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Researchers establish benchmark set of genotypes for human genome sequencing


   

David Mittelman David Mittelman

BLACKSBURG, Va., Feb. 26, 2014 – Led by biomedical engineer Justin Zook of the National Institute of Standards and Technology, a team of bioinformaticians from Harvard University and the Virginia Bioinformatics Institute at Virginia Tech has presented new methods to integrate data from different sequencing platforms, thus producing a highly reliable set of genotypes that will 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 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 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.

A university-level Research Institute of Virginia Tech, the Virginia Bioinformatics Institute was established in 2000 with an emphasis on informatics of complex interacting systems scaling the microbiome to the entire globe. It helps solve challenges posed to human health, security, and sustainability. Headquartered at the Blacksburg campus, the institute occupies 154,600 square feet in research facilities, including state-of-the-art core laboratory and high-performance computing facilities, as well as research offices in the Virginia Tech Research Center in Arlington, Virginia.

Written by Emily Kale.


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