QIAGEN Multiplex PCR Handbook[1]

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  • QIAGEN Multiplex PCR Handbook

    For fast and efficient multiplex PCR without optimization

    February 2008

    Sample & Assay Technologies

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  • QIAGEN Sample and Assay TechnologiesQIAGEN is the leading provider of innovative sample and assay technologies, enablingthe isolation and detection of contents of any biological sample. Our advanced, high-quality products and services ensure success from sample to result.

    QIAGEN sets standards in:

    Purification of DNA, RNA, and proteins Nucleic acid and protein assays microRNA research and RNAi Automation of sample and assay technologiesOur mission is to enable you to achieve outstanding success and breakthroughs. Formore information, visit www.qiagen.com .

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  • QIAGEN Multiplex PCR Handbook 02/2008 3

    ContentsKit Contents 4

    Shipping and Storage Conditions 4

    Technical Assistance 4

    Safety Information 5

    Product Use Limitations 5

    Product Warranty and Satisfaction Guarantee 5

    Quality Control 6

    Product Specifications 6

    Introduction 7

    HotStarTaq DNA Polymerase 8

    QIAGEN Multiplex PCR Buffer 8

    Q-Solution 8

    Important Notes 9

    Primers 9

    Methods of analysis 9

    Template DNA 11

    Choosing the correct protocol 14

    Multiplex PCR using Q-Solution 14


    Standard Multiplex PCR 16

    Amplification of Microsatellite Loci Using Multiplex PCR 20

    Multiplex PCR Using Q-Solution 23

    Troubleshooting Guide 26

    Appendix A: Design of Multiplex PCR Primers 33

    Appendix B: Handling and Storage of Primers 34

    Appendix C: PCR Cycling Protocols 36

    Appendix D: Analysis of Multiplex PCR Products 37

    Appendix E: Special Multiplex PCR Applications 37

    Appendix F: Optimization of Reaction Conditions for Special Multiplex PCR Applications 42

    Ordering Information 44

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  • 4 QIAGEN Multiplex PCR Handbook 02/2008

    Kit ContentsQIAGEN Multiplex PCR KitCatalog no. 206143 206145No. of 50 l reactions 100 1000

    2x QIAGEN Multiplex PCR Master Mix, 3 x 0.85 ml 1 x 25 mlcontaining: HotStarTaq DNA Polymerase, Multiplex PCR Buffer*, dNTP Mix

    Q-Solution, 5x 1 x 2.0 ml 1 x 10 ml

    RNAse-Free Water 2 x 1.7 ml 1 x 20 ml

    Handbook 1 1

    * Contains 6 mM MgCl2.

    Shipping and Storage ConditionsThe QIAGEN Multiplex PCR Kit is shipped on dry ice, but retains full activity at roomtemperature (1525C) for 2 days. The QIAGEN Multiplex PCR Kit, including Q-Solution and RNase-free water, should be stored immediately upon receipt at 20Cin a constant-temperature freezer. When stored under these conditions and handledcorrectly, these products can be kept at least until the expiration date (see the inside ofthe kit lid) without showing any reduction in performance. The QIAGEN Multiplex PCRMaster Mix can be stored at 28C for up to 6 months.

    Technical AssistanceAt QIAGEN we pride ourselves on the quality and availability of our technical support.Our Technical Service Departments are staffed by experienced scientists with extensivepractical and theoretical expertise in molecular biology and the use of QIAGENproducts. If you have any questions or experience any difficulties regarding the QIAGENMultiplex PCR Kit, or QIAGEN products in general, please do not hesitate to contact us.

    QIAGEN customers are a major source of information regarding advanced orspecialized uses of our products. This information is helpful to other scientists as well asto the researchers at QIAGEN. We therefore encourage you to contact us if you haveany suggestions about product performance or new applications and techniques.

    For technical assistance and more information, please see our Technical Support centerat www.qiagen.com/goto/TechSupportCenter or call one of the QIAGEN TechnicalService Departments or local distributors (see back cover or visit www.qiagen.com ).

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  • QIAGEN Multiplex PCR Handbook 02/2008 5

    Safety InformationWhen working with chemicals, always wear a suitable lab coat, disposable gloves,and protective goggles. For more information, please consult the appropriate materialsafety data sheets (MSDSs). These are available online in convenient and compact PDFformat at www.qiagen.com/ts/msds.asp where you can find, view, and print the MSDSfor each QIAGEN kit and kit component.

    24-hour emergency information

    Emergency medical information in English, French, and German can be obtained 24 hours a day from:

    Poison Information Center Mainz, Germany

    Tel: +49-6131-19240

    Product Use LimitationsThe QIAGEN Multiplex PCR Kit is developed, designed, and sold for research purposesonly. It is not to be used for human diagnostic or drug purposes or to be administeredto humans unless expressly cleared for that purpose by the Food and DrugAdministration in the USA or the appropriate regulatory authorities in the country of use.All due care and attention should be exercised in the handling of many of the materialsdescribed in this text.

    Product Warranty and Satisfaction GuaranteeQIAGEN guarantees the performance of all products in the manner described in ourproduct literature. The purchaser must determine the suitability of the product for itsparticular use. Should any product fail to perform satisfactorily due to any reason otherthan misuse, QIAGEN will replace it free of charge or refund the purchase price. Wereserve the right to change, alter, or modify any product to enhance its performanceand design. If a QIAGEN product does not meet your expectations, simply call yourlocal Technical Service Department or distributor. We will credit your account orexchange the product as you wish.

    A copy of QIAGEN terms and conditions can be obtained on request, and is alsoprovided on the back of our invoices. If you have questions about product specificationsor performance, please call QIAGEN Technical Services or your local distributor (seeback cover) or visit www.qiagen.com .

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  • 6 QIAGEN Multiplex PCR Handbook 02/2008

    Quality ControlQIAGEN Multiplex PCR Master Mix

    Multiplex PCR performance assay PCR performance, reproducibility, and sensitivityare tested in parallel multiplex reactions.

    HotStarTaq DNA Polymerase Amplification efficiency and reproducibility in PCR(included in QIAGEN Multiplex are tested. Functional absence of exonucleases andPCR Master Mix) endonucleases is tested.

    Buffers and reagents

    QIAGEN Multiplex PCR Buffer Density, pH, and content of cationic componentsare tested.

    Q-Solution Conductivity, density, pH, and performance in PCRare tested.

    RNase-Free Water Conductivity, pH, and RNase activities are tested.

    Product Specifications2x QIAGEN Multiplex PCR Master Mix contains:

    HotStarTaq DNA Polymerase HotStarTaq DNA Polymerase is a modified form of a recombinant 94 kDa DNA polymerase,originally isolated from Thermus aquaticus, clonedin E. coli. (Deoxynucleoside-triphosphate: DNAdeoxynucleotidyltransferase, EC

    QIAGEN Multiplex PCR Buffer Contains 6 mM MgCl2, pH 8.7 (20C)

    dNTP Mix Contains dATP, dCTP, dGTP, dTTP; ultrapurequality

    Q-Solution 5x concentrated

    RNase-Free Water Ultrapure quality, PCR-grade

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  • QIAGEN Multiplex PCR Handbook 02/2008 7

    IntroductionMultiplex PCR is a powerful technique that enables amplification of two or more productsin parallel in a single reaction tube. It is widely used in genotyping applications anddifferent areas of DNA testing in research, forensic, and diagnostic laboratories. MultiplexPCR can also be used for qualitative and semi-quantitative gene expression analysis usingcDNA as a starting template (Table 1). DNA tested typically originates from a variety ofeukaryotic (human, animal, and plant) and prokaryotic (bacterial and viral) sources.

    Table 1. Applications of Multiplex PCR

    Source of DNA Application

    Animals/human Analysis of satellite DNA (e.g., short tandem repeat [STR] analysis or variable number of tandem repeats [VNTR] analysis)

    Typing of transgenic animals

    Lineage analysis (e.g., of farm animals)

    Detection of pathogens

    Food analysis

    Sex determination

    Detection of mutations

    Amplification of SNP loci

    Qualitative and semi-quantitative gene expression analysis

    Plants Analysis of satellite DNA (e.g., STR or VNTR analysis)

    Typing of transgenic plants

    Lineage analysis

    GMO analysis

    Detection of pathogens

    Qualitative and semi-quantitative gene expression analysis

    Bacteria/viruses Hygiene analysis

    Detection of pathogens/diagnostics

    Qualitative and semi-quantitative gene expression analysis

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  • 8 QIAGEN Multiplex PCR Handbook 02/2008

    The QIAGEN Multiplex PCR Kit is the first commercially available kit for multiplex PCR. Itminimizes the need for optimization, making the development of multiplex PCR assays bothsimple and fast. The kit contains a master mix whose composition and elements werespecifically developed for multiplex PCR applications. The master mix contains pre-optimized concentrations of HotStarTaq DNA Polymerase and MgCl2, plus dNTPs, anda PCR buffer that contains the novel factor MP. Use of a master-mix format reduces time andhandling for reaction setup and increases reproducibility by eliminating many possiblesources of pipetting errors.

    HotStarTaq DNA Polymerase

    The QIAGEN Multiplex PCR Master Mix contains HotStarTaq DNA Polymerase, amodified form of QIAGEN Taq DNA Polymerase. HotS