Reference Materials for Pharmacogenetics

Reference Materials for Pharmacogenetics
TPMT and NUDT15 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 (J Mol Diag 2022 24:1079-1088). The data from each method and consensus diplotypes for each sample can be viewed here.  The assays used and alleles tested can be viewed here.
CYP2C8, CYP2C9 and CYP2C19 (Next Generation sequencing) 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.  The data from each test method and consensus diplotypes for each sample can be viewed here
VKORC1 warfarin resistant variants, CYP2C9*13, CYP2C10*35, CYP2C cluster, GGCX 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 (J. Mol Diag 2021 23:952-958)A subscription to the journal is required to view the article until 2022; after that it will be available to the public. The data from each test method and consensus diplotypes for each sample can be viewed here Tier 2 GeT-RM website table
CYP2D6 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 (J Mol Diag 2019 21:1034-1052). The data from each test method and consensus diplotypes for each sample, assays used, and alleles tested can be viewed here.
CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP3A4, CYP3A5, CYP4F2, DPYD, GSTM1, GSTP1, GSTT1, NAT1, NAT2, SLC15A2, SLC22A2, SLCO1B1, SLCO2B1, TPMT, UGT1A1, UGT2B7, UGT2B15, UGT2B17, VKORC1 DNA from 137 cell lines was characterized by the GeT-RM for 28 PGx genes using a variety of methods. (J Mol Diag 2016 Jan:18(1): 109-23). The assays used and alleles tested can be viewed with this link. Consensus genotype data and data by platform are presented in the following tables for all 28 loci together and for each of the 28 loci individually:
  • 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
CYP2D6, CYP2C19, CYP2C9, VKORC1 and UGT1A1 DNA from 107 cell lines was characterized for CYP2D6, CYP2C19, CYP2C9, VKORC1 and UGT1A1 by the GeT-RM using a variety of methods. (J Mol Diag 2010 12(6):835-846). The assays used and alleles tested in this study can be viewed with this link. (106 of these samples were also characterized by GeT-RM for HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQA1, DQB1, DPA1, and DPB1, see Inherited Genetic Reference Material and HLA page. (J Mol Diag 2018, 20: 703-715) Data are presented in the following tables for all 5 loci together and for each of the 5 loci individually:
Additional GeT-RM Data
Additional GeT-RM Data
ABCC2, ABCC4, CDA, CYP1B1, CYP2A13, CYP2F1, CYP2J2, CYP2S1, CYP3A7, CYP3A43, CYP4B1, CYP19A1, FMO2, G6PD, IFNL3, ITPA, PTGIS, SULT1A1, TBXAS1, UGT1A3, UGT1A4, UGT1A6, UGT1A7, UGT1A8, UGT1A9, and UGT1A10 These are additional data for 137 DNA samples obtained during the GeT-RM PGx characterization study (J Mol Diag 2016 Jan:18(1) 109-23). Data are from one assay only. The assay used to characterize each gene is indicated.
CYP4F2, EPHX1, ABCB1, HLAB, KIF6, CYP3A4, CYP3A5, TPMT, DPD. These are additional data about 107 DNA samples obtained during the GeT-RM PGx characterization study (J Mol Diag 2010 12(6):835-846). Data are from only one laboratory.

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