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Journal of Clinical Microbiology, May 1998, p. 1318-1323, Vol. 36, No. 5
0095-1137/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

Computerized Analysis of Restriction Fragment Length Polymorphism Patterns: Comparative Evaluation of Two Commercial Software Packages

P. Gerner-Smidt,1,* L. M. Graves,2 Susan Hunter,2 and B. Swaminathan2

Department of Gastrointestinal Infections, Statens Seruminstitut, Copenhagen, Denmark,1 and Foodborne and Diarrheal Diseases Branch, Division of Bacterial and Mycotic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia2

Received 15 July 1997/Returned for modification 14 January 1998/Accepted 13 February 1998

Two computerized restriction fragment length polymorphism pattern analysis systems, the BioImage system and the GelCompar system (Molecular Analyst Fingerprinting Plus in the United States), were compared. The two systems use different approaches to compare patterns from different gels. In GelCompar, a standard reference pattern in one gel is used to normalize subsequent gels containing lanes with the same reference pattern. In BioImage, the molecular sizes of the fragments are calculated from size standards present in each gel. The molecular size estimates obtained with the two systems for 12 restriction fragments of phage lambda  were between 97 and 101% of their actual sizes, with a standard deviation of less than 1% of the average estimated size for most fragments. At the window sizes used for analysis, the GelCompar system performed somewhat better than BioImage in identifying visually identical patterns generated by electrophoretic separation of HhaI-restricted DNA of Listeria monocytogenes. Both systems require the user to make critical decisions in the analysis. It is very important to visually verify that the systems are finding all bands in each lane and that no artifacts are being detected; both systems allow manual editing. It is also important to verify results obtained in the pattern matching or clustering portions of the analysis.

* Corresponding author. Mailing address: Department of Gastrointestinal Infections, Statens Seruminstitut, Artillerivej 5, DK-2300 Copenhagen S, Denmark. Phone: (45) 32 68 37 98. Fax: (45) 32 68 38 73. E-mail: PGS{at}SSI.DK.

Journal of Clinical Microbiology, May 1998, p. 1318-1323, Vol. 36, No. 5
0095-1137/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.


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