Precision Medicine at Mount Sinai

Integrating a Patient’s Clinical and Molecular Information for Improved Diagnosis and Treatment

We often hear about the “potential” that biomedical science and technology have to offer “the future of medicine.” At The Mount Sinai Medical Center, some 25,000 patients are living that future and receiving more precise, personalized care—in real time—based on their own DNA.

Each has enrolled in BioMe (TM), our robust biobank which is among the largest such repositories in the United States. It is also unique in that each patient has broadly consented to DNA sequencing, contact from researchers, and longitudinal studies stemming from the electronic medical record (EMR). Mount Sinai has implemented the Epic EMR system throughout its inpatient and outpatient services, the emergency department, pharmacy, and in many affiliate offices across the city.

The Future of Medicine Is Here

A team of physicians, genetic scientists, and experts in information technology are now launching CLIPMERGE, a first-in-nation and potentially revolutionary data management and analysis platform that will guide clinical care, in real time, based on patients’ genetic makeup. CLIPMERGE (for Clinical Implementation of Personalized Medicine through Electronic Health Records and Genomics) communicates with the EHR—right in the doctor’s office—to give point-of-care therapeutic guidance based on a patient’s genetic profile.

Once a patient has consented to take part in a CLIPMERGE study, their DNA derived from saliva is analyzed for genetic variations that may affect how a drug works in that individual. With its interoperable BioMe and CLIPMERGE platforms as flagship institutional infrastructures, Mount Sinai has the unique ability to close the loop between genomic discovery and the implementation of genomic medicine in clinical care.

Real-time feedback on optimal, DNA-based therapeutics will be available for conditions related to cardiovascular disease, blood clots, high cholesterol, depression and pain. CLIPMERGE will alert a doctor if a medication prescribed to a patient has a lower likelihood of being effective, or a higher chance of side effects, due to that patient’s particular type of genetic information. This process of providing relevant information to physicians at the point of care, right when they are treating patients, is called “clinical decision support.” Just as it sounds, it is intended to support physicians in their clinical decision making. As science yields greater insights into the role that genetics plays in drug efficacy and reactions, genome-guided clinical decision support systems will become even more robust, leading to more precise treatment.

From Pixel to Whole Picture: The Goal of Genomics

BioMe and CLIPMERGE are critical parts of Mount Sinai’s larger genomics enterprise which is built on the knowledge that modern medicine does not begin to take into account the multitude of factors that influence health and healing. Consider this analogy: when you watch a movie, your brain is processing unfathomable amounts of information in order to follow the plot. You would never be able to understand the movie based on a single pixel from a single shot in the film.

The same is true in medicine, and considered from this view, the current practice of diagnosing Type 2 diabetes, for example, based on a high glucose reading is akin to seeing one pixel and trying to understand a whole movie. A better and more precise diagnosis would analyze glucose readings over time along with DNA, RNA, metabolites, and other high-dimensional proteomic information to distinguish Type 2 diabetes from a condition that might be stand-alone high glucose.

The focus of the genomics enterprise, therefore, is associating a tsunami of molecular data with phenotype, or all observable characteristics—no matter how microscopic—then building models that allow scientists to manipulate biological systems and control that phenotype for individual and public health benefit. Such sophisticated mathematical modeling is the norm in space exploration, weather forecasting, financial markets, and in consumer industries that are driven to understand and influence buying habits. It is revolutionary, however, in academic medicine.

Similar to a GPS in a car, pathology and treatment in the genomic arena includes data on the spatial organization of cells and tissues which allows scientists to navigate in human tissues with more precision than ever before. In essence, patient-specific characteristics and molecular phenotypes are becoming the new foundation for patient management.

Enter Minerva, Mount Sinai’s Supercomputer

In diabetes, cancer, brain diseases, and other areas Mount Sinai is generating among the largest datasets in medicine. The information is housed in BioMe and in the institution’s data warehouse that accesses de-identified clinical information from the EMRs Mount Sinai’s very diverse patient population. On a per-patient basis, Mount Sinai collects several terabytes of data, or 1,000 gigabytes—think 100 DVDs—including the whole genome sequencing of the tumor DNA, DNA from adjacent normal tissue, RNA sequencing in both tissues, and epigenomic profiling. Depending on the type of cancer, these data can be collected on hundreds or thousands of patients, producing petabyte scales of data, or 1,000,000 gigabytes—think 100,000 DVDs.

Amassing this much data is one step. Analyzing and integrating it to build more precise predictive models of a particular cancer—and of all cancers, and all diseases—is another. That’s where Minerva, Mount Sinai’s supercomputer, comes in. It is among the largest high-performance computer clusters in academic medicine in the U.S., processing the Internet-scale data that Mount Sinai is amassing.

Modern medicine needs supercomputers in the way climatologists require them to accurately model the weather. But in medicine, the data are much more complicated, and many more factors are at play.

What’s Next?

CLIPMERGE is opening the door to wider real-time applications of genomic medicine in the clinical setting. With BioMe, Minerva, and a robust genomics enterprise that allow for big data computations and accelerated sequencing of genomic information, we are looking to grow our portfolio of clinical tools—for the benefit of all patients today and in the future.

Erwin Bottinger, MD
Director, Charles Bronfman Institute for Personalized Medicine

Omri Gottesman, MD
Assistant Professor of Medicine (General Internal Medicine)

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