New system matches genetic anomalies with precision cancer treatments

February 2, 2018, University of Delaware
A system developed at the University of Delaware and Georgetown matches genetic anomalies with studied treatments. Credit: University of Delaware

A team of computer scientists from the University of Delaware and Georgetown University has developed a new system to rapidly determine which cancer drugs are likely to work best given a patient's genetic markers. The first publicly available system of its kind, their database, eGARD (extracting Genomic Anomalies association with Response to Drugs), is described in PLoS One.

When your genes work correctly, they function like miniature factory plant managers, directing the production of life-sustaining proteins. But sometimes, a gene goes rogue and manufactures a cancerous tumor instead. When cancer experts identify these faulty genes, they can devise treatment plans based on past evidence.

However, until now, the data linking genetic factors and treatment results has been spread among hundreds of academic journals. It would take days for doctors, doing nothing else, to find and read all these reports. Now, they may be able to spend that time delivering optimized treatments instead.

The promise of eGARD

eGARD is a text mining system that analyzes words and phrases in medical literature to find relationships between genomic anomalies and drug responses.

"Clinicians have no time to read all of the reports and literature for each tumor," said Peter McGarvey, a study author and associate professor of biochemistry at Georgetown University. "eGARD is a way to help surface the important ones for clinicians, medical geneticists or maybe companies that already are doing this in other ways."

The research team applied eGARD on roughly 36,000 article abstracts, retrieving 50 genes and 42 , including cell cycle inhibitors, kinase inhibitors and antibody treatments.

The research team first trained the system to identify indications of genetic anomalies, with very scientific names such as "over-expression of ERCC1" or "C677T and A1298C polymorphisms of MTHFR gene." Then, they trained it to look for text suggesting treatment outcomes, such as "significantly poorer response" or "survival rate." Next, they sought words and phrases connecting a genetic anomaly and outcome, such as "correlate," "associate" or "sensitize."

By extracting and processing key pieces of text, eGARD can match genetic signatures with outcomes with 95 percent precision.

"We hope this could make a difference for oncologists and cancer patients alike," said study author Vijay Shanker, a professor of computer and information sciences at UD.

UD researchers developed the code and data processing for eGARD, and clinically focused researchers at Georgetown provided use cases, terminology, curated datasets and insight on what information was most important to clinicians working in precision medicine. Both groups tested and refined the system.

The team will make a public interface for eGARD. It may also be incorporated into other software eventually.

A team led by Mahmood and Gang Li, also a graduate student in computer and , took some top honors in the precision medicine track.

Participants were given information about a patient's disease, relevant genetic variants and other key factors. Then they were asked to retrieve clinical trial information and abstracts of biomedical articles relevant to the patient and judged on three measures of their ability to do each. In a competition with 32 teams, the UD team ranked first on all three measures related to clinical trials. For abstracts, the UD team earned rankings of first, fourth and fifth.

iTextMine for knowledge integration

eGARD is not the first or last system from this group of big data experts. A suite of text mining tools has been developed by students and research scientists over the years through the long-standing collaborations between Shanker and Wu. Funded by another NIH grant, the UD research team has developed the iTextMine (Integrated Text Mining System for Large-Scale Knowledge Extraction from Literature), which uses an automated workflow to run multiple text-mining tools on the entire PubMed with millions of citations for biomedical literature.

"By analyzing scientific texts with multiple tools, researchers may further gain knowledge on gene-drug-disease relationships and better understand the underlying molecular mechanisms," said Wu.

This tool allows users to browse the text evidence for multiple biomarkers and view integrated results through a network visualization. The iTextMine will be presented by Jia Ren, a student in the Bioinformatics and Systems Biology Ph.D. program, at the International Biocuration Conference in China this April.

Explore further: Team presents an online tool to extract drug toxicity information from text

More information: A. S. M. Ashique Mahmood et al. eGARD: Extracting associations between genomic anomalies and drug responses from text, PLOS ONE (2017). DOI: 10.1371/journal.pone.0189663

Related Stories

Team presents an online tool to extract drug toxicity information from text

June 1, 2017
There is an increasing interest in more sophisticated search engines that are tailored to cope with the complexity of biomedical data, not only enabling more targeted search queries but also easier integration and construction ...

Team develops technology to find optimum drug target for cancer

December 18, 2017
A KAIST research team led by Professor Kwang-Hyun Cho of the Department of Bio and Brain Engineering developed technology to find the optimum drug targets for specific types of cancer cells. The team used systems biology ...

New precision medicine tool helps optimize cancer treatment

December 22, 2016
Columbia University Medical Center (CUMC) researchers have created a computational tool that can rapidly predict which genes are implicated in an individual's cancer and recommend treatments. It is among the most comprehensive ...

Recommended for you

Researchers identify a mechanism that fuels cancer cells' growth

November 14, 2018
Scientists at the UCLA Jonsson Comprehensive Cancer Center have identified sodium glucose transporter 2, or SGLT2, as a mechanism that lung cancer cells can utilize to obtain glucose, which is key to their survival and promotes ...

A new approach to detecting cancer earlier from blood tests: study

November 14, 2018
Cancer scientists led by principal investigator Dr. Daniel De Carvalho at Princess Margaret Cancer Centre have combined "liquid biopsy", epigenetic alterations and machine learning to develop a blood test to detect and classify ...

New antibody breakthrough to lead the fight against cancer

November 14, 2018
Scientists at the University of Southampton have developed a new antibody that could hold the key to unlocking cancer's defence against the body's immune system.

Photoacoustic imaging may help doctors detect ovarian tumors earlier

November 14, 2018
Ovarian cancer claims the lives of more than 14,000 in the U.S. each year, ranking fifth among cancer deaths in women. A multidisciplinary team at Washington University in St. Louis has found an innovative way to use sound ...

Solving the mystery of NPM1 in acute myeloid leukemia

November 13, 2018
Although it has long been recognized that mutations of gene NPM1 play an important role in acute myeloid leukemia, no one has determined how the normal and the mutated forms of the protein NPM1 function.

Cognitive decline—radiation—brain tumor prevented by temporarily shutting down immune response

November 13, 2018
Treating brain tumors comes at a steep cost, especially for children. More than half of patients who endure radiation therapy for these tumors experience irreversible cognitive decline, a side-effect that has particularly ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.