DNA Sequencing & Genotyping at AWRI/GVSU

Fragment Analysis Guidelines

The DNA sequencing and genotyping facility can run fragment analysis applications like microsatellites and amplified fragment length polymorphisms (AFLPs).


The most important thing to remember before submitting samples for fragment analysis is that the ABI3130xl needs to be “trained” to detect any dye that you utilize in your fragment analysis applications.  There are two dye sets that the facility currently maintains:


DS33 6-FAM™, VIC®, NED, and PET® dyes with LIZ® as the size standard.

The dye LIZ® is reserved for the standard and you will encounter difficulty in analyzing the data if you label fragments with this color.


DS32 (dye set F) 5-FAM™, JOE™, and NED™ with ROX™ as the size standard.

            The dye ROX™ is reserved for the size standard.


The Genetic Analyzer is capable of viewing up to five different colors of fluorescent dyes at the same time. This allows the researcher to combine several fragments all in the same well. Some dyes are incompatible with other dyes and so “dye sets” have been created to avoid problems.


We encourage you to use one of the two existing dye sets for any new projects. Please talk to Ryan Thum or Jeremy Newton if you would like help deciding which best suits your needs. If you currently have research in progress that uses other dyes, please contact Jeremy to set up use of the facility.


We suggest you perform a few dilution trials to optimize your samples when submitting samples for the first time. Our methods may differ from your current genotyping facility so optimization may be warranted.



Facility technician prepares sample for the run - $2 per sample.

Prepare and load your own sample - $1 per sample. (You will receive training on how to prepare samples if you choose to do your own bench work.)

Reduced per sample costs can apply to large projects that involve running lots of samples (e.g., entire plates).  Please inquire with Dustin Wcisel for these types of projects.

Questions?  Please contact Jeremy Newton at 616-331-3990 or newtojer@gvsu.edu

Page last modified August 13, 2012