The Geisinger MyCode community health initiative: an electronic health record-linked biobank for precision medicine research

Abstract

Purpose: Geisinger Health System (GHS) provides an ideal platform for Precision Medicine. Key elements are the integrated health system, stable patient population, and electronic health record (EHR) infrastructure. In 2007, Geisinger launched MyCode, a system-wide biobanking program to link samples and EHR data for broad research use.

Methods: Patient-centered input into MyCode was obtained using participant focus groups. Participation in MyCode is based on opt-in informed consent and allows recontact, which facilitates collection of data not in the EHR and, since 2013, the return of clinically actionable results to participants. MyCode leverages Geisinger's technology and clinical infrastructure for participant tracking and sample collection.

Results: MyCode has a consent rate of >85%, with more than 90,000 participants currently and with ongoing enrollment of ~4,000 per month. MyCode samples have been used to generate molecular data, including high-density genotype and exome sequence data. Genotype and EHR-derived phenotype data replicate previously reported genetic associations.

Conclusion: The MyCode project has created resources that enable a new model for translational research that is faster, more flexible, and more cost-effective than traditional clinical research approaches. The new model is scalable and will increase in value as these resources grow and are adopted across multiple research platforms.Genet Med 18 9, 906-913.

Figure 1. MyCode^® enrollment and biobanking flow chart

Steps from determining patient eligibility to sample analysis are shown. Whenever possible, existing processes and infrastructure are utilized to maximize efficiency. Steps that use existing health information technology (HIT) or clinical work flows are indicated by blue and tan boxes.

Figure 2. EHR data available for MyCode^® participants

Panel A: The duration of available EHR data for 51,893 adult MyCode^® participants, defined as the length of time between the most recent clinical encounter and the first encounter recorded for that individual in the GHS EHR; the spike at approximately 160 months corresponds to the completion of EHR implementation in GHS outpatient clinics; Panel B: the total number of clinical encounters recorded in the GHS EHR for the same MyCode participants, stratified as participants between 18 and 55 years (current age) or >55 years. The median number of encounters is 120 for age >55 years, and 50 for 18–55 years.

Figure 3. Lipid lab values of carriers and non-carriers of APOC3 variants

Laboratory values for triglycerides, low density lipoprotein cholesterol (LDL), and high density lipoprotein cholesterol (HDL) were extracted from electronic health record data of 11,499 individuals with both array genotype and blood lipid data. Each point represents the mean value of an individual carrier or non-carrier of the indicated genomic variants. For individuals with no record of a lipid lowering medication a lifetime mean value was calculated; for individuals prescribed a lipid lowering medication, the pre-medication values were averaged. Bars indicate median and inter quartile ranges. APOC3 variants were determined by array genotyping using the Illumina HumanExome array V1.1. The groups were compared by ANOVA and Dunn’s multiple comparison test. Unless indicated, differences among groups were not significant.