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DNA Fragment Analysis


Genetic marker analysis experiments rely on the detection of changes in the length of a specific DNA fragment to indicate the presence or absence of a genetic marker. Our DNA Sequencing team offers a fast and reliable automated DNA fragment analysis service where fluorescently labeled DNA fragments are electrophoretically separated using the ABI3730xl Genetic Analyzer.

Fragment Analysis Chromatogram Image

For selected applications (Microsatellite and MLPA), we also offer the final data interpretation as an add-on service for samples labeled with 6-FAM. We perform quality DNA sizing, allele calling, and relative quantitation using the GeneMapper v6.0 analysis software package.

Key Features

  • Accurate size calling, consistent band intensities, and low run-to-run migration variations by electrophoresis on ABI 3730xl DNA Analyzer

  • Sizing to within 1 bp resolution for fragments in the approximate size range of 50 bp to 500 bp

  • Supported dye labels: 6-FAM (blue), NED (yellow), PET (red), VIC (green)

    • Our instrument is calibrated for use with Dye Set DS-33 (filter set G5) and will not work optimally with other dyes.

    Please note: Data analysis can only be performed here at the Core when 6-FAM is selected. Analysis of any other dye label or multiplexing more than one dye is to be performed by the end user.

  • Multiplex option (up to 4 fluorescent dyes)

  • Sizing by comparison with GeneScan 500 LIZ Size Standard

    • Standard size marker (orange dye label) is loaded with each sample.


  • On-site data interpretation (Microsatellite and MLPA applications only!) using GeneMapper v6.0 analysis software (add-on service option)
    Please note: Data interpretation of NED, PET, VIC, and multiplexed samples are the responsibility of the user. The core will analyze data when samples are labeled with 6-FAM only.

  • Direct email notification upon service completion

  • Secure website access to fragment analysis results

  • Prompt technical support and consultation

  • Daily (Mon-Fri) processing and free sample pickup at our remote sample drop-off locations

  • Turnaround time: 24 hours or less


Supported DNA Fragment Analysis Applications:

  • Microsatellite Analysis (short tandem repeats (STRs), variable nucleotide tandem repeats (VNTRs))
  • MLPA Analysis (multiplex ligation-dependent probe amplification)

We are performing our standard fragment analysis services utilizing an ABI 3730xl protocol that has been specifically developed and optimized for Microsatellite and MLPA applications.

If you are interested in another application, please contact us to inquire about technical feasibility.

Additional Fragment Analysis Applications:

  • AFLP Analysis (amplified fragment lengths polymorphisms)
  • Electrophoresis of fluorescent PCR amplicons
  • T-RFLP Analysis (terminal restriction length polymorphism)
  • Single Nucleotide Polymorphism Genotyping (SNP)
  • Relative Fluorescent Quantitation (Loss of Heterozygosity, LOH)

Please refer to our Fragment Analysis Guidelines prior to submitting samples.

If you should require any assistance or have questions regarding sample submission or setting up an account with us, please contact us.