An algorithm for comparing two-dimensional electrophoretic gels, with particular reference to the study of mutation.

Abstract

An algorithm dedicated to the detection of presumed mutational events involving the polypeptides displayed with two-dimensional polyacrylamide gel electrophoresis has been described. Because of the large number of gels necessary in most studies of mutation, the algorithm has been designed to minimize operator intervention in its execution. The basic principle involves a comparison of the graph structures of the gels of a father, mother, and one or more children, searching for protein spots in the child not found in either parent. These so-called "orphan" spots are considered a probable manifestation of mutation only after other possible causes of such an isolated event have been excluded as rigorously as possible. At present, the analysis of gels prepared from a platelet or erythrocyte lysate yields about 2% "false-positive" findings, i.e., results in the incorrect designation of a unique spot in a child. These errors can be disposed of by technician intervention. In an experiment designed to simulate the occurrence of mutational events, the algorithm operated with 70% accuracy. Most of the "errors" ("false negatives") occurred when the position of the simulated mutant polypeptide coincided in whole or part with that of a preexisting polypeptide, resulting in a class of mutation not detectable by the eye either. With correction for this fact, the accuracy was 84%. Possible improvements in the algorithm which would substantially increase accuracy have been discussed at some length, as have some ideas as to how to manage the large body of data resulting from the operation of the algorithm. A murine experiment designed to validate the approach has been outlined.