Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting

L V Kalman; Jag Agúndez; M Lindqvist Appell; J L Black; G C Bell; S Boukouvala; C Bruckner; E Bruford; K Caudle; S A Coulthard; A K Daly; Al Del Tredici; J T den Dunnen; K Drozda; R E Everts; D Flockhart; R R Freimuth; A Gaedigk; H Hachad; T Hartshorne; M Ingelman-Sundberg; T E Klein; V M Lauschke; D R Maglott; H L McLeod; G A McMillin; U A Meyer; D J Müller; D A Nickerson; W S Oetting; M Pacanowski; V M Pratt; M V Relling; A Roberts; W S Rubinstein; K Sangkuhl; M Schwab; S A Scott; S C Sim; R K Thirumaran; L H Toji; R F Tyndale; Rhn van Schaik; M Whirl-Carrillo; Ktj Yeo; U M Zanger

doi:10.1002/cpt.280

Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting

Clin Pharmacol Ther. 2016 Feb;99(2):172-85. doi: 10.1002/cpt.280. Epub 2015 Nov 20.

Authors

L V Kalman¹, Jag Agúndez², M Lindqvist Appell³, J L Black⁴, G C Bell⁵, S Boukouvala⁶, C Bruckner⁷, E Bruford⁸, K Caudle⁹, S A Coulthard¹⁰, A K Daly¹⁰, Al Del Tredici¹¹, J T den Dunnen¹², K Drozda¹³, R E Everts¹⁴, D Flockhart¹⁵, R R Freimuth⁴, A Gaedigk¹⁶, H Hachad¹⁷, T Hartshorne¹⁸, M Ingelman-Sundberg¹⁹, T E Klein²⁰, V M Lauschke¹⁹, D R Maglott²¹, H L McLeod⁵, G A McMillin²², U A Meyer²³, D J Müller²⁴, D A Nickerson²⁵, W S Oetting²⁶, M Pacanowski¹³, V M Pratt¹⁵, M V Relling⁹, A Roberts²⁷, W S Rubinstein²¹, K Sangkuhl²⁰, M Schwab²⁸, S A Scott²⁹, S C Sim¹⁹, R K Thirumaran³⁰, L H Toji³¹, R F Tyndale³², Rhn van Schaik³³, M Whirl-Carrillo²⁰, Ktj Yeo³⁴, U M Zanger²⁸

Affiliations

¹ Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
² Department of Pharmacology, University of Extremadura, Cáceres, Spain.
³ Division of Drug Research, Department of Medical and Health Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
⁴ Mayo Clinic, Rochester, Minnesota, USA.
⁵ Moffitt Cancer Center, Tampa, Florida, USA.
⁶ Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
⁷ Affymetrix, Santa Clara, California, USA.
⁸ HUGO Gene Nomenclature Committee (HGNC), EMBL-EBI, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, UK.
⁹ St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
¹⁰ Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.
¹¹ Millennium Health, LLC, San Diego, California, USA.
¹² Department of Human Genetics and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
¹³ US Food and Drug Administration, Silver Spring, Maryland, USA.
¹⁴ Agena Bioscience, San Diego, California, USA.
¹⁵ Indiana University School of Medicine, Indianapolis, Indiana, USA.
¹⁶ Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Kansas City and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA.
¹⁷ Translational Software, Bellevue, Washington, USA.
¹⁸ Department of Genetic Analysis, Thermo Fisher Scientific, South San Francisco, California, USA.
¹⁹ Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
²⁰ Department of Genetics, Stanford University, Stanford, California, USA.
²¹ National Institutes of Health / National Library of Medicine / National Center for Biotechnology Information, Bethesda, Maryland, USA.
²² University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA.
²³ University of Basel, Basel, Switzerland.
²⁴ Department of Psychiatry, University of Toronto, CAMH, Toronto, Ontario, Canada.
²⁵ Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
²⁶ Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA.
²⁷ Aegis Science Corporation, Nashville, Tennessee, USA.
²⁸ Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart and Department of Clinical Pharmacology, University Hospital, Tuebingen, Germany.
²⁹ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
³⁰ Genelex Corporation, Seattle, Washington, USA.
³¹ Coriell Institute for Medical Research, Camden, New Jersey, USA.
³² CAMH and the Departments of Psychiatry and Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada.
³³ Department of Clinical Chemistry, Erasmus MC Rotterdam, International Federation for Clinical Chemistry (IFCC) Task Force Pharmacogenetics, Rotterdam, The Netherlands.
³⁴ Department of Pathology, The University of Chicago, Chicago, Illinois, USA.

PMID: 26479518
PMCID: PMC4724253
DOI: 10.1002/cpt.280

Abstract

This article provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward.

Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review

MeSH terms

Alleles*
Genes
Genetic Testing / standards*
Genetic Testing / trends
Genetic Variation
Humans
Pharmacogenetics / standards*
Pharmacogenetics / trends
Precision Medicine
Terminology as Topic*

Abstract

Publication types

MeSH terms

Grants and funding