Loading ...Hitachi Software recently released a free software tool to automate the design of SNP genotyping assays using Allele Specific Primer Extension (ASPE) on the xMAP platform. The ASPE approach utilizes Luminex Corporation’s xTAG (formerly FlexMAP) microspheres which are pre-coupled to oligonucleotide sequences (anti-tags) that are optimized to be an isothermal set and to have minimum cross-reactivity. The detection probes have the tag sequence synthesized on the 5′ end. The use of the pre-coupled xTAG microspheres simplifies the assay greatly.
In the past designing an ASPE assay was the most difficult aspect of utilizing the xMAP technology for SNP genotyping. The ASPE design software helps researchers create a multiplex SNP assay by automatically designing the primers and probes while optimizing for Tm and identifying any potential cross reactivity between the probe and primer sets of the multiplex reaction.
The ASPE design tool is part of a free web based suite of sequence analysis tools built around an electronic notebook called DNASIS SmartNote. The SmartNote tool takes the best of the free bioinformatics tools on the web and puts them together in one environment. SmartNote also offers some of the new “Web 2.0″ social networking features to allow easier collaboration and information sharing among colleagues.
How to use the ASPE design tool in SmartNote:
- Create a free account here.
- Upload the sequences in your SNP assay. SmartNote offers several options from grabbing fasta files on your computer to automatically retrieving sequences from the SNP dB at NCBI using the rs accession numbers. (Hint: Enter rs numbers separated by commas to retrieve multiple sequence in batch: rs1000,rs1001,rs1002 etc.)
- Select the sequences you would like to design a multiplex assay around and click the analyze button. At this point you will see all of the bioinformatics tools SmartNote has available. Select the Probe design tool for ASPE.
- Enter the allelic variants for each SNP and the bp location within the target sequence. If you have uploaded your sequences from SNP dB then this information is automatically populated!
After you submit your query the software will begin the design process. You are notified by email when the results are available. You have the option of opening the results in an Excel file (csv) for easy viewing. Click here to see example results.
As of July 1st, 2008 you will be able to order the xTAG microspheres online from Hitachi Software. The final step is to send the probe-tag sequences to your favorite oligo synthesis company.
You can find more information about the ASPE assay including recommended protocols and reagents here.
If you have already designed your ASPE assay and are looking for a tool to help pick the correct xTAG sequences SmartNote has a tool for that as well. The xTAG Software (Formerly TagIT Software) is one of the available tools in SmartNote. Click here to learn more about it.
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