Fragment Analysis

Contact: Elizabeth Jensen
Location: DE-302
Contact phone: (206) 667-4470
Contact fax: (206) 667-2825
Contact e-mail: ejensen@fredhutch.org

Lab Introduction and Consulting

The Genomics Resource's Genetic Analysis Lab runs fragment analysis and SNP analysis for genotyping using Applied Biosystems (ABI) 3730xl DNA Analyzers. An overview of ABI's platform and applications is available at their website.

Reagent and Consumable Purchases

Investigators should select a filter set, purchase their own reagents, and run the reactions in their laboratory. When starting a new project, it is often necessary to run a dilution series to determine the optimum concentration for the reactions.

Sample submission

For fragment analysis, bring 1-2 ul of your processed samples to the Genetic Analysis lab in room DE-302 and put samples into the Styrofoam box labeled "Genotyping samples" in the freezer. You should also bring a completed request form with you (see below). Genetic analysis staff will add a size standard and formamide to each sample and run the samples on the ABI 3730xl.

If you are doing SNPlex, run the assays and bring the plate(s) to DE-302, place the plates in the freezer, and the staff will load the plate onto the machine for analysis.

ABI genotyping request forms:
If you are using a Fred Hutch project id for billing, please fill out the Internal submission form at the Hutchbase site, print the completed form and bring with your sample.

If you are using a UW budget number or are not a Fred Hutch or Cancer Consortium member, fill out the External Request Form.

Results and Downstream Analysis

Researchers who deliver samples, accompanied by a completed submission form, by 4 PM Mon-Thur or by the Fri deadline of 2PM will typically receive results the following business day (M-F). Please note that the stated turnaround estimates will be affected by holidays, equipment malfunctions, and staffing issues.

For quality control, Genetic analysis will ensure that the size standard added by the resource has produced expected results.

Data generated in the resource are transferred to servers supported by Fred Hutch's IT department. Data are transferred into the user's FRED account, in the researcher's 'geneticanalysis' directory. or can be sent to investigator via email. Please indicate on the request form which method you would prefer.

Results sent electronically will have a project file (.ser) and a chromatogram file (.fsa)

GeneMapper is the software recommended by staff and is available in the Computing Center in the library. ABI also has a free software download on their website called "Peak Scanner."