Featured Research

from universities, journals, and other organizations

Researchers establish benchmark set of human genotypes for genome sequencing

Date:
February 19, 2014
Source:
Virginia Tech
Summary:
Researchers have presented new methods to integrate data from different sequencing platforms, thus producing a reliable set of genotypes to serve as a benchmark for human genome sequencing.

Led by biomedical engineer Justin Zook of the National Institute of Standards and Technology, a team of scientists from Harvard University and the Virginia Bioinformatics Institute of Virginia Tech has presented new methods to integrate data from different sequencing platforms, thus producing a reliable set of genotypes to serve as a benchmark for human genome sequencing.

“Understanding the human genome is an immensely complex task and we need great methods to guide this research,” Zook says. “By establishing reference materials and gold standard data sets, scientists are one step closer to bringing genome sequencing into clinical practice.”

The methods put forth by the researchers make it increasingly possible to use an individual’s genetic profile to guide medical decisions to prevent, diagnose, and treat diseases — a priority of the National Institutes of Health. Their work was published in the Feb. 16 issue of Nature Biotechnology.

“We minimize biases toward any sequencing platform or data set by comparing and integrating 11 whole human genome and three exome data sets from five sequencing platforms,” says Zook.

The National Institute of Standards and Technology organized the Genome in a Bottle Consortium to make well-characterized, whole-genome reference materials available to research, commercial, and clinical laboratories.

The team addressed the challenge with the expertise of David Mittelman, an associate professor of biological sciences at the Virginia Bioinformatics Institute, who creates tools that analyze vast amounts of genomic information.

The researchers created a metric to determine the accuracy of gene variations and understand biases and sources of error in sequencing and bioinformatics methods.

Their findings are available to the public on the Genome Comparison and Analytic Testing website, known as GCAT, to enable real-time benchmarking of any DNA-sequencing method. The collaborative, free online resource comparesmultiple analysis tools across a variety of crowd-sourced metrics and data sets.

GCAT was built with the help of Virginia Tech Intellectual Properties and a faculty-owned, start-up company called Arpeggi, which Mittelman cofounded. Arpeggi has since been acquired by Gene by Gene Ltd, a company that offers clinical and direct-to-consumer genetic testing. Mittelman is a partner and equity holder in Gene by Gene Ltd.


Story Source:

The above story is based on materials provided by Virginia Tech. Note: Materials may be edited for content and length.


Journal Reference:

  1. Justin M Zook, Brad Chapman, Jason Wang, David Mittelman, Oliver Hofmann, Winston Hide, Marc Salit. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nature Biotechnology, 2014; DOI: 10.1038/nbt.2835

Cite This Page:

Virginia Tech. "Researchers establish benchmark set of human genotypes for genome sequencing." ScienceDaily. ScienceDaily, 19 February 2014. <www.sciencedaily.com/releases/2014/02/140219075207.htm>.
Virginia Tech. (2014, February 19). Researchers establish benchmark set of human genotypes for genome sequencing. ScienceDaily. Retrieved September 19, 2014 from www.sciencedaily.com/releases/2014/02/140219075207.htm
Virginia Tech. "Researchers establish benchmark set of human genotypes for genome sequencing." ScienceDaily. www.sciencedaily.com/releases/2014/02/140219075207.htm (accessed September 19, 2014).

Share This



More Health & Medicine News

Friday, September 19, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

The Cost of Ebola

The Cost of Ebola

Reuters - Business Video Online (Sep. 18, 2014) As Sierra Leone prepares for a three-day "lockdown" in its latest bid to stem the spread of Ebola, Ciara Lee looks at the financial implications of fighting the largest ever outbreak of the disease. Video provided by Reuters
Powered by NewsLook.com
What HealthKit Bug Means For Your iOS Fitness Apps

What HealthKit Bug Means For Your iOS Fitness Apps

Newsy (Sep. 18, 2014) Apple has delayed the launch of the HealthKit app platform, citing a bug. Video provided by Newsy
Powered by NewsLook.com
U.S. Food Makers Surpass Calorie-Cutting Pledge

U.S. Food Makers Surpass Calorie-Cutting Pledge

Newsy (Sep. 18, 2014) Sixteen large food and beverage companies in the United States that committed to cut calories in their products far surpassed their target. Video provided by Newsy
Powered by NewsLook.com
Residents Vaccinated as Haiti Fights Cholera Epidemic

Residents Vaccinated as Haiti Fights Cholera Epidemic

AFP (Sep. 18, 2014) Haitians receive the second dose of the vaccine against cholera as part of the UN's vaccination campaign. Duration: 00:34 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:
from the past week

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