Researchers from the CIT and CIT spin-out NSilico Life Science collaborated with the George Washington University to publish an article in PLOS Biology
Researchers from CIT collaborated with the George Washington University (GW) and the US Food and Drug Administration (FDA) to publish an article in PLOS Biology, describing a standardized communication method for researchers performing high-throughput sequencing (HTS) called BioCompute.
HTS is a catalyst for novel drug development and personalized medicine inroads. This new technology has outpaced the development of much-needed infrastructure around its use. Lead author Raja Mazumder, PhD, associate professor of biochemistry and molecular medicine at the GW School of Medicine and Health Sciences, collaborated with CIT’s Professor Paul Walsh on this paper.
Mazumder, colleagues at the FDA, and several industry leaders collaborated on the BioCompute Object Specification Project, which enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This project includes a framework, which facilitates communication and promotes interoperability. The standard is freely accessible as a GitHub organization.
Professor Walsh was responsible for inputting into the standard from both an academic and Industry perspective. He advised on technical aspects of the standard and helped to build some experimental prototypes to explore its practical application.
Professor Walsh explains that “advances in sequencing and ITC technology offer untold promises in the area of personalised medicine, which promises to radically transform healthcare and medical treatment in the 21st century by precisely and accurately retargeting medical treatment. Effective medicine is one that treats the person not just the disease, so being able to gather vast information about the patient suffering from a condition allows researchers and clinicians to develop precise interventions. For example in cancer research we can now gather vast amounts of information, including medical imaging, patient records and even genetic data. By integrating this information with powerful bioinformatics and machine learning algorithms we are able to get deep insight not just for diseases but also for a specific patients suffering from those diseases. The BioCompute project allows researchers to accurately capture information not just about the data but also the algorithms and processes used to analyse that data, thereby allowing other researchers and clinicians to evaluate, understand, and reuse that insight.”
“Enabling precision medicine via standard communication of HTS provenance, analysis, and results” was published in PLOS Biology.