SNP Genotyping- Mass Array

In addition to Real Time PCR methods, UAGC offers SNP genotyping on the Agena Bioscience MassARRAY® MALDI–TOF instrument. Using this technology we can multiplex SNPs for up to 36 loci.

Sample Input

Each reaction requires 1µL of 10ng/µL DNA.

The DNA can be submitted in 96-well or 384-well plates with at least 2 open wells for negative controls.

Expected Results

Genotypes are determined through ratio analysis of the MALDI-TOF mass spectrometer.

Click on the 'Details' tab above for rate information and how to submit samples.

Sample Preparation Details
  • The DNA samples should be eluted in RNase free or HPLC water.The instrument is very sensitive to salt, so please avoid TE buffer.
  • Each reaction requires 1µL of 10ng/µL DNA. It is best if 260/280 ratio is between 1.7 and 2.0.
  • The DNA can be submitted in 96-well or 384-well plates with at least 2 open wells per every 384 for negative controls.
  • The instrument utilizes 384-well plate format.

UAGC can extract and prepare your samples for SNP genotyping.


How to Get Started with your Sample Submission: 

  • Contact UAGC to discuss SNPs of interest and multiplex design
  • Login to Sample Lifecycle Manager (SLM) and select 'Sequenom Genotyping' as your workflow.
  • Upload your sample information.
  • Click submit tubes.
  • Click Set test and enter the multiplex assay name designed with UAGC.
  • Click Submit Test.
  • Record and attach the 4 letter code at the end of your SLM submission to your samples and send or deliver to UAGC. 

Multiplex Design Information:This instrument can perform up to a 36-plex, but we typically achieve between 25 and 30 loci. To optimize the largest multiplex possible, it is best to provide 40-50 loci with specific notes about their relative importance. Provide the SNP ID (rs#) and the sequence. Within the sequence the SNP should be denoted in brackets (i.e. [G/A]), with 100-200 bases of flanking sequence on either side. Tri-allelic SNPs are also detectable. Multiplex PCR assays target ~100bp amplicons containing SNPs of interest. 

If there are other known polymorphisms within the sequence please denote them as "X" so we can design the primers around them. There cannot be polymorphisms bracketing the SNP of interest within 20bp; however, if there is a polymorphism upstream of the SNP of interest, we can design the primer on the antisense strand.

Three primers are utilized per SNP, two for amplification and one for the extension reaction. Primers are unlabeled and usually 15-25 bp in length.

For more information, please see our Agena Bioscience Mass Array FAQ page


Academic(UofA): $2700.00 | Industry: $4050.00 | Unit: 384-well Plate

Turnaround Time


Additional Information

Price listed is per 384 well plate. If multiplexed at 30 SNPS cost ~ $0.20 per SNP

Primers are not included in the above pricing. These typically run ~$8/SNP.

For more information about the Agena Bioscience MassARRAY® system, please visit our FAQ page or go to:

  • The Agena Bioscience Mass Array instrument is a great option when genotyping multiple SNPs for a large number of samples.

    Crystal Richt

For this service, please contact