AUTOMATED DNA SEQUENCING FACILITY

The Sequencing Facility provides Fox Chase investigators with computer-readable sequences of their DNA templates in a timely and cost effective manner. The facility now includes an Applied Biosystems Model 373A "Stretch" and two Model 377XL genetic analyzers. Besides sequencing, analysis of DNA polymorphisms, important in genetic mapping studies, is also available using "GeneScan" software. The facility performs taq cycle sequencing reactions on user-supplied templates and routinely generates sequences of 700-800 bases, with an average of 1-2% ambiguities. Recent upgrades allow up to 48 (373A), 64, or 96 (377XLs) samples per run. Short PCR product sequencing or GeneScan runs are done during the day, with most sequencing run overnight. The facility provides sequencing primers for all routine vectors. Primer design software is available to investigators on a computer in the facility for large sequencing projects. Investigators are provided with a printout of their sequence, including electropherogram traces. Additionally, sequence files are available from a networked file server so that investigators can re-analyze their data on local Macintosh computers and import the sequence data into software of their choosing for further analysis. There is also a computer workstation in the facility, independent of the sequencers, that allows simultaneous processing of samples while data is being collected, enhancing throughput. In the past year, one of the 377 systems has been upgraded for 96-lane use. All sequence analysis samples are processed using a plate-based setup, providing significantly increased sample throughput. The facility is now routinely processing up to 1500 sequence samples per month.

The facility has averaged 1200-1400 runs per month over the previous year and has provided sequences to investigators from the following laboratories: A. Bellacosa, M. Bosma, J. Burch, J. Chernoff, M. Clapper, T. Coleman, R. Edwards, J. Feng, J. Gallo, A. Godwin, E. Golemis, T. Hamilton, R. Hardy, K. Hayakawa, L. Henske, K. Hunter, D. Kappes, W. Kruger, G. Kruh, W. Mason, Y. Matsumoto, E. Moss, M. Murphy, R. Raftogianis, C. Seeger, A. Skalka, R. Strich, J. Taylor, J. Testa, K. Tew, J. Tricoli, L. Weiner, D. Wiest, H. Yan, T. Yen, and A. Yeung. These investigators represent usage by all 13 of our programs.

Illustrations or unpublished data in these reports should not be used without permission of the author.

Fox Chase Cancer Center

Scientific Report 1998