Navigation Links
Research team establishes benchmark set of human genotypes for sequencing
Date:2/18/2014

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 benchmark 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 this week in 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.

Though several methods to integrate genomic information have been put forth by the 1000 Genomes Project an international research effort to establish a detailed catalogue of human genetic variation the idea to arbitrate between data sets from different sequencing methods on the same genome had never been done.

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 compares multiple 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 co-founded. 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.


'/>"/>

Contact: Tiffany Trent
ttrent@vt.edu
540-231-6822
Virginia Tech
Source:Eurekalert

Related biology news :

1. Researchers shed new light on the genetic history of the European beaver
2. Two NYU faculty win Sloan Foundation research fellowships
3. Researchers identify new way to control stone fruit disease
4. Researchers warn against abrupt stop to geoengineering method
5. Researchers hijack cancer migration mechanism to move brain tumors
6. CU-Boulder stem cell research may point to new ways of mitigating muscle loss
7. MLB largely responsible for players steroid abuse, UTA researcher says
8. Hot issues in climate change research to be debated at AAAS Annual Meeting
9. Plastic shopping bags make a fine diesel fuel, researchers report
10. GVSU researchers draw link between zebra mussels, risk of algae blooms
11. Population bomb may be defused, but research reveals ticking household bomb
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/20/2016)... 2016 Securus Technologies, a leading provider ... public safety, investigation, corrections and monitoring announced that ... has secured the final acceptance by all three ... Access Systems (MAS) installed. Furthermore, Securus will have ... installed by October, 2016. MAS distinguishes between legitimate ...
(Date:6/7/2016)...  Syngrafii Inc. and San Antonio Credit Union ... integrating Syngrafii,s patented LongPen™ eSignature "Wet" solution into ... result in greater convenience for SACU members and ... existing document workflow and compliance requirements. ... Highlights: ...
(Date:6/1/2016)... 2016 Favorable Government Initiatives Coupled ... Criminal Identification to Boost Global Biometrics System Market Through ... Research report, " Global Biometrics Market By Type, ... Opportunities, 2011 - 2021", the global biometrics market is ... account of growing security concerns across various end use ...
Breaking Biology News(10 mins):
(Date:6/24/2016)... DIEGO , June 24, 2016 ... more sensitively detects cancers susceptible to PARP inhibitors ... circulating tumor cells (CTCs). The new test has ... HRD-targeted therapeutics in multiple cancer types. ... targeting DNA damage response pathways, including PARP, ATM, ...
(Date:6/23/2016)... 2016   Boston Biomedical , an industry ... to target cancer stemness pathways, announced that its ... Drug Designation from the U.S. Food and Drug ... including gastroesophageal junction (GEJ) cancer. Napabucasin is an ... cancer stemness pathways by targeting STAT3, and is ...
(Date:6/23/2016)... MONICA, Calif. , June 23, 2016  The Prostate Cancer Foundation ... pioneer increasingly precise treatments and faster cures for prostate cancer. Members of the ... institutions across 15 countries. Read More About the Class ... ... ...
(Date:6/23/2016)... ... June 23, 2016 , ... In a new case report ... detail how a patient who developed lymphedema after being treated for breast cancer benefitted ... change the paradigm for dealing with this debilitating, frequent side effect of cancer treatment. ...
Breaking Biology Technology: