Methylation-sensitive, single-strand conformation analysis (MS-SSCA): A rapid method to screen for and analyze methylation

We have developed methylation-sensitive, single-strand conformation analysi s (MS-SSCA) as a method of screening for methylation changes, Bisulfite mod ification converts cytosines to thymines, but methylated cytosines remain u nchanged. This modification creates sequence differences between methylated and unmethylated samples, which can be resolved by SSCA. SSCA is 70-95% ef ficient at detecting single base changes in a fragment. As bisulfite modifi cation of methylated DNA would typically involve several base changes in a fragment, the efficiency of detecting methylation using MS-SSCA could appro ach 100%. We applied this method to analyze the BRCA1 promoter CpG island i n breast cancer samples. About 20% of sporadic breast cancers are hypermeth ylated at the BRCA1 promoter CpG island, MS-SSCA rapidly detected those tum ors that had previously been shown to be methylated by Southern blotting. T he variant bands detected by SSCA were analyzed by sequencing and shown to be methylated. MS-SSCA is a simple method for screening large numbers of sa mples for methylation and can accelerate genomic sequencing, as all bands c an be isolated and sequenced directly. Hum Mutat 14:289-293, 1999. (C) 1999 Wiley-Liss, Inc.