Genomics England announced that it will be using technology co-developed in a partnership between the University of Utah and Omicia, and exclusively commercialized through Omicia, to interpret the DNA of Britons as part of the 100,000 Genomes Project, a national effort to hasten creation of diagnostics and treatments that are tailored to a person's genetic make-up. The VAAST (Variant Annotation, Analysis and Search Tool) and Phevor (Phenotype Driven Variant Ontological Re-ranking tool) algorithms are core components of the Omicia Opal platform, which transforms genomic data into clinically relevant information.
Published in 2011, VAAST has become a benchmark in genome analysis, and is already in use at over 300 sites throughout the world. VAAST is best recognized for discovering a genetic variation that leads to Ogden syndrome, one of the first disease genes found through genome sequencing. A newer algorithm, Phevor, has been used in conjunction with VAAST to identify disease-causing genes found in a single patient or in a small family of two or three, the most common clinical situation for undiagnosed and rare diseases.
"What we want to be able to do is help the kid who is born with a hard-to-diagnose genetic disorder," says the creator of VAAST and Phevor, Mark Yandell, Ph.D., also professor of human genetics at the University of Utah and co-director of the USTAR Center for Genetic Discovery. "Our genome interpretation tools will be able to identify that disorder and guide treatment."
Omicia's Opal platform, which incorporates VAAST and Phevor, was a top performer in a Genomics England competition that challenged 28 companies from across the world to clinically assess genomic data from patients. Four finalists were invited to analyze the first 8,000 patients in the pilot phase of the 100,000 Genomes Project. Omicia and Congenica were selected to search for genetic causes of rare disease, Nanthealth for cancer, and Wuxi Nextcode for both types of conditions.
"The genetic testing industry is advancing from single gene tests, to panels and exomes and soon to whole genomes," says Martin Reese, Ph.D., CSO and Founder of Omicia. "This transformation can only be accomplished by changing from a solely molecular biology driven industry to an information driven industry with a full understanding of the biological and genetic concepts. Our long-standing collaboration with the University of Utah, a powerhouse in genetics, has pioneered the approach of automation and scalability for intelligent interpretation of NGS sequence data."
Rare diseases pose a particularly vexing problem for health care. In the U.S., rare diseases are defined as conditions that affect no more than 200,000 people. Although the numbers with each condition are small, it is estimated that there are nearly 7,000 rare diseases, which cumulatively affect 10 percent of the American population. Today, relatively few drugs and therapies exist for these patients; a major goal of precision medicine is to reverse this trend.
The 100,000 Genomes Project pilot phase is expected to commence in August 2015.
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Listen to Mark Yandell explain Phevor on The Scope Radio: Using Computer Logic to Diagnose Rare Diseases
About the USTAR Center for Genetic Discovery
From DNA to diagnosis, the mission of the USTAR Center for Genetic Discovery is to integrate patient genome information into health care. The USTAR Center for Genetic Discovery is developing big data management, disease discovery, and genome interpretation tools for research and clinical applications. USTAR CGD is also the computational engine behind the Utah Genome Project, an initiative that leverages the Utah Population Database - the world's largest repository of genealogies, public health and medical records- to discover disease-causing genes. The center is funded by the University of Utah and Utah Science Technology and Research (USTAR).