Comparison of germ line minisatellite mutation detection at the CEB1 locus by Southern blotting and PCR amplification

Abstract

Identification of de novo minisatellite mutations in the offspring of parents exposed to mutagenic agents offers a potentially sensitive measure of germ line genetic events induced by ionizing radiation and genotoxic chemicals. Germ line minisatellite mutations (GMM) are usually detected by hybridizing Southern blots of unamplified size-fractionated genomic DNA with minisatellite probes. However, this consumes a relatively large amount of DNA, requires several steps and may lack sensitivity. We have developed a polymerase chain reaction (PCR)-based GMM assay, which we applied to the hypermutable minisatellite, CEB1. Here, we compare the sensitivity and specificity of this assay with the conventional Southern hybridization method using DNA from 10 spouse pairs, one parent of each pair being a survivor of cancer in childhood, and their 20 offspring. We report that both methods have similar specificity but that the PCR method uses 250 times less DNA, has fewer steps and is better at detecting GMM with single repeats provided that specific guidelines for allele sizing are followed. The PCR GMM method is easier to apply to families where the amount of offspring DNA sample is limited.

Fig. 1

(A and B) Representative gel images obtained for Families 2–6 using the (A) Southern and (B) PCR-based CEB1 genotyping assays. The two sets of images were assembled independently by the two laboratories, the Southern images from five separate assays and the PCR images from a single gel. Family members are denoted as: F, father; M, mother; C1, Child 1; C2, Child 2. The vertical black downward arrows show the position of 1-kb allele-sizing ladders; this only approximates to allele sizes in the Southern images of Families 2, 3, 4 and 6 because assays were carried out on separate occasions. The asterisk shows germ line mutant bands and the vertical black upward arrows , the appropriate parental progenitor alleles.