Development of LOINC for Integrating Constitutional Cytogenetic Test Result Reports into Electronic Health Records

Abstract

Objective: To develop Logical Observation Identiers Names and Codes (LOINC) codes to represent constitutional cytogenetic test results for electronically exchanging coded and structured result reports. The LOINC codes developed must be exible and sustainable for easy maintenance. The goal is to create a standard set of codes that are exible enough to be used for all unique conventional and molecular cytogenetic results. Design: Patient de-identied sample result reports were obtained from ARUP Laboratories for a variety of normal and abnormal constitutional studies using G-banding, FISH and array-CGH. Information models were created to capture the semantic relationships of the key data elements that existed in the reports. Sample reports were subsequently obtained from Emory and Mayo Clinic Cytogenetics Laboratories to verify the information models. The information models were then used to guide the systematic creation of the LOINC codes. Results: A post-coordinated approach was used in developing the LOINC codes for cytogenetics test results. LOINC panel codes were created to represent the hierarchical structures implied by the reports. A master panel was created to contain three LOINC subpanels; each of the three subpanels held the structure for chromosome analysis results that uses a dierent technique. Conclusion: The LOINC codes we created met our objective and will allow the use of well established health informatics standards to exchange coded and structured cytogenetic test results between testing laboratories and ordering institutions. Use of standard structures and terminologies for cytogenetic results is critical for eective communication between testing laboratories and clinicians. This minimizes misinterpretation, leads to consistency, and provides the EHR systems exibility of customizing formatting to present more clinician-friendly reports.

Genetic testing behavior and reporting patterns in electronic medical records for physicians trained in a primary care specialty or subspecialty

“…Third, the findings may not be generalizable and we acknowledge that attempting to classify genetic testing data from the EMR of a single institution will be imperfect and give patient, provider, and genetic test characteristics that will likely differ across organizations. 40 Finally, the LOINC coding system, in its current form, limited our ability to accurately classify every genetic test result in the EMR. Although widely adopted and capable of describing most laboratory results, the LOINC system currently has gaps for cytogenetic results that may lead to potential under-representation of such tests in our analysis.…”

Supporting interoperability of genetic data with LOINC

“…LOINC has been widely adopted as the standard for laboratory test result names in the United States, where it is a national standard, 16,17 and internationally. 18,19 Many genetic test reporting initiatives, 20,21 including the HL7 Clinical Genomics Working Group, 22,23 have adopted LOINC.…”

“…The axes produce names detailed enough to distinguish among similar observations. 18 For naming genetic tests that target specific genetic variations, LOINC uses the Human Genome Organization Gene Nomenclature Committee's terminology 24 to name the gene(s) and the Human Genome Variation Society's (HGVS) syntax to name the variation(s) 25 of interest. We are aware of the challenges due to misnaming and version changes in these nomenclatures 26 ; however, the thousands of LOINC users tend to detect and report such problems.…”

“…The genetic variation collection consists of a number of LOINC panels, including one that reports the overall results of the study, another that reports the details about each variation found, and yet another that describes the region of interest and the gene chip as applicable (see figure 1). To improve the integration of cytogenetic test results into EHRs, Heras et al 18 examined a range of sample cytogenetic test names and result reports and, from this empirical effort, created a LOINCenabled HL7 specification for reporting cytogenetic tests in a fully structured form. 22 The LOINC codes for this specification are organized under the Chromosome analysis master panel [62389-2], which includes a choice of subpanels for discrete reporting of the 3 major testing approaches-chromosome banding, fluorescence in situ hybridization, and microarrays.…”

“…However, it is better to provide the report in Heras's full structured cytogenetic specification. 18,22 Cytogenetic tests should also include an observation for the reference assembly build identifier such as Human reference sequence assembly release number .…”