Genotyping - ABI

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.

The following is information pertinent to Fred Hutchinson and other Cancer Consortium members accessing genotyping services at FHCRC. Those new to this technology or new to using the Genetic Analysis Lab are strongly encouraged to meet with lab personnel prior to planning a project. For non-consortium members interested in services please contact the Genomics Resource at (206) 667-4470 or one of the individuals below.

Contacts:

• For questions regarding services and related fees, please contact Elizabeth Jensen at ejensen@fhcrc.org or 206.667.4470.
  

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. Fill out and submit the request form at this time. 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:
FHCRC and Cancer Consortium members using an FHCRC budget number should fill out the Internal request form.

If you are using a UW budget number or are not an FHCRC 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 the Hutchinson Center's Research Computing Support Shared Resource. 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 Research Computing Center. See other options available for visualizing and analyzing your data. ABI also has a free software download on their website called "Peak Scanner".