Assay Design

As we offer SNP genotyping based on several different technologies, the procedure for assay design and ordering of assays/probes etc. will also vary.

MassARRAY (Sequenom)
To be able to give an exact price for a specific SNP project, we normally need to test design assays to localize the final multiplexing level as well as the total number of multiplexes we need to run.

We currently design and run assays from single-plex and up to 29-plexes with good results.

Using the MassARRAY Assay Design software, we are able to design single or multiplexed SNP assays based on a text file containing the SNP, SNP-id and the sequence flanking the SNP.

Additional Design Information:

• A demo text file for assay design --> here
• Input Format rules/specifications --> here

Each assay design produces a set of three primer sequences: two PCR primers and a third primer for the extension reaction.

An important (for economical reasons) part of the primer design is to create multiplexed assays (i.e. sets of assays that can be run in the same initial PCR reaction) which, after the extension reaction, will be clearly identified in the resulting mass spectrum. In this process it is crucial to avoid multiplexed primer combinations that may cause unintended products by extending from primers or amplification products from various assays.

SNPlex (Applied Biosystems)
For SNPlex, total pricing is not dependent on the results from the assay design. This is due to the fact that all reactions and prices are based on full 48 plexes and 5000 reactions (this is the size of all SNPlex kits from Applied Biosystems). Your final price pr. genotype needs to take into account these fixed parameters.

The SNPlex Genotyping System provides for the simultaneous genotyping of up to 48 SNPs. To be able to design full 48 plexes, submission of approximately 70 sequences will normally be necessary.

All assay designs are carried out by Applied Biosystems and we normally recommend that all users do this directly with Applied Biosystems. If necessary, we will of course assist in this process.

• A demo text file for assay submission --> here
• To submit your sequences --> here