchers around the country easy access to data in an effort to improve research practices.

“This data is available to any scientist basically who wants to take this data and do analytics on them,” Toga said. “These are important things because it really kind of democratizes access to vast amounts of data that would be expensive in your own center.”  

Toga collaborated with The Michael J. Fox Foundation for Parkinson’s Research (MJFF) in adding the new RNA sequencing data to the database.

RNA sequencing is a process that involves analyzing blood samples, giving researchers a better understanding of how genetic scripts are expressed in various biological processes such as disease states with the long-term goal of identifying some of the earliest hallmarks of Parkinson disease that may appear prior to symptoms arising.

Prior to the database becoming available for researchers, investigators were required to download massive files and go through a time-consuming process of organizing, harmonizing and, analyzing raw data.

PPMI researchers adhere to strict protocols for obtaining and storing data, rendering the data highly reliable, while reducing inconsistencies or potential sources of bias.

Toga’s team has also begun co-locating visualization, analytic, and data storage technologies, enabling researchers to instantly conduct preliminary analysis online without needing to download any files.

"PPMI has built the most robust Parkinson's dataset to date, collecting clinical, imaging and biological information from volunteers over at least five years to better understand disease onset and progression," Todd Sherer, CEO of the MJFF, said in a statement. "The PPMI RNA Sequencing Project significantly increases the study's value and moves us closer to its goals to better define, measure and treat Parkinson's disease."

The database currently stores data from nearly 50,000 subjects in 125 different studies, has also pioneered secure methods for processing, sharing and visualizing large datasets. 

The RNA sequencing project alone amounts to 108 terabytes, the equivalent of 47,520,000,000 single-spaced typed pages--along with the open-access portal that combines storage, analytic and visualization functionalities.

Ultimately, Toga said the PPMI database will accelerate the pace of discoveries and lead to better drugs and therapies to treat the disease.

“The PPMI data has really done wonders in terms of characterizing the disease and its progression over time and I think these are the kinds of things that will help provide a testbed to evaluate the efficacy of new treatments,” Toga said.
 

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