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.
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.
Tiffany Trent | EurekAlert!
A new potential biomarker for cancer imaging
05.02.2016 | Universiti Putra Malaysia (UPM)
NIH researchers identify striking genomic signature shared by 5 types of cancer
05.02.2016 | NIH/National Human Genome Research Institute
Automobiles increase the mobility of their users. However, their maneuverability is pushed to the limit by cramped inner city conditions. Those who need to...
Advance in biomedical imaging: The University of Würzburg's Biocenter has enhanced fluorescence microscopy to label and visualise up to nine different cell structures simultaneously.
Fluorescence microscopy allows researchers to visualise biomolecules in cells. They label the molecules using fluorescent probes, excite them with light and...
NASA's follow-on to the successful ICESat mission will employ a never-before-flown technique for determining the topography of ice sheets and the thickness of sea ice, but that won't be the only first for this mission.
Slated for launch in 2018, NASA's Ice, Cloud and land Elevation Satellite-2 (ICESat-2) also will carry a 3-D printed part made of polyetherketoneketone (PEKK),...
In the last decades, sea level has been rising continuously – about 3.3 mm per year. For reef islands such as the Maldives or the Marshall Islands a sinister picture is being painted evoking the demise of the island states and their cultures. Are the effects of sea-level rise already noticeable on reef islands? Scientists from the ZMT have now answered this question for the Takuu Atoll, a group of Pacific islands, located northeast of Papua New Guinea.
In the last decades, sea level has been rising continuously – about 3.3 mm per year. For reef islands such as the Maldives or the Marshall Islands a sinister...
The ‘Internet of Things’ is growing rapidly. Mobile phones, washing machines and the milk bottle in the fridge: the idea is that minicomputers connected to these will be able to process information, receive and send data. This requires electrical power. Transistors that are capable of switching information with a single electron use far less power than field effect transistors that are commonly used in computers. However, these innovative electronic switches do not yet work at room temperature. Scientists working on the new EU research project ‘Ions4Set’ intend to change this. The program will be launched on February 1. It is coordinated by the Helmholtz-Zentrum Dresden-Rossendorf (HZDR).
“Billions of tiny computers will in future communicate with each other via the Internet or locally. Yet power consumption currently remains a great obstacle”,...
02.02.2016 | Event News
26.01.2016 | Event News
26.01.2016 | Event News
05.02.2016 | Life Sciences
05.02.2016 | Materials Sciences
05.02.2016 | Physics and Astronomy