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

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
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 2,800+ scientific posters on ePosters
  • More than 4,000+ 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 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

Autism Mutation Isolated – Could Be Treated with Specific Enzyme
The research shows the precise cellular mechanisms that could increase risk for the disorder and how an existing drug might help thousands of people with autism.
Monday, August 10, 2015
New Gene Therapy For Hemophilia Shows Potential As Safe Treatment
Research showed that bleeding events were drastically decreased in animals with hemophilia B. Using a viral vector to swap out faulty genes proved safe and could be used for the more common hemophilia A.
Tuesday, March 17, 2015
Genetically Speaking, Mammals Are More Like Their Fathers
A first of its kind study shows that who we inherit genetic variants from – our mother or father – is crucial for the development of diseases and for research studies aimed at finding causes and potential treatments.
Wednesday, March 04, 2015
Researchers Silence Leading Cancer-Causing Gene
A novel siRNA-based molecule successfully targets KRAS, a well-studied but hard to halt protein important for cancer development and metastasis.
Monday, November 17, 2014
New Gene Therapy Proves Promising as Hemophilia Treatment
Researchers package specialized blood platelets with genes that express clotting factor, leading to fewer bleeding events.
Wednesday, December 18, 2013
New Findings Regarding DNA Damage Checkpoint Mechanism in Oxidative Stress
Scientists uncover previously unknown surveillance mechanism.
Thursday, June 20, 2013
Molecular Twist Helps Regulate the Cellular Message to Make Histone Proteins
Researchers show for the first time how two key proteins in messenger RNA communicate via a molecular twist to help maintain the balance of histones to DNA.
Monday, January 21, 2013
Molecular Delivery Truck Serves Gene Therapy Cocktail
University of North Carolina scientists have devised a gene therapy cocktail that has the potential to treat some inherited diseases associated with “misfolded” proteins.
Tuesday, August 23, 2011
Clinical Trial of Molecular Therapy for Muscular Dystrophy Yields Significant Positive Results
A molecular technique originally developed at the University of North Carolina at Chapel Hill has taken one step closer to becoming a treatment for the devastating genetic disease Duchenne muscular dystrophy.
Tuesday, July 26, 2011
Structure of 450 Million Year Old Protein Reveals Evolution’s Steps
Researchers have determined the atomic structure of an ancient protein, revealing in detail how genes evolved their functions.
Wednesday, August 22, 2007
Gene Discovered by Researchers Tied to Pancreatic Cancer
The gene, palladin, is involved is involved in the formation of scar tissue on nerve cells in the brain or spinal cord.
Monday, December 18, 2006
Three Lung Tumor Subtypes Identified in DNA Profiling Study
The finding may provide clinical information about patient survival in early- or late-stage disease.
Thursday, November 02, 2006
Studies Find General Mechanism of Cellular Aging
Studies suggest tumor suppressor gene is key.
Friday, September 08, 2006
Novel Enzyme Offers new Look at Gene Regulation
Scientists show that a protein called JHDM1A is able to remove a methyl group from histone H3.
Wednesday, December 28, 2005
Scientific News
New Tech Vastly Improves CRISPR/Cas9 Accuracy
A new CRISPR/Cas9 technology developed by scientists at UMass Medical School is precise enough to surgically edit DNA at nearly any genomic location, while avoiding potentially harmful off-target changes typically seen in standard CRISPR gene editing techniques.
New Class of RNA Tumor Suppressors Identified
Two short, “housekeeping” RNA molecules block cancer growth by binding to an important cancer-associated protein called KRAS. More than a quarter of all human cancers are missing these RNAs.
Biologists Induce Flatworms to Grow Heads and Brains of Other Species
Findings shed light on role of a new kind of epigenetic signaling in evolution, could yield clues for understanding birth defects and regeneration.
Turning up the Tap on Microbes Leads to Better Protein Patenting
Mining millions of proteins could become faster and easier with a new technique that may also transform the enzyme-catalyst industry, according to University of California, Davis, researchers.
Mathematical Model Forecasts the Path of Breast Cancer
Chances of survival depend on which organs breast cancer tumors colonize first.
Exploring the Causes of Cancer
Queen's research to understand the regulation of a cell surface protein involved in cancer.
Ancient Viral Molecules Essential for Human Development
Genetic material from ancient viral infections is critical to human development, according to researchers at the Stanford University School of Medicine.
Tardigrade's Are DNA Master Thieves
Tardigrades, nearly microscopic animals that can survive the harshest of environments, including outer space, hold the record for the animal that has the most foreign DNA.
The Secret Behind the Power of Bacterial Sex
Migration between different communities of bacteria is the key to the type of gene transfer that can lead to the spread of traits such as antibiotic resistance, according to researchers at Oxford University.
Farming’s in Their DNA
Ancient genomes reveal natural selection in action.
Skyscraper Banner

Skyscraper Banner
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
2,800+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,000+ scientific videos