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Personalized Medicine Gets Practical

April 26, 2009
by Dale Sanders and Thomas Kmiecik
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At Northwestern, sophisticated genetic testing is turning the dream of personalized medicine into reality

Dale sanders

Dale Sanders

Personalized medicine's goal is to optimize treatment based on genetic variations. Due to recent technological advances, information can now be collected on individual genetic variation quickly enough to allow practical use of the data in clinical practice. Personalized medicine is already known to be beneficial in medication and chemotherapy tailoring. Now, finally, we can screen patients for genetic variations that predispose them to disease, and intervene proactively with preventive treatment and lifestyle adjustments to delay or prevent the onset of disease.

Thomas kmiecik

Thomas Kmiecik

At Northwestern in Chicago, we are actively pursuing this new and exciting field. Our Feinberg School of Medicine works with Northwestern Memorial Hospital (NMH), an 897-bed inpatient and ambulatory care facility, in tight affiliation with the 650-physician Northwestern Memorial Faculty Foundation (NMFF), a specialty faculty practice plan. The school also has a close relationship with Children's Memorial Hospital (CMH) and the Rehabilitation Institute of Chicago (RIC).

We are taking several approaches to incorporate personalized medicine into clinical practice, and to use translational medicine to deliver the benefits of increased genetic knowledge to patient care.

At NMH, a variety of genetic laboratory tests are currently being used. Many of the tests are performed in-house, particularly in the areas of coagulation and hematology/oncology. We send other tests to external reference labs. NMH has an inbound interface from Genzyme (Cambridge, Mass.) to capture those results in a structured fashion, but results from Athena (athenahealth, Watertown, Mass.) and Prometheus (San Diego, Calif.) are scanned into PowerChart (Cerner, Kansas City, Mo.). Ideally, all results would be obtained in electronic structured format through an interface, but since considerable time and expense are required for each interface to an external lab, there is a strong incentive to conduct as many tests as possible in-house.

In the transplant division, the transplant immunology laboratory is using genetic tests to screen for compatibility between patients and donors. For bone marrow stem cells, patients and living unrelated donors are characterized with a high-resolution DNA sequencing assay. With related donors, a genetic test is first conducted, which allows multiple samples to be characterized at low cost. A genetic test is also used prior to solid organ transplantation to characterize the compatibility of the patient and donor.

Genetic typing data from these assays will typically be stored in HistoTrac (SystemLink, Washington, D.C.) and the Online Transplant Tracking Record (OTTR) computer systems used in the transplant lab, and is not sent to the Cerner or Epic EMRs. Raw instrument data is stored locally with the instrument software.

The Northwestern campus is developing and utilizing an Enterprise Data Warehouse (EDW), which is intended to function as a consolidated and standardized clinical data repository of all Northwestern patients. The EDW combines patient data from the NMH, the Feinberg School of Medicine, and NMFF, and currently stores details on over 2 million patient records. The EDW has given us a secure and efficient means of using clinical data in translational research.

In addition to other uses, the EDW is used to create standardized disease registries. These registries will play an increasingly important role in phenotyping and genotyping patients before they manifest symptoms of a particular disease. The EDW will also soon be used to create medication registries to track patients' specific reactions to medications that are known to have a strong genetic influence.

The NUgene Project ( is a biobank of several thousand DNA data samples coupled to EMR data from participating patients at Northwestern's affiliated medical centers. Study participants' DNA samples are combined with data from a one-time questionnaire and health data from participants' EMRs for their ongoing care at the medical center.

This NUgene project is being used to help identify genetic mechanisms underlying common diseases, with the intention that information gained will ultimately help integrate genetics into clinical care. The NUgene database securely stores the data representing the genotype and questionnaire data, while the EDW stores medical record information representing the phenotype generated through routine clinical care. An additional system, NOTIS, Northwestern's clinical trial information system, contains the participants' protected health identifiers and is used to link the NUgene and EDW databases via an encrypted connection. A combination of EDW data and self-reported questionnaire data is used to select subpopulations of NUgene participants for individual research studies.

Research use of NUgene requires approval by a sample access committee, in addition to the typical IRB approvals.