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Multiplex SNP Detection and High Throughput Genotyping

With PrimerPlex, you can design multiplex PCR primers flanking the SNP, ASPE primers with SNPs at the 3' end and capture probes with SNPs at their center. PrimerPlex enables you to detect all the mutations of a medium sized genomic sequence by designing oligos for each one of them. These primers and probes are checked for multiplexing and the best possible set is displayed.

Multiplex PCR Primer Design

Designing primer sets that work well for a multiplex assay can be a challenging task. PrimerPlex uses innovative and proprietary algorithms to design optimal multiplex primer sets, minimizing Tm mismatches. All sets are analyzed for cross reactivity to ensure specific and efficient amplification. You can choose the set best suited for your experimental needs from a list of alternates presented in variously sortable order. Using PrimerPlex, you have the flexibility of designing primers either towards the 3' end, the 5' end, at a specified distance from these ends or anywhere within the sequence.

For SNP genotyping assays, the program designs primers flanking mutations such as SNPs, DIPs (Deletion/Insertion Polymorphisms) and MNPs (Multiple Nucleotide Polymorphisms).

Comprehensive Assay Support

Using PrimerPlex, design oligos for multiplex PCR, ASPE and direct hybridization assays. The oligos are screened for cross reactivity to ensure high signal strength, minimizing Tm mismatches. The oligos are screened for dimers, runs and repeats.

Next Generation Sequencing Assay

With PrimePlex, designing multiplex oligos for pre-sequencing sample preparation and mutation detection such as SNPs, DIPs (Deletion/Insertion Polymorphisms) and MNPs (Multiple Nucleotide Polymorphisms) is as easy as clicking a few buttons.

Primer Specificity

The program BLAST searches multiple sequences in a single search run. The results are automatically interpreted and the homologies identified are avoided during primer design, ensuring that the design is highly specific.

Evaluate Pre-Designed Primers and Probes

PrimerPlex can use pre-designed well proven oligos to build a multiplex set. After specifying the oligos for each sequence, their properties are analyzed and the user is alerted for any deviations so found. For the sequences where pre-designed oligos are not available, PrimerPlex designs them, checks them for multiplexing and highlights compatibility issues if any. The user can then decide to accept the design or create a separate pool. This functionality gives complete control in the hands of the user.

Addition of MagPlex TAGs

The program now also supports a database of MagPlex TAGs along with the MicroPlex xTAGs (formerly known as FlexMAP TAGs) for automatic addition of appropriate tags to each ASPE primer. The tags are so chosen that they minimize dimerization and do not fold back on the oligos they are attached. In addition, a user can override the program's recommendation and select a tag on their own. PrimerPlex alerts the user if the tags are not unique or if the tag chosen is incompatible with the oligo.

Oligo Design for Multiplex PCR & High Throughput SNP Genotyping and Analysis

PrimerPlex is an efficient and sophisticated tool for designing oligos for multiplex assays. Multiplex assays facilitate amplification of multiple targets in a single reaction vessel, reducing both the time and cost of experimentation.

Primer design for multiplex PCR presents several challenges which include primer dimers, inability to separate amplicons with similar electrophoretic mobility and mis-priming due to nonspecific binding to non-target DNA templates. PrimerPlex uses proprietary algorithms to design optimal multiplex primer sets under uniform reaction conditions for over 100 sequences. The primer sets are identified after screening all the primers in a pool and minimizing Tm mismatches to ensure specific amplification and high signal strength. In this process, it analyzes millions of possible multiplex primer sets in a few seconds and presents a list of alternate sets. You can specify minimum product size differences amongst the set of designed primer pairs for better visualization of bands on a gel. To assure primer specificity, primers can be BLAST searched from PrimerPlex against any of the genomic databases available at NCBI.


  • Multiplex SNP Detection and High Throughput Genotyping
  • Multiplex PCR Primer Design
  • Comprehensive Assay Support
  • Next Generation Sequencing Assay
  • Primer Specificity
  • Evaluate Pre-Designed Primers and Probes
  • Addition of MagPlex TAGs


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