Biobank expands in pursuit of 'precision medicine'


Biobank expands in pursuit of 'precision medicine'

Mount Sinai Medical Center announced this week that 25,000 people have signed on to participate in its biobank program, BioMe, with each patient consenting to DNA sequencing and longitudinal studies related to data embedded in their electronic medical records.

The Mount Sinai Medical Center includes the Mount Sinai Hospital and Icahn School of Medicine at Mount Sinai. Officials there say the participants in the BioMe program represent one of the most diverse patient populations in the world.

"Biobank participants represent the ancestral diversity of the local Upper Manhattan communities, with self-reported 25 percent of African ancestry, 30 percent of European ancestry, 36 percent of Hispanic Latino, and 9 percent of other ancestry," said Erwin P. Böttinger, MD, director of the Charles Bronfman Institute for Personalized Medicine at Mount Sinai.

"To assess representativeness of the Biobank population for the local communities from which they are recruited, we obtained publicly available individual-level data from the annual New York City Community Healthy Survey, which provides robust data on the health of New Yorkers, including neighborhood, borough and citywide estimates on a broad range of chronic disease and behavioral risk factors," he added.

Mount Sinai researchers published a report in 2011 that found that ethnic labels may be of little help in predicting individuals' disease risk or determining their response to certain medications. It found that nearly 1,000 biobank participants who self-identified as European-American, African-American or Hispanic, had considerable parts of their genome coming from mixed ancestry.

"These findings emphasize the importance of considering the unique genotype of the individual patient rather than grouping patients by self-reported ethnicity," said Böttinger.  "Individual genomic disease risk and treatment response information will allow us to provide highly effective, personalized care." 

Funded by The Charles Bronfman Institute for Personalized Medicine at Mount Sinai, the BioMe program – in addition to serving as a repository of DNA and plasma samples that allows for secure, de-identified molecular research – accesses a wide array of clinical and environmental data stored in the Epic EMR and links it with genetic information.

Beyond its broader mission of biomedical research, BioMe is helping doctors give enrolled patients more targeted care. More than 600 new patients, on average, sign on to the project each month. The goal, ultimately, is to enroll 100,000.

"The large collection of DNA and plasma samples and large-scale genomic data are stored in a way that protects patients' privacy while allowing research to be performed on de-identified clinical information from Mount Sinai's data warehouse system," said Böttinger.

That warehouse "contains a wealth of clinical and transactional data, including all data in the Epic EMR, supporting high-throughput phenotyping of diseases and medically relevant traits," he explained – noting that, by using existing electronic clinical information in the warehouse, "the time, effort and cost involved in conducting genomic, biomarker and pharmacogenomics studies can be dramatically reduced."

On target
Key to delivering on BioMe's promise of personalized care is a component of the program called CLIPMERGE. It stands for Clinical Implementation of Personalized Medicine through Electronic Health Records and Genomics. It was developed by physicians, geneticists and IT experts at Mount Sinai to communicate with the EMR and offer physicians real-time guidance based on patients' genetic profiles.

"The emergence of electronic health records in mainstream healthcare, together with the inherent ability to provide clinical decision support, has the potential to provide the necessary level of point-of-care personalized guidance," said Böttinger.

CLIPMERGE, he said, "implements a novel clinical decision support engine for delivering guidelines with genetic variants of clinical significance in a way that integrates with busy physician work processes."

The program deploys an "advanced information management system developed by the Institute for Personalized Medicine, that is external to, but communicates with, Epic EHR  – and takes advantage of decision support capabilities executable at the point-of-care," said Böttinger.

CLIPMERGE decision support rules "are based on actionable variants distilled from each patient's genotype data and combined with relevant phenotypic data in our CLIPMERGE database," he noted, which includes "longitudinal clinical data extracted from Mount Sinai's Epic EMR and ancillary systems, for all consented patients."

Meanwhile, a technology called the CLIPMERGE Risk Assessment Engine "relates actionable genotype-phenotype pairs to genome-based advice messages," said Böttinger.

"If predefined rules are met, customized decision support is delivered in near real-time. Decision support messages consist of a short text segment, a link to our reference knowledge database server [reference material for providers] and an Epic SmartSet [order set] if appropriate."

By working in tandem, BioMe and CLIPMERGE essentially "close the loop" between genomic discovery and deployment of that knowledge in clinical care, said Mount Sinai officials.

"Enrolling 25,000 patients in the biobank is a significant achievement for Mount Sinai, propelling us to the forefront of precision medicine and its application in the clinical setting," said Dennis S. Charney, MD, the Anne and Joel Ehrenkranz Dean of Mount Sinai School of Medicine, in a press statement. "The future of medicine lies in genomics research and translating it to the bedside – and Mount Sinai's commitment to translational research makes us uniquely poised to lead that revolution."