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Expert Panel Publishes Standardized PGx Terms

NEW YORK (GenomeWeb) – A panel of experts has published a set of pharmacogenetics terms in Genetics in Medicine today with the aim of enabling greater integration of test results into electronic health records.

The publication, from the Clinical Pharmacogenetics Implementation Consortium, includes standardized terms for allele functional status and three sets of terms for inferred phenotypes for drug-metabolizing enzymes such as CYP2D6; transporters such as SLCO1B1; and high-risk genotypes such as HLA-B.

"We anticipate that broad adoption of these proposed standardized pharmacogenetics terms will improve understanding and interpretation of pharmacogenetic tests by clinicians and patients and reduce confusion by maintaining nomenclature consistency among pharmacogenes," the authors led by Kelly Caudle from St. Jude Children's Research Hospital wrote in GIM. "These uniform references will reduce the complexity of the underlying coded vocabulary needed to transmit pharmacogenetic phenotypes between independent laboratories and sites of care and to trigger clinical decision support."

CPIC, established in 2009, is a group of experts who develop guidelines for incorporating PGx into patient care. For the latest publication, CPIC members invited experts from groups, such as the Global Alliance for Genomics and Health, the PGx working groups within the Clinical Genome Resource (ClinGen), eMERGE, and the College of American Pathologists, to weigh in on terms through five structured surveys.

Close to 60 clinicians, researchers, genetic testing lab professionals, PGx specialists, and informaticians participated in the process. Consensus was defined as greater than 70 percent agreement.

Experts held a call to discuss and recommend final terms in the fifth survey, and after the final survey 100 percent agreed on terms describing allele function status for drug-metabolizing enzymes and transporters; nearly 92 percent agreed to terms for drug-metabolizing enzyme phenotypes; and the same portion of experts agreed to terms for transporter phenotypes.

For example, the experts decided on using the term "normal metabolizer," instead of "extensive metabolizer," which many thought was too confusing. They decided to apply the term "normal metabolizer" when discussing normally functioning drug-metabolizing enzymes, such as TPMT and DPYD, which previously have been described with the term "wild type."

However, the experts couldn't reach consensus on VKORC1, which is commonly tested to establish a starting dose for warfarin. Many labs reported the phenotype as "greatly increased sensitivity to warfarin," which made it complicated to standardize the term for this gene in the same format used for other genes, according to the paper.

These published standard terms will be used in CPIC guidelines going forward. "We recommend that these terms be considered standard terminology across all areas of clinical pharmacogenetics, including clinical genetic testing laboratory reporting," the authors wrote in GIM. The Association for Molecular Pathology, an organization representing 2,000 molecular and genomics lab professionals, has endorsed the terms put out by CPIC.

CPIC also registered the PGx terms under the Logical Observation Identifier Names and Codes, which is a well-known standard for reporting test results and interpretations. Caudle and colleagues said in the paper that using LOINC will facilitate PGx clinical decision support with EHRs, and make it easier to share tests results across EHRs as patients move between healthcare systems.

The authors further noted that these terms could be useful for collaborative genomic variation curation and interpretation efforts, such as ClinGen, the genetic variation archive ClinVar, and for proficiency testing programs designed to improve the quality of genetic tests.