Satellite Banner
Informatics
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

Informatics Approach Helps Doctors, Patients Make Sense of Genome Data

Published: Friday, September 21, 2012
Last Updated: Friday, September 21, 2012
Bookmark and Share
Researchers from UNC unveil an analysis framework aimed at helping clinicians spot “medically actionable findings” from genetic tests in an efficient manner.

The cost of sequencing the entire human genome, or exome – the regions of the genome that are translated into proteins that affect cell behavior – has decreased significantly, to the point where the cost of looking at the majority of a patient’s genomic data may be less expensive than undertaking one or two targeted genetic tests.  While efficient, the acquisition of this much genetic data – in some cases as many as 1.5 to 2 million variants – creates other challenges.

In a paper that appears today in the advance online edition of Genetics in Medicine, researchers from the University of North Carolina at Chapel Hill unveil an analysis framework aimed at helping clinicians spot “medically actionable findings” from genetic tests in an efficient manner.

“The challenge for medical geneticists is what do we do with the ‘incidentalome’ – the large amount of genetic data that these tests generate which may be important but which was incidental – that is, had nothing to do with why the patient underwent DNA analysis in the first place,” said Jonathan Berg, MD, PhD, assistant professor of clinical genetics and a member of UNC Lineberger Comprehensive Cancer Center.

“Our team is faced with this issue in a clinical trial we are conducting called the NC GENES study.  So we put together a framework that classifies genetic variations into three different ‘bins’:  those that are linked to a treatable or preventable condition (the medically actionable); those that have a known link to conditions for which we don’t have treatment options; and those for which there is no known direct association between a genetic variation and a disorder,” he said.

The team then created an informatics approach to carry out a structured analysis on these three ‘bins’.

“While there are still some challenges, we believe that this approach facilitates the analysis and streamlines the ability of the molecular analyst to go through a lot of data very quickly, providing more timely results to physicians and patients,” says Berg.

Berg notes that the researchers had to set a very high bar for the genetic variants reported to patients and physicians, taking into account that there are errors in all of the current databases of known disease-causing mutations and that they contain variants that are probably not disease causing, due to unavoidable errors in data processing and other aspects of genetic research.  However, because most hereditary disorders are very rare, disease causing mutations are highly unlikely.

“In epidemiologic terms we valued specificity over sensitivity.  We will have some false negatives because we are ignoring some genetic variants that we don’t understand well or that are very unlikely to occur.  However, as researchers who also work with patients, we know that there are significant consequences to false positive results for genetic disorders and given the rarity of many of these disorders we think this is an appropriate risk,” he argues.

Berg and his collaborators, which include James Evans, MD, PhD, Bryson Distinguished Professor of Genetics Research and a member of UNC Lineberger, are also studying the practical consequences of our ability to pinpoint disease-causing mutations in the genome.

“We hope that this methodology will enhance our ability to quickly translate a large amount of data into findings that are useful to physicians and patients, allowing us to study important issues like patient preference for learning about their likelihood of developing or passing along a hereditary disease for which there is no treatment,” said Evans.

“These are important ethical considerations, and currently there exist no best practices because this technology is still relatively new,” he added.

In addition to Berg and Evans, the research team included Michael Adams, MS, and Kristy Lee, MS from the UNC Department of Genetics, Kirk Wilhelmsen, MD, PhD from the Department of Genetics, the Carolina Center for Genome Sciences (where Berg and Evans are also members), and the Renaissance Computing Institute, and Nassib Nassar, PhD, Chris Bizon, PhD, and Charles Schmitt, PhD, from the Renaissance Computing Institute.


Further Information

Join For Free

Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 3,900+ scientific posters on ePosters
  • More than 5,300+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Hamner Institutes and UNC Launch International Drug Safety Institute
Scientific collaboration aims at improving drug safety and advancing drug development.
Wednesday, June 17, 2009
Scientific News
Accelerating the Detection of Foodborne Bacterial Outbreaks
The speed of diagnosis of foodborne bacterial outbreaks could be improved by a new technique developed by researchers at the Georgia Institute of Technology.
Largest Resource of Protein-Protein Interactions
Researchers have developed the largest ever database of protein-protein interactions.
NVIDIA Awards $400k to Trailblazers in Cancer Research
NVIDIA Foundation furthers research that could lead to new and more targeted treatments with investments.
Computers Learn to Recognize Molecules That Can Enter Cells
Researchers discover peptides with antimicrobial properties, but also that many known human proteins also had this ability.
Big Data for Infectious Disease Surveillance
NIH-led effort examines use of big data from health records and other digital sources for uses in infectious disease surveillance.
Clinical Screening Test for Gut Health Developed
uBiome has created an entirely new approach to support the clinical diagnosis of gut health conditions.
Computational Tool May Speed Drug Discovery
Scientists are able to see beyond static images of proteins with the help of a new computational tool.
Scientists Develop a Novel Method to Benchmark and Improve the Performance of Protein Measurement Techniques
A wide range of laboratories around the world are benefiting from this work, which enables researchers to analyze or compare the results of quantitative proteomics assays in a standardized way.
Uncovering the Cellular Environment
Researchers have shown how molecules move within a crowded bacterial cell using Japan's K supercomputer.
Tracking Alzheimer's Progression
MRI data reveals structural asymmetries that vary among individuals and are greater among those who develop dementia.
Scroll Up
Scroll Down
SELECTBIO

SELECTBIO Market Reports
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
3,900+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
5,300+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!