University of Calgary
UofC Navigation

Genetic Fragment Analysis for Microsatellite, Genotype, SNP, and other Analyses

 

 

The University Core Genetic Analysis Laboratory provides automated multicolour fluorescent analysis of PCR-based DNA fragments. Examples of the types of projects that may be undertaken include: gene mapping using amplified fragment length polymorphisms (AFLP), detecting microsatellite instability of replication error (RER), determining loss of heterozygosity (LOH), and screening for single nucleotide polymorphisms (SNP) using single strand conformation polymorphisms (SSCP) or fluorescent allele specific PCR. Massively parallel genotyping using next-generation DNA sequencing is available through the Centre for Health Genomics and Informatics.

Up to four different fluorescent dyes may be used for labeling, allowing for a greater amount of multiplexing in a single lane for higher throughput. An internal size standard, labeled with a fifth dye, provides accurate and reproducible size determination and quantification, and eliminates problems associated with lane-to-lane or run-to-run electrophoretic variability.

Fragment analysis kits may be purchased through Applied Biosystems. Alternately, custom synthesized fluorescently labeled primers may be obtained directly from the our DNA/RNA synthesis laboratory (dnalab@ucalgary.ca or telephone 403-220-4277). Purchase of the appropriate kit and primers, sample set-up and amplification, and (optional) multiplexing of samples into 96-well sample plates is done prior to submitting the samples for analysis. The DNA Sequencing Laboratory will acquire the data using our Applied Biosystems 96 capillary 3730XL analyzer.

Due to the complexity of assigning genotypes, the automatically called data analysis is not done by our laboratory staff. Instead, researchers are invited to use the copy of GeneMapper we have installed in our laboratory.  Alternatively, the GeneMapper software may be purchased from Applied Biosystems (we are not licensed to allow its use outside our lab) or Applied Biosystems free Peak Scanner software can be downloaded. Information about GeneMapper features and operation can be found by going to the Applied Biosystems web site or by downloading the GeneMapper 3.0 or  GeneMapper 3.7 product bulletins.

A copy of LaserGene (version 7) from DNASTAR is also available for use in our laboratory. This is a commercial multifunctional sequence analysis package which includes a module for SNP detection.

Peak Scanner Software - Free from Applied Biosystems

An easy to use software tool from Applied Biosystems is available as a free download. This software allows users to view, edit, analyse, print and export fragment analysis data from files generated by Applied Biosystems instruments. For many researchers, this free software will eliminate the need to purchase GeneMapper (see above). For more information on this software see www.appliedbiosystems.com/peakscanner 

Size Standards

We stock the following sets of size markers:

  • GeneScan 400 HD ROX size standard
  • GeneScan 500 ROX and 500 LIZ size standard
  • Liz 1200

Any other size standard required must be provided with your samples.

Pricing

See our full list of sequencing and genomic analysis prices.

Ordering

All request for fragment analysis (or sequencing) services must be submitted through our new dnaLIMS system. To go directly to the dnaLIMS server click on www.sequencing.ucalgary.ca or click here for instructions on how to use the dnaLIMS.