MBCF Genotyping Services

There are a number of different fragment analysis genotyping applications that are available using our Applied Biosystems 3730 DNA Analyzers and Genemapper 4.0 software. Some of the most common applications are microsatellite analysis, spectratyping, LOH studies, and multi-plexed SNP analysis (Applied Biosystems SNPlex).

Pricing

$150 optimization/software training fee
$1 per sample
Volume discounting can be discussed.
Please contact Zach with any questions:

zachary_herbert@research.dfci.harvard.edu
(617) 632-3082

Download Free Peak Scanner Software from Applied Biosystems.

Labeling Fragments

PCR products can be labeled using a number of different florophores such as 6-FAM, VIC, NED, PET, HEX, etc. You should check with us to make sure that we can support your dye set prior to sample submission, especially if you are considering a multiplex reaction. The dye labels should be attached to the 5' end of the PCR product. Although we do have the ability to synthesize dye labeled primers in our lab, it is probably more cost and time effective for you to order them from a commercial vender such as Applied Biosystems or IDT. Additionally, we are not set up to run PCR reactions so they must be run in YOUR lab.

Sample Prep/Guidelines

Following PCR, you can drop off 5-10ul of the product. We do not have a set volume because it is highly variable depending on the particular sample and PCR conditions. Typically, for the first few samples we will run serial dilutions with water to determine what volume of your products will yield the best results. 10ul of formamide containing a size standard are added to each sample, prior to analysis. (If you are planning on running many samples, we can provide you with formamide and size standard for you to add prior to submission. This can help improve turnaround time.) IMPORTANT NOTE: Samples are loaded into the capillaries through an electrophoretic injection therefore results can be severely affected by charged contaminants such as salts, buffers, primer dimmers, and very short PCR products. This means that your samples may require some form of post-PCR clean-up in order to optimize your results.

Data Analysis and Output

There are a number of different applications that can be performed using the Genemapper 4.0 software, and therefore, data analysis and output will vary depending on the specific nature of the project. For some of the more straightforward applications results can be sent out by e-mail in a simple spread sheet format. However, some of the more interpretative analysis may require the use of the Genemapper 4.0 software, which may have to be done at MBCF (a great excuse to come visit us at DFCI North campus).

SNPlex (New Service)

This application allows for multi-plexed SNP genotyping of up to 48 SNPs per sample. Please contact us for details and price quotes.