Genotyping is the characterization of an organism by its DNA. Genotyping using microsatellite markers involves PCR amplification of the microsatellite region and measurement of the size of the amplified fragment. SNP typing is a method of identifying and characterizing single base changes.

The genotyping core is available for microsatellite marker analysis using a 3730xL DNA Analyzer.

The primers for microsatellite genotyping are designed from DNA sequences adjacent to regions of tandem repeat units. The variable length of these repeat regions produces polymorphic allele fragments during PCR that can be analyzed through capillary electrophoresis. Along with size differences we take advantage of three different fluorescent channels to run a multiplex analysis of your fragments in a single capillary.

  • Applied Biosystem's 3730xL DNA Analayzer

3730xL Fragment Analysis

Clients who have fluorescently labeled microsatellite fragments using Applied Biosystems chemistry may submit whole plates for 3730xL analysis. You may either submit pooled PCR fragments or samples in HiDi formamide with a size standard. You will need to generate a plate sheet based on our template file and then e-mail your completed data table to our genotyping core at: genotype@genome.med.harvard.edu.

All 3730xL fragment analysis samples should be prepared in an ABI compatible plate such as ABgene/Marsh T0296PE with a total volume of 12ul.
Service Harvard Internal Harvard Affiliate/Academic Commercial
3730xL Analysis - full plate of PCR Products $126.72 $145.73 $164.74
3730xL Analysis - full plate of Samples in HiDi with Ladder $77.00 $88.55 $100.10

When analysis is complete your data will be posted to our secure FTP server as a ".fsa" file which can be opened with GeneMapper.

The data can be analyzed using Applied Biosystem's GeneMapper or PeakScanner. We have a license for GeneMapper at our computer facility and can be signed up for use. PeakScanner is a freeware and can be downloaded to your personal computer directly from ABI's website.