TaqMan Drug Metabolism Genotyping Assays on OpenArray Plates
|
|
|
- Hollie Kelley
- 7 years ago
- Views:
Transcription
1 TaqMan Drug Metabolism Genotyping Assays on OpenArray Plates June 28, 2014 The world leader in serving science 1
2 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: 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 Thermo Fisher Scientific. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. 2
3 CYP2D6*2A g.-1584c>g, rs C _30 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. 3
4 CYP2D6 g.2850c>t, rs16947 C _ C>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. 4
5 CYP2D6*2 g.4180g>c, rs C _ G>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. 5
6 CYP2D6*3 g.2549dela, rs C _50 6
7 CYP2D6*4 g.1846g>a, rs C _D0 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. 7
8 CYP2D6*6 g.1707delt, rs C _20 8
9 CYP2D6*7 g.2935a>c, rs C _A0 recommended *7 assay version C _A0 is an improved version of C _30 (slide 10). It has higher amplification signal due to reduction of NTC signal. We recommend using C _A0 to interrogate CYP2D6*7 g.2935a>c. 9
10 CYP2D6*7 g.2935a>c, rs C _30 - improved assay version is available* The high NTC signal seen with C _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 _A0 (slide 9). It has higher amplification signal due to reduction of NTC signal. 10
11 CYP2D6*8 g.1758g>t, rs C_ C_K0 recommended *8 assay version C_ C_K0 reports the major (G) and one minor (T) allele (CYP2D6*8) of a triallelic SNP. C_ D_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_ C_K0 is an improved version of C_ C_20 (slide 12), which has higher amplification signal due to a decrease in amplicon size. 11
12 CYP2D6*8 g.1758g>t, rs C_ C_20 - improved assay version is available* C_ C_20 reports the major (G) and one minor (T) allele (CYP2D6*8) of a triallelic SNP. C_ D_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_ C_K0 (slide 11). It has higher amplification signal due to a decrease in amplicon size. 12
13 CYP2D6*9 g.2613_2615delaga, rs C _60 C _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 K
14 CYP2D6*10 g.100c>t, rs C _40 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. 14
15 CYP2D6*11 g.883g>c, rs C _A0 C _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 _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. 15
16 CYP2D6*12 g.124g>a, rs C _A0 16
17 CYP2D6*14 g.1758g>a, rs C_ D_M0 recommended *14 assay version C_ D_M0 reports the major (G) and one minor (A) allele (CYP2D6*14) of a triallelic SNP. C_ C_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_ D_M0 is an improved version of C_ D_30 (slide 18), which has higher amplification signal due to a decrease in amplicon size. 17
18 CYP2D6*14 g.1758g>a, rs C_ D_30 - improved assay version is available* C_ D_30 reports the major (G) and one minor (A) allele (CYP2D6*14) of a triallelic SNP. C_ C_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_ D_M0 (slide 17). It has higher amplification signal due to a decrease in amplicon size. 18
19 CYP2D6*15 g inst, rs C _40 19
20 CYP2D6*17 g.1023c>t, rs C _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 _A0 is an improved version of C _40 (slide 21). It has been observed that C _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 _A0 whereas they run as *17/*17 homozygotes with C _40. 20
21 CYP2D6*17 g.1023c>t, rs C _40 - improved assay version is available* 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 _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 _40 whereas they run as *17 heterozygotes with C _A0. *We recommend using the improved assay: C _A0 (slide 20) to interrogate CYP2D6*17 g.1023c>t. 21
22 CYP2D6*29 g 3183G>A, rs C _20 22
23 CYP2D6*35 g.31g>a, rs C _80 Cycle 30 gdna Sample 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. 23
24 CYP2D6*41 g.2988g>a (splicing defect), rs C _20 24
25 CYP2C9*2 c.430c>t g.3608c>t, rs C _10 25
26 CYP2C9*3/*18 c.1075a>c, g.42614a>c, rs C _10 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 _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/* C 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. 26
27 CYP2C9*4 c. 1076T>C, g.42615t>c, rs C _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 _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/* C 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. 27
28 CYP2C9*5 c.1080c>g g.42619c>g, rs C _40 Cycle 27 28
29 CYP2C9*6 c.818dela g.10601dela C _20 29
30 CYP2C9*8 c.449g>a g.3627g>a, rs C _10 30
31 CYP2C9*11 c.1003c>t g.42542c>t, rs C _70 31
32 CYP2C9*13 c.269t>c g.3276t>c, rs C _20 32
33 CYP2C9*27 c.449g>t g.3627g>t, rs C_ D_20 33
34 CYP2C19*2 g.19154g>a. c.681g>a (splicing defect), rs C _70 The polymorphic CYP2C19*2 c.681g>a SNP is adjacent to the rare CYP2C19*10 c.680c>t SNP that is detected by C _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. 34
35 CYP2C19*10 c.680c>t g.19153c>t, rs C _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 _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. 35
36 CYP2C19*3 g.17948g>a, rs C _10 36
37 CYP2C19*4 c.1a>g g.1a>g, rs C _10 37
38 CYP2C19*5 g.90033c>t, rs C _10 38
39 CYP2C19*6 g.12748g>a, rs C _10 39
40 CYP2C19*7 g.19294t>a, rs C _10 40
41 CYP2C19*8 g.12711t>c, rs C _30 41
42 CYP2C19*9 c.431g>a g.12784g>a, rs C _30 42
43 CYP2C19*17 g.-806c>t, rs C _10 43
44 CYP3A4*1B g.-392a>g, rs C _50 44
45 CYP3A4*2 g.15713t>c, rs C _10 45
46 CYP3A4*3 c.1334t>c, rs C _20 46
47 CYP3A4*12 c.1117 C>T g.21896c>t, rs C _10 47
48 CYP3A4*16 c.554c>g g.15603c>g, rs C _10 48
49 CYP3A4*17 c.566 T>C g.15615t>c, rs C _10 49
50 CYP3A4*22 g.15389c>t, rs C _10 50
51 CYP3A5*9 g.19386g>a, rs C _10 51
52 CYP3A5*3B g.3705c>t, rs C _50 52
53 CYP3A5*2 g.27289c>a, rs C _10 53
54 CYP3A5*3 g.6986a>g, rs C _30 54
55 CYP3A5*3/*10 g.31611c>t, rs15524 C _40 55
56 CYP3A5*6 g.14690g>a, rs C _10 56
57 CYP3A5*7 g.27131_27132inst, rs C _10 57
58 CYP3A5*8 g.3699c>t, rs C _10 58
59 CYP1A2*1 g.-3860g>a, rs C _30 59
60 CYP1A2*1 g.-2467delt, rs C _10 60
61 CYP1A2*1K g.-729c>t, rs C _10 61
62 CYP1A2*1 g.-739t>g, rs C _10 62
63 CYP1A2*1F g.-163c>a, rs C _40 Cycle 30 63
64 CYP1A2*4 g.2499a>t, rs C _10 64
65 CYP1A2*3 g.2116g>a, rs C _20 65
66 CYP1A2*6 g.5090c>t, rs C _20 66
67 CYP1A2*7 g.3533g>a, rs C _10 67
68 CYP1A2*8 g.5166g>a, rs C _10 68
69 CYP1A2*11 g.558c>a, rs C _10 69
70 CYP1A2*15 g.125c>g, rs C _10 70
71 CYP1A2*16 g.2473g>a, rs C _20 71
72 CYP1A2 g.5347t>c, rs C _10 72
73 CYP2B6 c.516g>t g.15631g>t, rs C _60 73
74 CYP2B6*5 c.1459c>t, g.25505c>t, rs C _40 74
75 CYP2B6*10 c.64c>t g.64c>t, rs C _20 Cycle 30 75
76 CYP2B6*16/*18 c.983t>c g.21011t>c, rs C _20 76
77 CYP2B6*22 g.-82t>c, rs C _10 77
78 CYP2C8*2 c.805a>t g.11054a>t, rs C _10 78
79 CYP2C8*3 c.1196a>g g.30411a>g, rs C _20 79
80 CYP2C8*4 c.792c>g g.11041c>g, rs C _20 80
81 COMT c.322g>a or c.472g>a, rs4680 C _50 81
82 DRD2*A C>T Taq1A, rs C _10 82
83 SLCO1B1*5 g.37041t>c, rs C _10 83
84 UGT1A1*6 c.211g>a g.211g>a, rs C _20 84
85 UGT1A1*60 g T>G, rs C _10 85
86 VKORC1-prom, rs C _20 86
87 VKORC1 358C>T P83L, rs C _10 Cycle 30 87
88 VKORC1 497T>G, rs C _20 88
89 VKORC1 1173C>T, rs C _10 89
90 VKORC1 3730G>A, rs7294 C _10 90
91 Apo-ε2 c.526c>t, rs7412 C _10 91
92 Apo-ε4 c.t388c, rs C _20 92
93 HLA-B*1502 tag rs , rs C _10 93
94 HTR2A -1438G>A, rs6311 C _10 94
95 HTR2C -759C>T, rs C _10 95
96 F2 G20210A, rs C _20 96
97 Factor V R506Q Leiden mutation, rs6025 C _10 97
98 F7 rs6042, rs6042 C _20 98
99 MTHFR C677T Ala222Val, rs C _20 99
100 MTHFR A1298C Glu429Ala, rs C _20 100
101 OPRM1 A118G Asn40Asp, rs C _1_ 101
102 VKORC1-1639G>A, rs C _20 102
103 VKORC1 1173C>T, rs C _10 103
104 VKORC1 3730G>A, rs7294 C _10 104
105 VKORC1 1542G>C, rs C _10 105
106 VKORC1 2255C>T, rs C _10 106
107 VKORC1 6009C>T, rs C _10 107
108 Gender Assay AMEL_Y-FAM_X-VIC, hcv C_ _10 C_ _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_ _10 assay should be run in combination with a Y-chromosome assay to identify any mistyped samples (e.g. C _20; see slide 109). 108
109 Y-chr assay, rs C _20 This Y-chromosome-specific assay will amplify only male samples; female samples run with or close to the NTCs. 109
110 Legal notification For Research Use Only. Not for use in diagnostic procedures Thermo Fisher Scientific. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. 110
A complete workflow for pharmacogenomics using the QuantStudio 12K Flex Real-Time
Application NOte QuantStudio 12K Flex Real-Time PCR System A complete workflow for pharmacogenomics using the QuantStudio 12K Flex Real-Time PCR System Introduction Pharmacogenomics (PGx) is the study
GENEWIZ, Inc. DNA Sequencing Service Details for USC Norris Comprehensive Cancer Center DNA Core
DNA Sequencing Services Pre-Mixed o Provide template and primer, mixed into the same tube* Pre-Defined o Provide template and primer in separate tubes* Custom o Full-service for samples with unknown concentration
Molecular analyses of EGFR: mutation and amplification detection
Molecular analyses of EGFR: mutation and amplification detection Petra Nederlof, Moleculaire Pathologie NKI Amsterdam Henrique Ruijter, Ivon Tielen, Lucie Boerrigter, Aafke Ariaens Outline presentation
10 µg lyophilized plasmid DNA (store lyophilized plasmid at 20 C)
TECHNICAL DATA SHEET BIOLUMINESCENCE RESONANCE ENERGY TRANSFER RENILLA LUCIFERASE FUSION PROTEIN EXPRESSION VECTOR Product: prluc-c Vectors Catalog number: Description: Amount: The prluc-c vectors contain
ALLERGY/MOLD Gene & Variation rsid # Risk Allele Your Alleles and Results HLA rs7775228 C TT -/- HLA rs2155219 T GG -/-
DETOX CYP1A1*2C A4889G rs1048943 C TT -/- CYP1A1*4 C2453A rs1799814 T GG -/- CYP1A2 C164A rs762551 C AA -/- CYP1B1 L432V rs1056836 C CC +/+ CYP1B1 N453S rs1800440 C TT -/- CYP1B1 R48G rs10012 C no call
(http://genomes.urv.es/caical) TUTORIAL. (July 2006)
(http://genomes.urv.es/caical) TUTORIAL (July 2006) CAIcal manual 2 Table of contents Introduction... 3 Required inputs... 5 SECTION A Calculation of parameters... 8 SECTION B CAI calculation for FASTA
(A) Microarray analysis was performed on ATM and MDM isolated from 4 obese donors.
Legends of supplemental figures and tables Figure 1: Overview of study design and results. (A) Microarray analysis was performed on ATM and MDM isolated from 4 obese donors. After raw data gene expression
Table S1. Related to Figure 4
Table S1. Related to Figure 4 Final Diagnosis Age PMD Control Control 61 15 Control 67 6 Control 68 10 Control 49 15 AR-PD PD 62 15 PD 65 4 PD 52 18 PD 68 10 AR-PD cingulate cortex used for immunoblot
SERVICES CATALOGUE WITH SUBMISSION GUIDELINES
SERVICES CATALOGUE WITH SUBMISSION GUIDELINES 3921 Montgomery Road Cincinnati, Ohio 45212 513-841-2428 www.agctsequencing.com CONTENTS Welcome Dye Terminator Sequencing DNA Sequencing Services - Full Service
Mutations and Genetic Variability. 1. What is occurring in the diagram below?
Mutations and Genetic Variability 1. What is occurring in the diagram below? A. Sister chromatids are separating. B. Alleles are independently assorting. C. Genes are replicating. D. Segments of DNA are
A guide to the analysis of KASP genotyping data using cluster plots
extraction sequencing genotyping extraction sequencing genotyping extraction sequencing genotyping extraction sequencing A guide to the analysis of KASP genotyping data using cluster plots Contents of
Single Nucleotide Polymorphisms (SNPs)
Single Nucleotide Polymorphisms (SNPs) Additional Markers 13 core STR loci Obtain further information from additional markers: Y STRs Separating male samples Mitochondrial DNA Working with extremely degraded
Hands on Simulation of Mutation
Hands on Simulation of Mutation Charlotte K. Omoto P.O. Box 644236 Washington State University Pullman, WA 99164-4236 omoto@wsu.edu ABSTRACT This exercise is a hands-on simulation of mutations and their
Commonly Used STR Markers
Commonly Used STR Markers Repeats Satellites 100 to 1000 bases repeated Minisatellites VNTR variable number tandem repeat 10 to 100 bases repeated Microsatellites STR short tandem repeat 2 to 6 bases repeated
DNA Sample preparation and Submission Guidelines
DNA Sample preparation and Submission Guidelines Requirements: Please submit samples in 1.5ml microcentrifuge tubes. Fill all the required information in the Eurofins DNA sequencing order form and send
TaqMan Genotyper Software v1.0.1 TaqMan Genotyping Data Analysis Software
TaqMan Genotyper Software v1.0.1 TaqMan Genotyping Data Analysis Software March 2011 Product Overview TaqMan Genotyper Software TaqMan Genotyper Software Standalone data analysis software for Applied Biosystems
Domain Antivirals tested Test methods for phenotype References. Aciclovir (ACV), Foscarnet (FOS) ACV, FOS ACV,
Sauerbrei A, Bohn-Wippert K, Kaspar M, Krumbholz A, Karrasch M, Zell R. 2015. Database on natural polymorphisms and resistance-related non-synonymous mutations in thymidine kinase and DNA polymerase genes
Forensic DNA Testing Terminology
Forensic DNA Testing Terminology ABI 310 Genetic Analyzer a capillary electrophoresis instrument used by forensic DNA laboratories to separate short tandem repeat (STR) loci on the basis of their size.
Custom TaqMan Assays For New SNP Genotyping and Gene Expression Assays. Design and Ordering Guide
Custom TaqMan Assays For New SNP Genotyping and Gene Expression Assays Design and Ordering Guide For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. Information in
Introduction To Real Time Quantitative PCR (qpcr)
Introduction To Real Time Quantitative PCR (qpcr) SABiosciences, A QIAGEN Company www.sabiosciences.com The Seminar Topics The advantages of qpcr versus conventional PCR Work flow & applications Factors
OpenArray Sample Tracker Software
QUICK REFERENCE OpenArray Sample Tracker Software For QuantStudio 12K Flex OpenArray Sample Block and the OpenArray Real-Time PCR System Publication Part Number 4460657 Rev. C Revision Date May 2012 Contents
Next Generation Sequencing
Next Generation Sequencing 38. Informationsgespräch der Blutspendezentralefür Wien, Niederösterreich und Burgenland Österreichisches Rotes Kreuz 22. November 2014, Parkhotel Schönbrunn Die Zukunft hat
The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics
The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics The GS Junior System The Power of Next-Generation Sequencing on Your Benchtop Proven technology: Uses the same long
Supplementary Online Material for Morris et al. sirna-induced transcriptional gene
Supplementary Online Material for Morris et al. sirna-induced transcriptional gene silencing in human cells. Materials and Methods Lentiviral vector and sirnas. FIV vector pve-gfpwp was prepared as described
rs1057909 CYP2C9 42612A>G G AA -/- rs4917639 CYP2C9 A6326C C AA -/-
Liver Detox - Phase I (Figure 1) rs1048943 CYP1A1*2C A4889G C CT +/- rs1799814 CYP1A1*4 C2453A T GG -/- rs2472304 CYP1A2*1F A AG +/- rs762551 CYP1A2*1F C164A C AA -/- rs2069526 CYP1A2*1K -739T>G G TT -/-
SNPbrowser Software v3.5
Product Bulletin SNP Genotyping SNPbrowser Software v3.5 A Free Software Tool for the Knowledge-Driven Selection of SNP Genotyping Assays Easily visualize SNPs integrated with a physical map, linkage disequilibrium
Gene Synthesis 191. Mutagenesis 194. Gene Cloning 196. AccuGeneBlock Service 198. Gene Synthesis FAQs 201. User Protocol 204
Gene Synthesis 191 Mutagenesis 194 Gene Cloning 196 AccuGeneBlock Service 198 Gene Synthesis FAQs 201 User Protocol 204 Gene Synthesis Overview Gene synthesis is the most cost-effective way to enhance
plaque reduction assay, modified dye uptake assay including formazan test, dye uptake assay
Sauerbrei A, Bohn-Wippert K, Kaspar M, Krumbholz A, Karrasch M, Zell R. 2015. Database on natural polymorphisms and resistance-related non-synonymous mutations in thymidine kinase and DNA polymerase genes
SeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications
Product Bulletin Sequencing Software SeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications Comprehensive reference sequence handling Helps interpret the role of each
pcas-guide System Validation in Genome Editing
pcas-guide System Validation in Genome Editing Tagging HSP60 with HA tag genome editing The latest tool in genome editing CRISPR/Cas9 allows for specific genome disruption and replacement in a flexible
Gene Mapping Techniques
Gene Mapping Techniques OBJECTIVES By the end of this session the student should be able to: Define genetic linkage and recombinant frequency State how genetic distance may be estimated State how restriction
ONLINE SUPPLEMENTAL MATERIAL. Allele-Specific Expression of Angiotensinogen in Human Subcutaneous Adipose Tissue
ONLINE SUPPLEMENTAL MATERIAL Allele-Specific Expression of Angiotensinogen in Human Subcutaneous Adipose Tissue Sungmi Park 1, Ko-Ting Lu 1, Xuebo Liu 1, Tapan K. Chatterjee 2, Steven M. Rudich 3, Neal
2. True or False? The sequence of nucleotides in the human genome is 90.9% identical from one person to the next. False (it s 99.
1. True or False? A typical chromosome can contain several hundred to several thousand genes, arranged in linear order along the DNA molecule present in the chromosome. True 2. True or False? The sequence
Association of IGF1 and IGFBP3 polymorphisms with colorectal polyps and colorectal cancer risk
DOI 10.1007/s10552-009-9438-4 ORIGINAL PAPER Association of IGF1 and IGFBP3 polymorphisms with colorectal polyps and colorectal cancer risk Elisabeth Feik Æ Andreas Baierl Æ Barbara Hieger Æ Gerhard Führlinger
UNIVERSITETET I OSLO Det matematisk-naturvitenskapelige fakultet
1 UNIVERSITETET I OSLO Det matematisk-naturvitenskapelige fakultet Exam in: MBV4010 Arbeidsmetoder i molekylærbiologi og biokjemi I MBV4010 Methods in molecular biology and biochemistry I Day of exam:.
INTERNATIONAL CONFERENCE ON HARMONISATION OF TECHNICAL REQUIREMENTS FOR REGISTRATION OF PHARMACEUTICALS FOR HUMAN USE E15
INTERNATIONAL CONFERENCE ON HARMONISATION OF TECHNICAL REQUIREMENTS FOR REGISTRATION OF PHARMACEUTICALS FOR HUMAN USE ICH HARMONISED TRIPARTITE GUIDELINE DEFINITIONS FOR GENOMIC BIOMARKERS, PHARMACOGENOMICS,
TaqMan Mutation Detection Assay
PROTOCOL TaqMan Mutation Detection Assay Competitive Allele-Specific TaqMan PCR Publication Part Number 4467011 Rev. B Revision Date April 2012 For Research Use Only. Not intended for any animal or human
Essentials of Real Time PCR. About Sequence Detection Chemistries
Essentials of Real Time PCR About Real-Time PCR Assays Real-time Polymerase Chain Reaction (PCR) is the ability to monitor the progress of the PCR as it occurs (i.e., in real time). Data is therefore collected
Answer Key Problem Set 5
7.03 Fall 2003 1 of 6 1. a) Genetic properties of gln2- and gln 3-: Answer Key Problem Set 5 Both are uninducible, as they give decreased glutamine synthetase (GS) activity. Both are recessive, as mating
SICKLE CELL ANEMIA & THE HEMOGLOBIN GENE TEACHER S GUIDE
AP Biology Date SICKLE CELL ANEMIA & THE HEMOGLOBIN GENE TEACHER S GUIDE LEARNING OBJECTIVES Students will gain an appreciation of the physical effects of sickle cell anemia, its prevalence in the population,
TITRATION OF raav (VG) USING QUANTITATIVE REAL TIME PCR
Page 1 of 5 Materials DNase digestion buffer [13 mm Tris-Cl, ph7,5 / 5 mm MgCl2 / 0,12 mm CaCl2] RSS plasmid ptr-uf11 SV40pA Forward primer (10µM) AGC AAT AGC ATC ACA AAT TTC ACA A SV40pA Reverse Primer
Genetics Lecture Notes 7.03 2005. Lectures 1 2
Genetics Lecture Notes 7.03 2005 Lectures 1 2 Lecture 1 We will begin this course with the question: What is a gene? This question will take us four lectures to answer because there are actually several
Real-time PCR: Understanding C t
APPLICATION NOTE Real-Time PCR Real-time PCR: Understanding C t Real-time PCR, also called quantitative PCR or qpcr, can provide a simple and elegant method for determining the amount of a target sequence
Real-Time PCR Vs. Traditional PCR
Real-Time PCR Vs. Traditional PCR Description This tutorial will discuss the evolution of traditional PCR methods towards the use of Real-Time chemistry and instrumentation for accurate quantitation. Objectives
Advances in RainDance Sequence Enrichment Technology and Applications in Cancer Research. March 17, 2011 Rendez-Vous Séquençage
Advances in RainDance Sequence Enrichment Technology and Applications in Cancer Research March 17, 2011 Rendez-Vous Séquençage Presentation Overview Core Technology Review Sequence Enrichment Application
Technical Note. Roche Applied Science. No. LC 18/2004. Assay Formats for Use in Real-Time PCR
Roche Applied Science Technical Note No. LC 18/2004 Purpose of this Note Assay Formats for Use in Real-Time PCR The LightCycler Instrument uses several detection channels to monitor the amplification of
Lecture 6: Single nucleotide polymorphisms (SNPs) and Restriction Fragment Length Polymorphisms (RFLPs)
Lecture 6: Single nucleotide polymorphisms (SNPs) and Restriction Fragment Length Polymorphisms (RFLPs) Single nucleotide polymorphisms or SNPs (pronounced "snips") are DNA sequence variations that occur
Y Chromosome Markers
Y Chromosome Markers Lineage Markers Autosomal chromosomes recombine with each meiosis Y and Mitochondrial DNA does not This means that the Y and mtdna remains constant from generation to generation Except
Tools for human molecular diagnosis. Joris Vermeesch
Tools for human molecular diagnosis Joris Vermeesch Chromosome > DNA Genetic Code Effect of point mutations/polymorphisms Effect of deletions/insertions Effect of splicing mutations IVS2-2A>G Normal splice
SeattleSNPs Interactive Tutorial: Web Tools for Site Selection, Linkage Disequilibrium and Haplotype Analysis
SeattleSNPs Interactive Tutorial: Web Tools for Site Selection, Linkage Disequilibrium and Haplotype Analysis Goal: This tutorial introduces several websites and tools useful for determining linkage disequilibrium
Quantifiler Human DNA Quantification Kit Quantifiler Y Human Male DNA Quantification Kit
Product Bulletin Human Identification Quantifiler Human DNA Quantification Kit Quantifiler Y Human Male DNA Quantification Kit The Quantifiler kits produce reliable and reproducible results, helping to
Real-time qpcr Assay Design Software www.qpcrdesign.com
Real-time qpcr Assay Design Software www.qpcrdesign.com Your Blueprint For Success Informational Guide 2199 South McDowell Blvd Petaluma, CA 94954-6904 USA 1.800.GENOME.1(436.6631) 1.415.883.8400 1.415.883.8488
QuantStudio 12K Flex Real-Time PCR System. The all-in-one qpcr instrument
QuantStudio 12K Flex Real-Time PCR System The all-in-one qpcr instrument Expand the boundaries of your research Life Technologies is taking qpcr to the next level. Designed for maximum throughput, flexibility,
Event-specific Method for the Quantification of Maize MIR162 Using Real-time PCR. Protocol
Event-specific Method for the Quantification of Maize MIR162 Using Real-time PCR Protocol 31 January 2011 Joint Research Centre Institute for Health and Consumer Protection Molecular Biology and Genomics
Factors Influencing Multiplex Real-Time PCR
APPLICATION NOTE Multiplex Real-Time PCR Factors Influencing Multiplex Real-Time PCR Introduction Multiplex PCR is the simultaneous amplification of more than one target sequence in a single reaction [1].
Getting Started Guide
Primer Express Software Version 3.0 Getting Started Guide Before You Begin Designing Primers and Probes for Quantification Assays Designing Primers and Probes for Allelic Discrimination Assays Ordering
DNA-Analytik III. Genetische Variabilität
DNA-Analytik III Genetische Variabilität Genetische Variabilität Lexikon Scherer et al. Nat Genet Suppl 39:s7 (2007) Genetische Variabilität Sequenzvariation Mutationen (Mikro~) Basensubstitution Insertion
UKB_WCSGAX: UK Biobank 500K Samples Genotyping Data Generation by the Affymetrix Research Services Laboratory. April, 2015
UKB_WCSGAX: UK Biobank 500K Samples Genotyping Data Generation by the Affymetrix Research Services Laboratory April, 2015 1 Contents Overview... 3 Rare Variants... 3 Observation... 3 Approach... 3 ApoE
Information leaflet. Centrum voor Medische Genetica. Version 1/20150504 Design by Ben Caljon, UZ Brussel. Universitair Ziekenhuis Brussel
Information on genome-wide genetic testing Array Comparative Genomic Hybridization (array CGH) Single Nucleotide Polymorphism array (SNP array) Massive Parallel Sequencing (MPS) Version 120150504 Design
BioBoot Camp Genetics
BioBoot Camp Genetics BIO.B.1.2.1 Describe how the process of DNA replication results in the transmission and/or conservation of genetic information DNA Replication is the process of DNA being copied before
Lecture 3: Mutations
Lecture 3: Mutations Recall that the flow of information within a cell involves the transcription of DNA to mrna and the translation of mrna to protein. Recall also, that the flow of information between
ISTEP+: Biology I End-of-Course Assessment Released Items and Scoring Notes
ISTEP+: Biology I End-of-Course Assessment Released Items and Scoring Notes Page 1 of 22 Introduction Indiana students enrolled in Biology I participated in the ISTEP+: Biology I Graduation Examination
Single-Cell DNA Sequencing with the C 1. Single-Cell Auto Prep System. Reveal hidden populations and genetic diversity within complex samples
DATA Sheet Single-Cell DNA Sequencing with the C 1 Single-Cell Auto Prep System Reveal hidden populations and genetic diversity within complex samples Single-cell sensitivity Discover and detect SNPs,
Gene Expression Assay Performance Guaranteed With the TaqMan Assays QPCR Guarantee Program
WHITE PAPER TaqMan Assays QPCR Guarantee Program Gene Expression Assay Performance Guaranteed With the TaqMan Assays QPCR Guarantee Program Real-Time PCR for the Quantification of Gene Expression Real-time
Gene Finding CMSC 423
Gene Finding CMSC 423 Finding Signals in DNA We just have a long string of A, C, G, Ts. How can we find the signals encoded in it? Suppose you encountered a language you didn t know. How would you decipher
The Search for Anticoagulant Resistance in Rats in New Zealand
The Search for Anticoagulant Resistance in Rats in New Zealand Phil Cowan, Dianne Gleeson, Robyn Howitt, Ana Ramon-Laca, Alexandra Esther, Hans-Joachim Pelz Resistance to anticoagulant toxins is a global
INTERNATIONAL CONFERENCE ON HARMONISATION OF TECHNICAL REQUIREMENTS FOR REGISTRATION OF PHARMACEUTICALS FOR HUMAN USE Q5B
INTERNATIONAL CONFERENCE ON HARMONISATION OF TECHNICAL REQUIREMENTS FOR REGISTRATION OF PHARMACEUTICALS FOR HUMAN USE ICH HARMONISED TRIPARTITE GUIDELINE QUALITY OF BIOTECHNOLOGICAL PRODUCTS: ANALYSIS
NS5B Sequencing and Phenotypic Resistance Assays for HCV Subtypes 1a and 1b
NS5B Sequencing and Phenotypic Resistance Assays for HCV Subtypes 1a and 1b 5th Intl. Workshop on Hepatitis C Resistance & New Compounds Jacqueline Reeves NS5B Resistance Assays for HCV Subtypes 1a and
Simplifying Data Interpretation with Nexus Copy Number
Simplifying Data Interpretation with Nexus Copy Number A WHITE PAPER FROM BIODISCOVERY, INC. Rapid technological advancements, such as high-density acgh and SNP arrays as well as next-generation sequencing
TaqMan OpenArray Genotyping. Getting Started Guide
TaqMan OpenArray Genotyping Getting Started Guide For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. Information in this document is subject to change without notice.
Integration of genomic data into electronic health records
Integration of genomic data into electronic health records Daniel Masys, MD Affiliate Professor Biomedical & Health Informatics University of Washington, Seattle Major portion of today s lecture is based
Association between Dopamine Gene and Alcoholism in Pategar Community of Dharwad, Karnataka
International Journal of Scientific and Research Publications, Volume 3, Issue 10, October 2013 1 Association between Dopamine Gene and Alcoholism in Pategar Community of Dharwad, Karnataka SOMASHEKHAR
The p53 MUTATION HANDBOOK
The p MUTATION HANDBOOK Version 1. /7 Thierry Soussi Christophe Béroud, Dalil Hamroun Jean Michel Rubio Nevado http://p/free.fr The p Mutation HandBook By T Soussi, J.M. Rubio-Nevado, D. Hamroun and C.
Data Analysis for Ion Torrent Sequencing
IFU022 v140202 Research Use Only Instructions For Use Part III Data Analysis for Ion Torrent Sequencing MANUFACTURER: Multiplicom N.V. Galileilaan 18 2845 Niel Belgium Revision date: August 21, 2014 Page
Focusing on results not data comprehensive data analysis for targeted next generation sequencing
Focusing on results not data comprehensive data analysis for targeted next generation sequencing Daniel Swan, Jolyon Holdstock, Angela Matchan, Richard Stark, John Shovelton, Duarte Mohla and Simon Hughes
Thermo Scientific Phusion Site-Directed Mutagenesis Kit #F-541
PRODUCT INFORMATION Thermo Scientific Phusion Site-Directed Mutagenesis Kit #F-541 Lot _ Store at -20 C Expiry Date _ www.thermoscientific.com/onebio CERTIFICATE OF ANALYSIS The Phusion Site-Directed Mutagenesis
Human Leukocyte Antigens - HLA
Human Leukocyte Antigens - HLA Human Leukocyte Antigens (HLA) are cell surface proteins involved in immune function. HLA molecules present antigenic peptides to generate immune defense reactions. HLA-class
The following chapter is called "Preimplantation Genetic Diagnosis (PGD)".
Slide 1 Welcome to chapter 9. The following chapter is called "Preimplantation Genetic Diagnosis (PGD)". The author is Dr. Maria Lalioti. Slide 2 The learning objectives of this chapter are: To learn the
Text file One header line meta information lines One line : variant/position
Software Calling: GATK SAMTOOLS mpileup Varscan SOAP VCF format Text file One header line meta information lines One line : variant/position ##fileformat=vcfv4.1! ##filedate=20090805! ##source=myimputationprogramv3.1!
Chapter 9. Applications of probability. 9.1 The genetic code
Chapter 9 Applications of probability In this chapter we use the tools of elementary probability to investigate problems of several kinds. First, we study the language of life by focusing on the universal
Genetic Testing for Mental Health Conditions
MEDICAL POLICY POLICY RELATED POLICIES POLICY GUIDELINES DESCRIPTION SCOPE BENEFIT APPLICATION RATIONALE REFERENCES CODING APPENDI HISTORY Genetic Testing for Mental Health Conditions Number 12.04.515
quantitative real-time PCR, grain, simplex DNA extraction: PGS0426 RT-PCR: PGS0494 & PGS0476
BioScience quantitative real-time PCR, grain, simplex DNA extraction: PGS0426 RT-PCR: PGS0494 & PGS0476 This method describes a Real-time semi-quantitative TaqMan PCR procedure for the determination of
Highly specific and sensitive quantitation
PRODUCT ULLETIN SYR Select Master Mix SYR Select Master Mix Highly specific and sensitive quantitation SYR Select Master Mix offers advanced performance at an affordable price. SYR Select Master Mix is
European Medicines Agency
European Medicines Agency July 1996 CPMP/ICH/139/95 ICH Topic Q 5 B Quality of Biotechnological Products: Analysis of the Expression Construct in Cell Lines Used for Production of r-dna Derived Protein
AS4.1 190509 Replaces 260806 Page 1 of 50 ATF. Software for. DNA Sequencing. Operators Manual. Assign-ATF is intended for Research Use Only (RUO):
Replaces 260806 Page 1 of 50 ATF Software for DNA Sequencing Operators Manual Replaces 260806 Page 2 of 50 1 About ATF...5 1.1 Compatibility...5 1.1.1 Computer Operator Systems...5 1.1.2 DNA Sequencing
Genomes and SNPs in Malaria and Sickle Cell Anemia
Genomes and SNPs in Malaria and Sickle Cell Anemia Introduction to Genome Browsing with Ensembl Ensembl The vast amount of information in biological databases today demands a way of organising and accessing
KASP genotyping chemistry User guide and manual
KASP genotyping chemistry User guide and manual KASP manual content 1. Introduction 3 2. Principal of the KASP genotyping assay 3 2.1 Mechanism of KASP chemistry 4 3. The KASP reaction component 5 3.1
Mutation. Mutation provides raw material to evolution. Different kinds of mutations have different effects
Mutation Mutation provides raw material to evolution Different kinds of mutations have different effects Mutational Processes Point mutation single nucleotide changes coding changes (missense mutations)
NimbleGen SeqCap EZ Library SR User s Guide Version 3.0
NimbleGen SeqCap EZ Library SR User s Guide Version 3.0 For life science research only. Not for use in diagnostic procedures. Copyright 2011 Roche NimbleGen, Inc. All Rights Reserved. Editions Version
2.500 Threshold. 2.000 1000e - 001. Threshold. Exponential phase. Cycle Number
application note Real-Time PCR: Understanding C T Real-Time PCR: Understanding C T 4.500 3.500 1000e + 001 4.000 3.000 1000e + 000 3.500 2.500 Threshold 3.000 2.000 1000e - 001 Rn 2500 Rn 1500 Rn 2000
2. The number of different kinds of nucleotides present in any DNA molecule is A) four B) six C) two D) three
Chem 121 Chapter 22. Nucleic Acids 1. Any given nucleotide in a nucleic acid contains A) two bases and a sugar. B) one sugar, two bases and one phosphate. C) two sugars and one phosphate. D) one sugar,
How many of you have checked out the web site on protein-dna interactions?
How many of you have checked out the web site on protein-dna interactions? Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail. Find and be ready to discuss
Overview of Genetic Testing and Screening
Integrating Genetics into Your Practice Webinar Series Overview of Genetic Testing and Screening Genetic testing is an important tool in the screening and diagnosis of many conditions. New technology is
Overview One of the promises of studies of human genetic variation is to learn about human history and also to learn about natural selection.
Technical design document for a SNP array that is optimized for population genetics Yontao Lu, Nick Patterson, Yiping Zhan, Swapan Mallick and David Reich Overview One of the promises of studies of human
Original article: DXS10079, DXS10074 and DXS10075: new alleles and SNP occurrence
EXCLI Journal 2007;6:177-182 ISSN 1611-2156 Received: December 14, 2006, accepted: June 21, 2007, published: June 26, 2007 Original article: DXS10079, DXS10074 and DXS10075: new alleles and SNP occurrence
Inverse PCR & Cycle Sequencing of P Element Insertions for STS Generation
BDGP Resources Inverse PCR & Cycle Sequencing of P Element Insertions for STS Generation For recovery of sequences flanking PZ, PlacW and PEP elements E. Jay Rehm Berkeley Drosophila Genome Project I.
Title : Parallel DNA Synthesis : Two PCR product from one DNA template
Title : Parallel DNA Synthesis : Two PCR product from one DNA template Bhardwaj Vikash 1 and Sharma Kulbhushan 2 1 Email: vikashbhardwaj@ gmail.com 1 Current address: Government College Sector 14 Gurgaon,
Next Generation Sequencing: Technology, Mapping, and Analysis
Next Generation Sequencing: Technology, Mapping, and Analysis Gary Benson Computer Science, Biology, Bioinformatics Boston University gbenson@bu.edu http://tandem.bu.edu/ The Human Genome Project took
Design of conditional gene targeting vectors - a recombineering approach
Recombineering protocol #4 Design of conditional gene targeting vectors - a recombineering approach Søren Warming, Ph.D. The purpose of this protocol is to help you in the gene targeting vector design
Methods 50 (2010) S10 S14. Contents lists available at ScienceDirect. Methods. journal homepage: www.elsevier.com/locate/ymeth
Methods 50 (2010) S10 S14 Contents lists available at ScienceDirect Methods journal homepage: www.elsevier.com/locate/ymeth Application Note ScreenClust: Advanced statistical software for supervised and