Genomics England, a subsidiary of the United Kingdom’s Department of Health, is leading the drive to sequence the genomes of 100,000 National Health Service patients through the United Kingdom’s 100k Genome Project. “The United Kingdom will become the first ever country to introduce this technology in its mainstream health system—leading the global race for better […]
Genomics England, a subsidiary of the United Kingdom’s Department of Health, is leading the drive to sequence the genomes of 100,000 National Health Service patients through the United Kingdom’s 100k Genome Project. “The United Kingdom will become the first ever country to introduce this technology in its mainstream health system—leading the global race for better tests, better drugs and above all better, more personalized care to save lives,” said Jeremy Hunt, the United Kingdom’s secretary of state for health, in a statement. In the United States, the only nationally coordinated sequencing efforts are being conducted through the Million Veteran Program (MVP) at the Department of Veterans Affairs (VA). The goal of MVP is to build one of the world’s largest medical databases integrating genomic, lifestyle, and clinical health information from 1 million veteran volunteers. Screened research projects from the VA, other federal health agencies, and U.S. academic institutions will be permitted access to anonymized data. To date MVP has enrolled more than 225,000 volunteers. Based on data collected through November 2013, the enrollment profile includes:
Participants from 50 VA Medical Centers nationally, with other sites to be added;
42 percent of enrollees to date are aged 60 to 69 years old and 30.9 percent are over the age of 70 years; and
82 percent are white and 13 percent are black.
“MVP represents a unique and timely opportunity for genomics to improve the health and health care of veterans along with all Americans,” says John Concato, M.D., director of the VA Clinical Epidemiology Research Center, one of two genomic coordinating centers for MVP. Among the strengths of the study are that a database of this magnitude can enable both initial discovery and replication research for both common and less common diseases, Concato explains. Ethnic and racial groups are represented in rough proportion to the U.S. population, although female representation is lower. Additionally, the genomic data and self-reported data are linked to clinical data in electronic health records in an integrated health system. “The challenge, and this is not only with MVP or the VA, but as a society, what do you do with this information? . . . We are talking about petabytes of information,” Ronald Przygodzki, M.D., associate director of genomic medicine at the VA., explains to DTET. “There are really scant publications that look at data tying this marker or variant and outcome. People continually forget that most of these studies are based on a small number of individuals. With MVP we hope to break that apart. What data is reliable? How do we present that information? Is genomic information useful in medical records. We will be determining how to work with this data.” Coordination Benefits Industry Are more federally directed efforts needed to ensure that the United States is a leader in the genomic revolution? Evidence shows that a coordinated national effort could both accelerate the pace of discovery and benefit private companies in the space. In 2013 the VA announced several MVP partnerships with the industry:
The BioProcessing Solutions Alliance, a partnership between RUCDR Infinite Biologics at Rutgers University, the State University of New Jersey, and BioStorage Technologies, a sample management solutions company, received a five-year contract for quality control and analysis of 100,000 samples from MVP using gene expression, sequencing, and genotyping. The agreement, announced in November, calls for a year one payment of $7.5 million and will in part use Affymetrix Genotype Solutions.
Claritas Genomics (Boston) received a $9 million contract in October to sequence exomes of MVP samples over the next 12 months. Claritas is supported in this by Life Technologies with its Ion Proton sequencing platform and Lockheed Martin, which is applying its expertise in data security to manage the large amounts of data that will be generated.
Personalis (Menlo Park, Calif.) received a contract back in March to use its secure computing facility and proprietary algorithms to quality control all raw data, call variants against a reference sequence, and annotate both single nucleotide variants/indels, and structural variants for more than 1,000 samples. Personalis will subcontract the laboratory genetic analysis, including both DNA sequencing and genome-scale genotyping, to Illumina.
Takeaway: Expanding large-scale, nationally coordinated sequencing efforts may enhance the speed with which clinically useful genomic data is incorporated into medical practice, while providing an economic boost to private industry.
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