At a glance
Pharmacogenetics
This resource contains the up-to-date consensus PGx genotypes for 334 DNA samples characterized by GeT-RM. These samples were characterized during 8 GeT-RM pharmacogenetic or Human Leukocyte Antigen (HLA) studies covering 34 genes/loci.
Consolidated Table of all GeT-RM Pharmacogenetic Reference Material Genotypes
A searchable web-based tool, GeT-RM PGx Search, based on these data, is available on the Coriell Institute for Medical Research website.
Note: The files in the sections below contain the same data as the consolidated Excel table in this section.
DNA from 49 cell lines were characterized for alleles in CYP3A4 and CYP3A5 using a variety of methods.1 The document includes data from each method and consensus diplotypes for each sample.
The alleles were tested using genotyping assays.
Summary of CYP3A4 and CYP3A5 Platforms and Genotyping Assays
GeT-RM used a variety of methods to characterize DNA from 30 Coriell cell lines to create a panel of reference materials for TMPT and NUDT15.2 The data from each method and the consensus diplotypes for each sample are available for review.
Lab Data and Consensus TMPT and NUDT15 Diplotypes
Details on the assays used and the alleles tested can be found separately.
GeT-RM used targeted and whole genome sequencing analysis to recharacterize 137 DNA samples that were previously characterized using a variety of targeted genotyping assays to identify star allele diplotypes for CYP2C8, CYP2C9, and CYP2C19.34 Data from each test method and consensus diplotypes for each sample are available for review.
CYP2C8, CYP2C9 and CYP2C19 (Next Generation Sequencing) Results by Test Method
GeT-RM characterized 18 cell line DNA samples to create reference materials containing pharmacogenetic alleles classified as "Tier 2" by the Association for Molecular Pathology PGx Work Group.5 Data from each test method and consensus diplotypes for each sample are available for review.
The CYP2D6 gene in DNA from 179 cell lines including rare and/or difficult to analyze alleles and/or diplotypes were characterized by the GeT-RM using a variety of methods.6 The data from each test method and consensus diplotypes for each sample, assays used, and the tested alleles are available for review.
DNA from 137 cell lines was characterized by the GeT-RM for 28 PGx genes using a variety of methods.7 Consensus genotype data and data by platform are presented in the tables, covering all 28 loci collectively and individually for each locus. Details on the assays used and the alleles tested are provided separately.
- WGS data (FASTQ and BAM files) for 70 of these samples are freely available for download and use from the European Nucleotide Archive.
- Tables showing data from each of the platforms used to characterize each of the 28 PGx genes.
Consensus Genotypes for 28 PGx Genes
DNA from 107 cell lines was characterized for CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1 by the GeT-RM using a variety of methods.8 The assays used and the tested alleles in this study are in the Summary of Assays and Alleles Tested spreadsheet linked below. (106 of these samples were also characterized by GeT-RM for HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQA1, DQB1, DPA1, and DPB1.9) Data are presented in the documents listed below for all 5 loci together and for each of the 5 loci individually.
Summary of Assays and Alleles Test
CYP2D6, CYP2C19, CYP2C9, VKORC1 and UGT1A1 Characterized by GeT-RM
Inherited genetic disease
GeT-RM partnered with ClinGen to develop a publicly available list of expert curated, clinically important variants. This list serves as a resource for designing comprehensive validation studies. It is also used for creating in silico reference materials for clinical genomic test development and validation.10 ClinGen Variant Curation Expert Panels nominated 546 pathogenic and difficult to detect variants in 84 disease-associated genes.
The Ashkenazi Jewish Reference Material Panel includes the following diseases:
- Bloom syndrome
- Canavan disease
- Fanconi anemia type C
- Familial dysautonomia
- Gaucher disease
- Glycogen storage disease type 1a
- Mucolipidosis IV
- Neimann-Pick disease
- Tay-Sachs disease.
All cell lines in this table have been characterized using various methods by the GeT-RM program.11
All cell lines in this table have been characterized using various methods by the GeT-RM program.12
All cell lines in this table have been characterized using various methods by the GeT-RM program.3
All cell lines in this table have been characterized using various methods by the GeT-RM program and AMP.13
All cell lines in this table have been characterized using various methods by the GeT-RM program.14
All cell lines in this table have been characterized using various methods by the GeT-RM program.15
All cell lines in this table have been characterized using various methods by the GeT-RM program.16
All cell lines in this table have been characterized using various methods by the GeT-RM program.17
All cell lines in this table have been characterized using various methods by the GeT-RM program. The article is available to the public.18
Additional data
These are additional data for 137 DNA samples obtained during the GeT-RM PGx characterization study.7 Data are from one assay only. The assay used to characterize each gene is indicated.
These are additional data about 107 DNA samples obtained during the GeT-RM PGx characterization study.8 Data are from only one laboratory.
These are additional data about the DNA characterized in the GeT-RM MTHFR, SERPINA1, RET, BRCA1, and BRCA2 characterization study.15 These data come from only one laboratory.
These are additional data about 107 DNA samples in the GeT-RM PGx characterization study.8 Data are from only one or two (HFE) laboratories.
This document includes reference materials for conditions involving nonsyndromic deafness, craniosynostosis/Muenke, hemochromatosis, MTHFR, alpha-thalassemia, factor V, prothrombin, sickle cell disease.19
Contact information
For inquiries about the information on this page, contact DLSInquiries@cdc.gov.
For assistance reading the data tables in the PDF and Excel files, use the subject line “GeT-RM Data Tables: Assistance with Reading” in your email.
- Gaedigk A, Boone EC, Turner A, van Schaik R, Cheranova D, Wang WY, et al. Characterization of Reference Materials for CYP3A4 and CYP3A5- A GeT-RM Collaborative Project. J Mol Diag 2023 25:655-664.
- Pratt VM, Wang WY, Boone EC, Broeckel U, Cody N, Edelmann L, et al. Characterization of Reference Materials for TPMT and NUDT15 - A GeT-RM Collaborative Project. J Mol Diag 2022, 24:1079-1088.
- Kalman L, Leonard J, Gerry N, Tarleton J, Bridges C, Gastier-Foster JM, et al. Quality Assurance for Duchenne and Becker Muscular Dystrophy Genetic Testing: Development of a Genomic DNA Reference Material Panel. J Mol Diag 2011 Mar;13(2):167-74.
- Gaedigk A, Boone EC, Scherer S, Lee S, Numanagic I, Sahinalp C, et al. Characterization of Reference Materials for CYP2C8, CYP2C9 and CYP2C19 by Next Generation sequencing: A GeT-RM Collaborative Project. J Mol Diag 2022, 24:337-350.
- Pratt, VM, Turner A, Broeckel U, Dawson BD, Gaedigk A, Lynnes, et al. Characterization of Reference Materials for CYP2C9, CYP2C19, VKORC1, CYP2C Cluster Variant, GGCX, and Other Pharmacogenetic Alleles with an Association for Molecular Pathology (AMP) Pharmacogenetics Working Group Tier 2 Status – A GeT-RM Collaborative Project. J Mol Diag 2021, 23:952-958.
- Gaedigk A, Turner A, Everts RE, Scott SA, Aggarwal P, Broeckel U, et al. Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles A GeT-RM Collaborative Project. J Mol Diag 2019 21:1034-1052.
- Pratt VM, Everts RE, Aggarwal P, Beyer BN, Broeckel U, Epstein-Baak R, et al. Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes: A GeT-RM Collaborative Project. J Mol Diag 2016 18:109-123.
- Pratt VM, Zehnbauer B, Wilson JA, Baak R, Babic N, Bettinotti M, et al. Characterization of 107 genomic DNA reference materials for CYP2D6, CYP2C19, CYP2C9, VKORC1 and UGT1A1: A GeT-RM and Association for Molecular Pathology collaborative project. J Mol Diag 2010 12:835-846.
- Bettinotti MP, Ferriola D, Duke JL, Mosbruger TL, Tairis N, Jennings L, et al. Characterization of 108 Genomic DNA Reference Materials for 11 Human Leukocyte Antigen Loci: A GeT-RM Collaborative Project. J Mol Diag 2018, 20:703-715.
- Wilcox E, Harrison SM, Lockhart E, Voelkerding K, Lubin IM, Clingen Expert Panels, et al. Creation of an Expert Curated Variant List for Clinical Genomic Test Development and Validation: A ClinGen and GeT-RM Collaborative Project. J Mol Diag 2021 23:1501-1506.
- Kalman LV, Amos Wilson J, Buller A, Dixon J, Edelmann L, Geller L, et al. Characterization of Genomic DNA reference materials for genetic testing of disorders common in people of Ashkenazi Jewish decent. J Mol Diag 2009 Nov;11(6):530-6.
- Pratt VM, Caggana M, Bridges C, Buller AM, DiAntonio L, Highsmith EW, et al. Development of Genomic Reference Materials for Cystic Fibrosis Genetic Testing. J Mol Diag 2009 11:186-93.
- Wilson JA, Pratt VM, Phansalkar A, Muralidharan K, Highsmith Jr WE, Beck JC, et al. Consensus Characterization of 16 FMR1 Reference Materials: A Consortium Study. J Mol Diag 2008 10:2-12.
- Kalman L, Johnson MA, Beck J, Berry-Kravis E, Buller A, Casey B, et al. Development of genomic reference materials for Huntington disease genetic testing. Genetics in Medicine 2007 9:719-723.
- Barker SD, Bale S, Booker J, Buller A, Das S, Friedman K, Godwin AK, et al. Development and characterization of reference materials for MTHFR, SERPINA1, RET, BRCA1, and BRCA2 genetic testing J Mol Diag 2009 Nov;11(6):553-61.
- Kalman L, Tarleton J, Hitch M, Hegde M, Hjelm N, Berry-Kravis E, et al. Development of a Genomic DNA Reference Material Panel for Myotonic Dystrophy type 1 (DM1) Genetic Testing. J Mol Diag 2013 15:518-525.
- Kalman L, Tarleton J, Percy A, Aradhya S, Bale S, Barker S, et al. Development of a genomic DNA reference material panel for Rett Syndrome (MECP2-related disorders) Genetic Testing. J Mol Diag 2014 16:273-279.
- Prior TW, Bayrak-Toydemir P, Lynnes TC, Mao R, Metcalf JD, Muralidharan K, et al. Characterization of Reference Materials for Spinal Muscular Atrophy Genetic Testing: A Genetic Testing Reference Materials Coordination Program Collaborative Project. J Mol Diag 2021, 23:103-110.
- Bernacki SH, Beck JC, Stankovic AK, Williams LO, Amos J, Snow-Bailey K, et al. (2005). Genetically characterized positive control cell lines derived from residual clinical blood samples. Clinical chemistry, 51(11), 2013-2024. https://doi.org/10.1373/clinchem.2005.048694