Fragment Analysis

Fragment Analysis Submission Policies

Our DNA Analyzer uses fluorescence based detection to determine the size of DNA fragments. We will add the size standard and perform the electrophoresis on the samples. The current service charge is $72 for a 96 well plate regardless of how many samples are in the plate.

  • All samples must be submitted in ABI MicroAmp Optical Plates, part #N801-0560. (Available in the Yale stockrooms).
  • Plates must be sealed properly and wrapped in foil.
  • After the order is placed online, please email us the sample sheet. If a sample sheet is not supplied your sample files will be named Plate Name-Well number. Please click on link for sample sheet template. [Template]

We currently accept samples labeled with the following dye sets:

  1. DS-30: 6-FAM, HEX, NED and ROX, where ROX is the size standard. Please email for special requirements for this dye set before submitting a plate.
  2. DS-33: 6-FAM, VIC, NED, PET and LIZ, where LIZ is the size standard.
  3. DS-02: dR110, dR6G, dTAMRA, dROX and LIZ, where LIZ is the size standard.

Fragment Analysis Submission Protocol

(1) Before pooling multiplex PCR products:

  • We recommend running a mini-gel to verify that your PCR product works.
  • Determine optimal PCR concentration by serial dilution.
  • Example of possible Microsatellite optimized concentration: pre-PCR = 50ng/µl, post amplification 25ng/µl
  • To avoid Plus A problem order primer with tails. See User Bulletin: Plus A Artifacts for more information.

(2) Submit 1-2 µl of fluorescently labeled pooled PCR products and follow submission policy above.

Fragment Analysis Applications

  1. Microsatellite Analysis Fact Sheet: 106MI61
  2. BAC Fingerprinting on 3730/3730xl
  3. Screen for loss of heterozygosity

Standard Turn Around Time

Standard turnaround time is 1-2 business days. Results can be viewed using GeneMapper software through a remote desktop connection. Please email us at for login instructions.