An ancillary genomics system to support the return of pharmacogenomic results

Abstract

Existing approaches to managing genetic and genomic test results from external laboratories typically include filing of text reports within the electronic health record, making them unavailable in many cases for clinical decision support. Even when structured computable results are available, the lack of adopted standards requires considerations for processing the results into actionable knowledge, in addition to storage and management of the data. Here, we describe the design and implementation of an ancillary genomics system used to receive and process heterogeneous results from external laboratories, which returns a descriptive phenotype to the electronic health record in support of pharmacogenetic clinical decision support.

Keywords: electronic health record; genetic testing; pharmacogenomics.

Figure 1.

The Northwestern Medicine ancillary genomics system. Overall flow of data from external laboratories, which are imported into the ancillary genomics system, analyzed by the system to create computed observations (results), manually reviewed by a genetic counselor, and then released to the electronic health record (EHR). Steps denoted with an asterisk involve human interaction or decision making; all other steps are automated. HL7: Health Level 7.

Figure 2.

Translation and normalization steps from heterogeneous laboratory results to computed observations in the ancillary genomics system. For Lab A, the star variant results are converted to a normalized string representation and then translated to a computed observation. For Lab B, the single nucleotide polymorphism (SNP) results are normalized, translated to a star variant representation, and then translated to a computed observation.