The document outlines multiplex PCR, detailing its types—single and multiple template reactions—and advantages. It discusses primer design, highlighting software like PrimerPlex and Beacon Designer, and presents applications such as pathogen identification and SNP genotyping. Overall, it serves as a comprehensive guide for optimizing multiplex PCR techniques.

1. Prepared by:
Anfal Ibrahim Baher Eldeen

2. Contents
 Introduction
 Types
 Multiplex PCR primer design
 Advantages
 Applications

3. Introduction

4. Types of Multiplex PCR
1. Single Template PCR Reaction
This technique uses a single template which can be a
genomic DNA along with several pairs of forward and reverse
primers to amplify specific regions within a template.
2. Multiple Template PCR Reaction
It uses multiple templates and several primer sets in the
same reaction tube.

5. Types of Multiplex PCR
Qualitative
Quantities

6. Primer design – work plan

7. Examples of multiplex PCR primer
design software
 PrimerPlex is an efficient tool to design specific oligos for
multiplex PCR assays.
 Design Real time Multiplex PCR Primers using Beacon
Designer and AlleleID®

8. Good multiplex PCR primers properties

9. 0ptmising multiplex PCR condition

10. Multiplex Real time PCR

12. Example of stander multiplex PCR

14. Advantages of Multiplex PCR

15. Applications of Multiplex PCR
 Pathogen Identification
 High Throughput SNP Genotyping
 Mutation Analysis
 Gene Deletion Analysis
 Template Quantitation
 Linkage Analysis
 RNA Detection
 Forensic Studies