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Table 2 Concordance rate (%) between PGxSeq sequencing data compared to TaqMan-derived genotypes for clinically important SNVs as defined by PharmGKB

From: Targeted next generation sequencing as a tool for precision medicine

PharmGKB Gene Allele Nucleotide change Effect dbSNP Allele frequency TaqMan Concordanceª FP FN
Level of evidence 150 Study 1000G ExAC Patients genotyped (N) (%) (%) (%)
(n = 235) EUR EUR WT HET HOM
1A CYP2C19 *17 C > T promoter rs12248560 0.23 0.23 NR 23 11 1 100 0 0
1A CYP2C19 *2 G > A p.P227P rs4244285 0.14 0.15 0.15 25 11 0 100 0 0
1A CYP2C19 *3 G > A p.Y212X rs4986893 ND 0 1.80E-04 50 0 0 100 0 NA
1A CYP2C9 *2 C > T p.R144C rs1799853 0.13 0.12 0.13 72 23 3 100 0 0
1A CYP2C9 *3 A > C p.I359L rs1057910 0.06 0.06 0.07 87 13 0 100 0 0
1A CYP2D6 *10 C > T p.P34P rs1065852 0.21 0.2 0.25 30 19 3 98.1 0 1.9
1A CYP2D6 *4 G > A splice rs3892097 0.19 0.19 0.17 52 26 6 100 0 0
1A CYP2D6 *3A A > del p.R208fs rs35742686 0.03 0.02 0.02 50 2 0 100 0 0
1A CYP2D6 *41 G > A intronic rs28371725 0.12 0.09 0.09 38 14 0 100 0 0
1A CYP3A5 *3 A > G splice rs776746 0.93 0.95 NR 1 9 27 100 0 0
1A CYP4F2 *3 C > T p.V433 M rs2108622 0.30 0.27 0.29 23 17 0 100 0 0
1A DPYD *13 T > G p.I560S rs55886062 2.1E-03 1.3E-03 6.18E-04 97 1 0 100 0 0
1A DPYD *2A G > A splice rs3918290 0.02 0.01 0.01 100 1 0 100 0 0
1A DPYD   A > T p.D949V rs67376798 0.02 2.2E-03 4.09E-03 80 8 0 98.9 0 1.1
1A SLCO1B1 *5 T > C p.V174A rs4149056 0.18 0.17 0.16 67 31 4 100 0 0
1A TPMT *2 G > C p.A80P rs1800462 2.1E-03 6.00E-03 1.97E-03 51 1 0 100 0 0
1A TPMT *3B G > A p.A154T rs1800460 0.04 0.03 0.04 41 10 0 100 0 0
1A TPMT *4 G > A splice rs1800584 ND NR 3.01E-05 51 0 0 100 0 NA
1A TPMT *3C A > G p.Y240C rs1142345 0.04 0.03 0.04 41 10 0 100 0 0
1A UGT1A1 *28 (TA)6 > (TA)7 promoter rs3064744 0.32 0.29 NR 36 40 5 100 0 0
1A VKORC1   G > A intergenic rs9923231 0.40 0.40 NR 19 15 6 100 0 0
1B CYP2B6 *9 G > T p.Q172H rs3745274 0.21 0.23 0.24 22 9 0 100 0 0
2A ABCB1   C > T p.I1145I rs1045642 0.48 0.47 0.47 18 61 26 100 0 0
2A CYP2D6 *9 AAG > del p.K281del rs5030656 0.02 0.02 0.03 48 4 0 100 0 0
2A SLCO1B1 *1B A > G p.N130D rs2306283 0.41 0.40 0.41 40 46 15 100 0 0
2B ABCG2   C > A p.Q141K rs2231142 0.12 0.10 0.10 87 20 1 100 0 0
3 ABCC2   G > A p.V417I rs2273697 0.19 0.20 0.20 45 19 4 100 0 0
3 ABCG2   G > A p.V12 M rs2231137 0.04 0.06 0.05 81 9 0 100 0 0
3 CYP2B6   C > T p.R487C rs3211371 0.12 0.10 0.12 23 8 0 100 0 0
3 CYP3A4 *22 C > T intronic rs35599367 0.05 0.05 NR 36 8 0 100 0 0
3 DPYD HapB3 G > A p.E412E rs56038477 0.03 0.02 0.02 73 11 0 100 0 0
3 SLCO2B1   G > A p.R290Q rs12422149 0.06 0.10 0.11 62 6 0 100 0 0
  1. ª Percentage of total tested DNA samples with NGS-determined genotypes concordant with TaqMan results. False positive was defined as TaqMan determined “homozygous wildtype” and NGS determined “variant carrier”. False negative was defined as TaqMan determined “variant carrier” and NGS determined “homozygous wildtype”. PharmGKB definition for levels of evidence can be found at https://www.pharmgkb.org/page/clinAnnLevels. Nucleotide change presented as the change on the coding strand. Abbreviations: dbSNP 150 Single Nucleotide Polymorphism database build 150, ExAC Exome Aggregation Consortium European dataset, FP false positive, FN false negative, HET heterozygous genotype, HOM homozygous genotype, ND not detected in our patient database, NA not applicable as no variant carriers were found, NR, not reported in, 1000G EUR, or ExAC database, 1000G EUR 1000 Genomes Project European dataset, PharmGKB Pharmacogenomics Knowledge Base