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TaqMan® Drug Metabolism Genotyping Assays on OpenArray® Plates June 28, 2014

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TaqMan® Drug Metabolism Genotyping Assays on OpenArray® Plates

Life Technologies® has pretested over 300 TaqMan® DME and SNP assays to highly studied, important DME and other gene variants on OpenArray® plates run on the QuantStudio™ 12K Flex Real-Time PCR System. Assays were tested on this system with 44 Coriell gDNAs (22 each African American and Caucasian samples, a subset of the TaqMan® DME Assay 90 sample validation panel) and most were also tested with synthetic plasmid constructs representing each genotype. You can download the PGx Common Markers file that contains a list of the most commonly requested assays from this set at: www.lifetechnologies.com/pgx The file includes common allele names, context sequences, and other useful annotations. This PowerPoint document contains screen shots of the test data for the most commonly requested PGx and clinical research target assays.

For Research Use Only. Not for use in diagnostic procedures. © 2014 Thermo Fisher Scientific. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.

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CYP2D6*2A g.-1584C>G, rs1080985 C__32407252_30

Plasmid Samples

gDNA Samples

The CYP2D6*2 allele can be duplicated. Samples having 3 copies of CYP2D6 that are heterozygous for -1584C>G may run within or beside the heterozygous cluster.

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CYP2D6 g.2850C>T , rs16947 C__27102425_10

Plasmid Samples

2850C>T is a common SNP that is found in *2 and many other CYP2D6 star alleles. The *2 allele can be duplicated. Samples having 3 copies of CYP2D6 that are heterozygous for 2850C>T may run within or beside the heterozygous cluster.

gDNA Samples

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CYP2D6*2 g.4180G>C, rs1135840 C__27102414_10

Plasmid Samples

4180G>C is a common SNP that is found in *2 and many other CYP2D6 star alleles. The *2 allele can be duplicated. Samples having 3 copies of CYP2D6 that are heterozygous for 4180G>C may run within or beside the heterozygous cluster.

gDNA Samples

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CYP2D6*3 g.2549delA , rs35742686 C__32407232_50

Plasmid Samples

gDNA Samples

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CYP2D6*4 g.1846G>A , rs3892097 C__27102431_D0

Plasmid Samples

The CYP2D6 *4 allele can be duplicated. Samples having 3 copies of CYP2D6 that are heterozygous for 1846G>A may run within or beside the heterozygous cluster.

gDNA Samples

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CYP2D6*6 g.1707delT , rs5030655 C__32407243_20

Plasmid Samples

gDNA Samples

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CYP2D6*7 g.2935A>C, rs5030867 C__32388575_A0 – recommended *7 assay version

Plasmid Samples

C__32388575_A0 is an improved version of C__32388575_30 (slide 10). It has higher amplification signal due to reduction of NTC signal. We recommend using C__32388575_A0 to interrogate CYP2D6*7 g.2935A>C.

gDNA Samples

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CYP2D6*7 g.2935A>C , rs5030867 C__32388575_30 - improved assay version is available*

Plasmid Samples

The high NTC signal seen with C__32388575_30 is due to probe cleavage in the absence of template and amplification. It does not interfere with genotyping unless sample the amplification signal is low (e.g. due to low sample quantity). *We recommend using the improved assay design: C__32388575_A0 (slide 9). It has higher amplification signal due to reduction of NTC signal.

gDNA Samples

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CYP2D6*8 g.1758G>T, rs5030865 C_30634117C_K0 – recommended *8 assay version

C_30634117C_K0 reports the major (G) and one minor (T) allele (CYP2D6*8) of a triallelic SNP. C_30634117D_M0 reports the major (G) and other minor (A) allele (CYP2D6*14). Both assays should be independently run on samples and data analyzed as described in the PGx Experiments User Guide Chapter 5 section on triallelic and adjacent SNPs. C_30634117C_K0 is an improved version of C_30634117C_20 (slide 12), which has higher amplification signal due to a decrease in amplicon size.

gDNA Samples

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CYP2D6*8 g.1758G>T, rs5030865 C_30634117C_20 - improved assay version is available*

Plasmid Samples

C_30634117C_20 reports the major (G) and one minor (T) allele (CYP2D6*8) of a triallelic SNP. C_30634117D_30 reports the major (G) and other minor (A) allele (CYP2D6*14). Both assays should be independently run on samples and data analyzed as described in the PGx Experiments User Guide Chapter 5 section on triallelic and adjacent SNPs. * We recommend using the improved assay design: C_30634117C_K0 (slide 11). It has higher amplification signal due to a decrease in amplicon size.

gDNA Samples

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CYP2D6*9 g.2613_2615delAGA, rs28371720 C__32407229_60

Plasmid Samples

C__32407229_60 targets the CYP2D6*9 deletion variant, which can be denoted as g.2613_2615delAGA or g.2615_2617delAAG. The nucleotide deletion results in deletion of amino acid K281.

gDNA Samples

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CYP2D6*10 g.100C>T, rs1065852 C__11484460_40

Plasmid Samples Cycle 27

The CYP2D6*10 allele can be duplicated. Samples having 3 copies of CYP2D6 that are heterozygous for 100C>T may run within or beside the heterozygous cluster.

gDNA Samples

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CYP2D6*11 g.883G>C, rs5030863 C__30634118_A0

Plasmid Samples

C__30634118_A0 specifically amplifies CYP2D6 by targeting base differences between CYP2D6 and CYP2D7. Two of these base differences occur as SNPs in some CYP2D6*4 alleles, which thus cannot be amplified by the *11 assay. The CYP2D6*4 C__27102431_D0 assay should be run on the same samples for complete genotype analysis, as *4/*4 samples will not amplify with the *11 assay, and samples that run as *11/*11 may have *11/*11 or *4/*11 genotypes, which can be discerned by the *4 assay results.

gDNA Samples

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CYP2D6*12 g.124G>A , rs5030862 C__27531552_A0

Plasmid Samples

gDNA Samples

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CYP2D6*14 g.1758G>A, rs5030865 C_30634117D_M0 – recommended *14 assay version

C_30634117D_M0 reports the major (G) and one minor (A) allele (CYP2D6*14) of a triallelic SNP. C_30634117C_K0 reports the major (G) and other minor (T) allele (CYP2D6*8). Both assays should be independently run on samples and data analyzed as described in the PGx Experiments User Guide Chapter 5 section on triallelic and adjacent SNPs. C_30634117D_M0 is an improved version of C_30634117D_30 (slide 18), which has higher amplification signal due to a decrease in amplicon size.

gDNA Samples

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CYP2D6*14 g.1758G>A , rs5030865 C_30634117D_30 - improved assay version is available*

Plasmid Samples

C_30634117D_30 reports the major (G) and one minor (A) allele (CYP2D6*14) of a triallelic SNP. C_30634117C_20 reports the major (G) and other minor (T) allele (CYP2D6*8). Both assays should be independently run on samples and data analyzed as described in the PGx Experiments User Guide Chapter 5 section on triallelic and adjacent SNPs. * We recommend using the improved assay design: C_30634117D_M0 (slide 17). It has higher amplification signal due to a decrease in amplicon size.

gDNA Samples

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CYP2D6*15 g.137-138insT, rs72549357 C__32407245_40

Plasmid Samples

gDNA Samples

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CYP2D6*17 g.1023C>T, rs28371706 C___2222771_A0 – recommended *14 assay version

The CYP2D6*17 allele can be duplicated. Samples having 3 copies of CYP2D6 that are heterozygous for 1023C>T may run within or beside the heterozygous cluster.

C___2222771_A0 is an improved version of C___2222771_40 (slide 21). It has been observed that C___2222771_40 cannot amplify a subset of *4 alleles and thus some *4/*17 samples will run as *17 homozygotes. E.g. In the experiment shown, samples NA17116 and NA17121 run as heterozygotes with C___2222771_A0 whereas they run as *17/*17 homozygotes with C___2222771_40.

gDNA Samples

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CYP2D6*17 g.1023C>T, rs28371706 C___2222771_40 - improved assay version is available*

Plasmid Samples

The CYP2D6*17 allele can be duplicated. Samples having 3 copies of CYP2D6 that are heterozygous for 1023C>T may run within or beside the heterozygous cluster.

It has been observed that C___2222771_40 cannot amplify a subset of *4 alleles and thus some *4/*17 samples will run as *17 homozygotes. E.g. In the experiment shown, samples NA17116 and NA17121 run as homozygotes with C___2222771_40 whereas they run as *17 heterozygotes with C___2222771_A0. *We recommend using the improved assay: C___2222771_A0 (slide 20) to interrogate CYP2D6*17 g.1023C>T.

gDNA Samples

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CYP2D6*29 g 3183G>A, rs59421388 C__34816113_20

Plasmid Samples

gDNA Samples

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CYP2D6*35 g.31G>A, rs769258 C__27102444_80

Plasmid Samples gDNA Sample Cycle 30

The CYP2D6*35 allele can be duplicated. Samples having 3 copies of CYP2D6 that are heterozygous for 31G>A may run within or beside the heterozygous cluster.

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CYP2D6*41 g.2988G>A (splicing defect) , rs28371725 C__34816116_20

Plasmid Samples

gDNA Samples

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CYP2C9*2 c.430C>T g.3608C>T , rs1799853 C__25625805_10

Plasmid Samples

gDNA Samples

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CYP2C9*3/*18 c.1075A>C, g.42614A>C, rs1057910 C__27104892_10

Plasmid Samples Cycle 32

The polymorphic CYP2C9*3/*18 c.1075A>C SNP is adjacent to the rare CYP2C9*4 c.1076T>C SNP that is detected by C__30634131_20 (slide 27). The *3/*18 and *4 SNP assays can be used to detect the 3 possible haplotypes described for this locus (alleles *3/*18 1076C and *4 1075C do not occur together in a haplotype). Analyze data as described in the PGx Experiments User Guide Chapter 5 section ‘TaqMan® DME genotyping assays to triallelic SNPs and adjacent SNP targets’.

gDNA Samples

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CYP2C9*4 c. 1076T>C, g.42615T>C, rs56165452 C__30634131_20

Note: the samples with higher signal are wild type for the adjacent *3/*18 c.1075A>C SNP, those in the lower split cluster are heterozygous for this SNP, and the sample that does not amplify is homozygous for the 1075C allele.

The rare CYP2C9*4 c.1076T>C SNP is adjacent to the polymorphic CYP2C9*3/*18 c.1075A>C SNP, which is detected by C__27104892_10 (slide 26). The *3/*18 and *4 SNP assays can be used to detect the 3 possible haplotypes described for this locus (alleles *3/*18 1076C and *4 1075C do not occur together in a haplotype). Analyze data as described in the PGx Experiments User Guide Chapter 5 section ‘TaqMan® DME genotyping assays to triallelic SNPs and adjacent SNP targets’.

gDNA Samples

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CYP2C9*5 c.1080C>G g.42619C>G , rs28371686 C__27859817_40

Plasmid Samples Cycle 27

gDNA Samples

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CYP2C9*6 c.818delA g.10601delA C__32287221_20

Plasmid Samples

gDNA Samples

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CYP2C9*8 c.449G>A g.3627G>A, rs7900194 C__25625804_10

Plasmid Samples

gDNA Samples

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CYP2C9*11 c.1003C>T g.42542C>T, rs28371685 C__30634132_70

Plasmid Samples

gDNA Samples

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CYP2C9*13 c.269T>C g.3276T>C, rs72558187 C__34816136_20

Plasmid Samples

gDNA Samples

33

CYP2C9*27 c.449G>T g.3627G>T, rs7900194 C_25625804D_20

Plasmid Samples

gDNA Samples

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CYP2C19*2 g.19154G>A. c.681G>A (splicing defect) , rs4244285 C__25986767_70

Plasmid Samples

The polymorphic CYP2C19*2 c.681G>A SNP is adjacent to the rare CYP2C19*10 c.680C>T SNP that is detected by C__30634128_10 (slide 35). The *2 and *10 SNP assays can be used to detect the 3 possible haplotypes described for this locus (alleles *2 681A and *10 680T do not occur together in a haplotype). Analyze data as described in the PGx Experiments User Guide Chapter 5 section ‘TaqMan® DME genotyping assays to triallelic SNPs and adjacent SNP targets’.

gDNA Samples

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CYP2C19*10 c.680C>T g.19153C>T , rs6413438 C__30634128_10

The rare CYP2C19*10 c.680C>T SNP is adjacent to the polymorphic CYP2C19*2 c.681G>A SNP that is detected by C__25986767_70 (slide 34). The *2 and *10 SNP assays can be used to detect the 3 possible haplotypes described for this locus (alleles *2 681A and *10 680T do not occur together in a haplotype). Analyze data as described in the PGx Experiments User Guide Chapter 5 section ‘TaqMan® DME genotyping assays to triallelic SNPs and adjacent SNP targets’.

gDNA Samples

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CYP2C19*3 g.17948G>A , rs4986893 C__27861809_10

Plasmid Samples

gDNA Samples

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CYP2C19*4 c.1A>G g.1A>G, rs28399504 C__30634136_10

Plasmid Samples

gDNA Samples

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CYP2C19*5 g.90033C>T , rs56337013 C__27861810_10

Plasmid Samples

gDNA Samples

39

CYP2C19*6 g.12748G>A, rs72552267 C__27531918_10

Plasmid Samples

gDNA Samples

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CYP2C19*7 g.19294T>A , rs72558186 C__30634127_10

Plasmid Samples

gDNA Samples

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CYP2C19*8 g.12711T>C , rs41291556 C__30634130_30

Plasmid Samples

gDNA Samples

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CYP2C19*9 c.431G>A g.12784G>A, rs28399507 C__25745302_30

Plasmid Samples

gDNA Samples

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CYP2C19*17 g.-806C>T, rs12248560 C____469857_10

Plasmid Samples

gDNA Samples

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CYP3A4*1B g.-392A>G, rs2740574 C___1837671_50

gDNA Samples

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CYP3A4*2 g.15713T>C , rs55785340 C__30634204_10

Plasmid Samples

gDNA Samples

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CYP3A4*3 c.1334T>C, rs4986910 C__27535825_20

Plasmid Samples

gDNA Samples

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CYP3A4*12 c.1117 C>T g.21896C>T, rs12721629 C__30634202_10

Plasmid Samples

gDNA Samples

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CYP3A4*16 c.554C>G g.15603C>G, rs12721627 C__30634207_10

Plasmid Samples

gDNA Samples

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CYP3A4*17 c.566 T>C g.15615T>C, rs4987161 C__27859822_10

Plasmid Samples

gDNA Samples

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CYP3A4*22 g.15389C>T, rs35599367 C__59013445_10

gDNA Samples

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CYP3A5*9 g.19386G>A, rs28383479 C__30633863_10

gDNA Samples

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CYP3A5*3B g.3705C>T, rs28383468 C__30633871_50

gDNA Samples

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CYP3A5*2 g.27289C>A, rs28365083 C__30633862_10

Plasmid Samples

gDNA Samples

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CYP3A5*3 g.6986A>G , rs776746 C__26201809_30

Plasmid Samples

gDNA Samples

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CYP3A5*3/*10 g.31611C>T, rs15524 C___8303531_40

Plasmid Samples

gDNA Samples

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CYP3A5*6 g.14690G>A, rs10264272 C__30203950_10

Plasmid Samples

gDNA Samples

57

CYP3A5*7 g.27131_27132insT, rs41303343 C__32287188_10

Plasmid Samples

gDNA Samples

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CYP3A5*8 g.3699C>T, rs55817950 C__30633872_10

Plasmid Samples

gDNA Samples

59

CYP1A2*1 g.-3860G>A, rs2069514 C__15859191_30

Plasmid Samples

gDNA Samples

60

CYP1A2*1 g.-2467delT, rs35694136 C__60142977_10

Plasmid Samples

gDNA Samples

61

CYP1A2*1K g.-729C>T, rs12720461 C__30634146_10

Plasmid Samples

gDNA Samples

62

CYP1A2*1 g.-739T>G, rs2069526 C__16017734_10

Plasmid Samples

gDNA Samples

63

CYP1A2*1F g.-163C>A, rs762551 C___8881221_40

Plasmid Samples Cycle 30

gDNA Samples

64

CYP1A2*4 g.2499A>T, rs72547516 C__30634246_10

gDNA Samples

65

CYP1A2*3 g.2116G>A, rs56276455 C__30634247_20

gDNA Samples

66

CYP1A2*6 g.5090C>T, rs28399424 C__30634244_20

gDNA Samples

67

CYP1A2*7 g.3533G>A, rs56107638 C__30634145_10

Plasmid Samples

gDNA Samples

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CYP1A2*8 g.5166G>A, rs72547517 C__72649745_10

gDNA Samples

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CYP1A2*11 g.558C>A, rs72547513 C__34816151_10

gDNA Samples

70

CYP1A2*15 g.125C>G, rs72547511 C__72649743_10

gDNA Samples

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CYP1A2*16 g.2473G>A, rs72547515 C__72649744_20

gDNA Samples

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CYP1A2 g.5347T>C, rs2470890 C___1642455_10

Plasmid Samples

gDNA Samples

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CYP2B6 c.516G>T g.15631G>T, rs3745274 C___7817765_60

Plasmid Samples

gDNA Samples

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CYP2B6*5 c.1459C>T, g.25505C>T, rs3211371 C__30634242_40

Plasmid Samples

gDNA Samples

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CYP2B6*10 c.64C>T g.64C>T, rs8192709 C___2818162_20

Plasmid Samples Cycle 30

gDNA Samples

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CYP2B6*16/*18 c.983T>C g.21011T>C, rs28399499 C__60732328_20

Plasmid Samples

gDNA Samples

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CYP2B6*22 g.-82T>C, rs34223104 C__27830964_10

Plasmid Samples

gDNA Samples

78

CYP2C8*2 c.805A>T g.11054A>T, rs11572103 C__30634034_10

Plasmid Samples

gDNA Samples

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CYP2C8*3 c.1196A>G g.30411A>G, rs10509681 C__25625782_20

Plasmid Samples

gDNA Samples

80

CYP2C8*4 c.792C>G g.11041C>G, rs1058930 C__25761568_20

Plasmid Samples

gDNA Samples

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COMT c.322G>A or c.472G>A, rs4680 C__25746809_50

Plasmid Samples

gDNA Samples

82

DRD2*A1 32806C>T Taq1A, rs1800497 C___7486676_10

gDNA Samples

83

SLCO1B1*5 g.37041T>C, rs4149056 C__30633906_10

Plasmid Samples

gDNA Samples

84

UGT1A1*6 c.211G>A g.211G>A, rs4148323 C____559715_20

Plasmid Samples

gDNA Samples

85

UGT1A1*60 g. -3279T>G, rs4124874 C___1432134_10

Plasmid Samples

gDNA Samples

86

VKORC1-prom, rs9923231 C__30403261_20

Plasmid Samples

gDNA Samples

87

VKORC1 358C>T P83L, rs7200749 C__29057362_10

Plasmid Samples Cycle 30

gDNA Samples

88

VKORC1 497T>G , rs2884737 C__16147492_20

Plasmid Samples

gDNA Samples

89

VKORC1 1173C>T, rs9934438 C__30204875_10

Plasmid Samples

gDNA Samples

90

VKORC1 3730G>A, rs7294 C___7473918_10

Plasmid Samples

gDNA Samples

91

Apo-ε2 c.526C>T, rs7412 C____904973_10

gDNA Samples

92

Apo-ε4 c.T388C, rs429358 C___3084793_20

gDNA Samples

93

HLA-B*1502 tag rs3745274, rs3909184 C___8692805_10

gDNA Samples

94

HTR2A -1438G>A, rs6311 C___8695278_10

gDNA Samples

95

HTR2C -759C>T, rs3813929 C__27488117_10

gDNA Samples

96

F2 G20210A, rs1799963 C___8726802_20

gDNA Samples

97

Factor V R506Q Leiden mutation, rs6025 C__11975250_10

gDNA Samples

98

F7 rs6042, rs6042 C___3046089_20

gDNA Samples

99

MTHFR C677T Ala222Val, rs1801133 C___1202883_20

gDNA Samples

100

MTHFR A1298C Glu429Ala, rs1801131 C____850486_20

gDNA Samples

101

OPRM1 A118G Asn40Asp, rs1799971 C___8950074_1_

gDNA Samples

102

VKORC1 -1639G>A, rs9923231 C__30403261_20

gDNA Samples

103

VKORC1 1173C>T, rs9934438 C__30204875_10

gDNA Samples

104

VKORC1 3730G>A, rs7294 C___7473918_10

gDNA Samples

105

VKORC1 1542G>C, rs8050894 C___2847860_10

gDNA Samples

106

VKORC1 2255C>T, rs2359612 C__26291751_10

gDNA Samples

107

VKORC1 6009C>T, rs17708472 C__32928084_10

gDNA Samples

108

Gender Assay AMEL_Y-FAM_X-VIC, hCV990000001 C_990000001_10

C_990000001_10, targets a gender-specific polymorphic region in the amelogenin gene. A 6 base deletion occurring in the X-specific AMEL gene is detected by the VIC® dye probe, whereas the FAM™ dye probe detects Y-specific sequences. Male samples run in the heterozygous cluster position and female samples run in the VIC® homozygous cluster.

Note: some males lack the Y-specific amelogenin gene and will type as female. The C_990000001_10 assay should be run in combination with a Y-chromosome assay to identify any mistyped samples (e.g. C___8938211_20; see slide 109).

gDNA Samples

109

Y-chr assay, rs3913290 C___8938211_20

This Y-chromosome-specific assay will amplify only male samples; female samples run with or close to the NTCs.

gDNA Samples

110

For Research Use Only. Not for use in diagnostic procedures. © 2014 Thermo Fisher Scientific. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.

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