Fragment Analysis

Fragment Analysis Submission Policies

Our DNA Analyzer has the ability to determine the size of your DNA fragments by using fluorescence based detection system. We will add the size standard and perform the electrophoresis portion of fragment analysis technology. The current service charge is $110 for a 96 well plate regardless of how many samples are in the plate.

  • All samples must be submitted in ABI MicroAmp Optical Plates. Applied Biosystems Optical 96-Well Reaction (available in the Yale stockrooms). Part #N801-0560
  • Plates must be sealed properly, wrapped in foil and submitted along with a Submission Form: Yale Submission Form or Non-Yale Submission Form.
  • We must receive through email an excel sample sheet for each plate. If a sample sheet is not supplied your sample files will be named Plate Name-Well number. Please email dnasequencing@yale.edu for the excel sample sheet 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.

You must have access to Applied Biosystems Genemapper v3.5 or higher to analyze your sample files. Please email us for more information if you do not have this software.

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

Sample files are returned through FTP approximately 1-2 business days after the plate was received.