Featured Research

from universities, journals, and other organizations

Computational software provides rapid identification of disease-causing gene variations

Date:
June 24, 2011
Source:
University of Utah Health Sciences
Summary:
Scientists have developed a new software tool called VAAST, the Variant Annotation, Analysis and Selection Tool -- a probabilistic disease-causing mutation finder for individual human genomes.

Scientists from the University of Utah and Omicia, Inc., a privately held company developing tools to interpret personal genome sequences, have announced the publication in Genome Research of a new software tool called VAAST, the Variant Annotation, Analysis and Selection Tool -- a probabilistic disease-causing mutation finder for individual human genomes.

The dramatic decline in DNA sequencing costs is making personal genome sequencing a reality. Already, significant progress has been made in applying whole genome sequencing to cancer prognosis and early childhood disease. Examples include the 2010 publications on Miller Syndrome in Nature Genetics and Science, and similar studies aimed at identifying the unknown genetic defects responsible for some early childhood diseases.

However, a data interpretation bottleneck has limited the utility of personal genome information for medical diagnosis and preventive care. VAAST is a new algorithm to assist in overcoming this bottleneck. VAAST is the product of a collaboration between Mark Yandell, Ph.D., Associate Professor of Human Genetics at the University of Utah School of Medicine, and colleagues, and the Omicia scientific team under the leadership of Martin Reese, Ph.D., the company's CEO and Chief Scientific Officer.

In the Genome Research paper, Yandell and colleagues show that VAAST provides a highly accurate, statistically robust means to rapidly search personal genomes for genes with disease-causing mutations. The authors demonstrate that as few as three genomes from unrelated children, or those of the parents and their two children, are sufficient to identify disease causing mutations.

"The big challenge in genomic medicine today is how to sift through the millions of variants in a personal genome sequence to identify the disease-relevant variations," said Dr. Reese. "It's a classic needle in a haystack problem, and VAAST goes a long way toward solving it. We look forward to integrating VAAST into the Omicia Genome Analysis System currently under development for clinical applications."

Dr. Yandell added: "VAAST solves many of the practical and theoretical problems that currently plague mutation hunts using personal genome sequences. Our results demonstrate that this tool substantially improves upon existing methods with regard to statistical power, flexibility, and scope of use. Further, VAAST is automated, fast, works across all variant population frequencies and is sequencing platform independent."

In a separate paper published this week in the American Journal of Human Genetics, Gholson Lyon, M.D., Ph.D., previously at University of Utah and now at the Children's Hospital of Philadelphia, and colleagues report the use of VAAST as part of an international effort to identify the mutation responsible for a newly discovered childhood disease. This new illness, which they are tentatively calling Ogden Syndrome, is characterized by aged appearance, craniofacial abnormalities, cardiac arrhythmias and other symptoms. The team used X-chromosome exon capture and next-generation sequencing and the VAAST tool to quickly and unambiguously identify the disease-causing mutation in the NAA10 gene that has resulted in this fatal disease in children of two unrelated families.

"VAAST can identify disease-causing mutations with greater accuracy, using far fewer individuals and more rapidly than was previously possible," said Dr. Lyon. "We are now applying VAAST to many other unknown conditions, including rare Mendelian disorders and other common disorders such as ADHD and autism."

Commenting on the significance of this development, Eric J. Topol, M.D., Director, Scripps Translational Science Institute and Chief Academic Officer, Scripps Health, commented: "One of most important and exciting opportunities in genomic medicine is the newfound ability to pinpoint the root cause of an unknown idiopathic disease in an individual. The VAAST tool will markedly facilitate this and represents a major advance in the field. It fulfills a significant unmet need of interpreting whole genome sequences and will have a remarkable impact on accurate genomic diagnosis of many individuals going forward."

The development of VAAST was funded by the National Human Genome Research Institute through an American Recovery and Reinvestment Act Grand Opportunity (GO) grant. GO grants focus on transformative technologies and large, potentially high-impact projects.


Story Source:

The above story is based on materials provided by University of Utah Health Sciences. Note: Materials may be edited for content and length.


Journal References:

  1. Mark Yandell, Chad D. Huff, Hao Hu, Marc Singleton, Barry Moore, Jinchuan Xing, Lynn B. Jorde, Martin G. Reese. A probabilistic disease-gene finder for personal genomes. Genome Research, 2011; DOI: 10.1101/gr.123158.111
  2. Alan F. Rope, Kai Wang, Rune Evjenth, Jinchuan Xing, Jennifer J. Johnston, Jeffrey J. Swensen, W. Evan Johnson, Barry Moore, Chad D. Huff, Lynne M. Bird, John C. Carey, John M. Opitz, Cathy A. Stevens, Tao Jiang, Christa Schank, Heidi Deborah Fain, Reid Robison, Brian Dalley, Steven Chin, Sarah T. South, Theodore J. Pysher, Lynn B. Jorde, Hakon Hakonarson, Johan R. Lillehaug, Leslie G. Biesecker, Mark Yandell, Thomas Arnesen, Gholson J. Lyon. Using VAAST to Identify an X-Linked Disorder Resulting in Lethality in Male Infants Due to N-Terminal Acetyltransferase Deficiency. American Journal of Human Genetics, 2011; DOI: 10.1016/j.ajhg.2011.05.017

Cite This Page:

University of Utah Health Sciences. "Computational software provides rapid identification of disease-causing gene variations." ScienceDaily. ScienceDaily, 24 June 2011. <www.sciencedaily.com/releases/2011/06/110623130120.htm>.
University of Utah Health Sciences. (2011, June 24). Computational software provides rapid identification of disease-causing gene variations. ScienceDaily. Retrieved October 20, 2014 from www.sciencedaily.com/releases/2011/06/110623130120.htm
University of Utah Health Sciences. "Computational software provides rapid identification of disease-causing gene variations." ScienceDaily. www.sciencedaily.com/releases/2011/06/110623130120.htm (accessed October 20, 2014).

Share This



More Health & Medicine News

Monday, October 20, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Microneedle Patch Promises Painless Pricks

Microneedle Patch Promises Painless Pricks

Reuters - Innovations Video Online (Oct. 18, 2014) Researchers at The National University of Singapore have invented a new microneedle patch that could offer a faster and less painful delivery of drugs such as insulin and painkillers. Video provided by Reuters
Powered by NewsLook.com
Raw: Nurse Nina Pham Arrives in Maryland

Raw: Nurse Nina Pham Arrives in Maryland

AP (Oct. 17, 2014) The first nurse to be diagnosed with Ebola at a Dallas hospital walked down the stairs of an executive jet into an ambulance at an airport in Frederick, Maryland, on Thursday. Pham will be treated at the National Institutes of Health. (Oct. 16) Video provided by AP
Powered by NewsLook.com
Raw: Cruise Ship Returns to US Over Ebola Fears

Raw: Cruise Ship Returns to US Over Ebola Fears

AP (Oct. 17, 2014) A Caribbean cruise ship carrying a Dallas health care worker who is being monitored for signs of the Ebola virus is heading back to Texas, US, after being refused permission to dock in Cozumel, Mexico. (Oct. 17) Video provided by AP
Powered by NewsLook.com
Spanish Govt: Four Suspected Ebola Cases in Spain Test Negative

Spanish Govt: Four Suspected Ebola Cases in Spain Test Negative

AFP (Oct. 17, 2014) All four suspected Ebola cases admitted to hospitals in Spain on Thursday have tested negative for the deadly virus in a first round of tests, the government said Friday. Duration: 00:55 Video provided by AFP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Health & Medicine

Mind & Brain

Living & Well

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins