Combined SSCP/duplex analysis by capillary electrophoresis for more efficient mutation detection

SSCP and heteroduplex analysis (HA) continue to be the most popular methods of mutation detection due to their simplicity, high sensitivity and low co st. The advantages of these methods are most clearly visible when large gen es, such as BRCA1 and BRCA2, are scanned for scattered unknown mutations an d/or when a large number of DNA samples is screened for specific mutations. Here we describe a novel combined SSCP/duplex analysis adapted to the mode rn capillary electrophoresis (CE) system, which takes advantage of multicol or labeling of DNA fragments and laser-induced fluorescence detection. In d eveloping this method, we first established the optimum conditions for homo duplex and heteroduplex analysis by CE. These were determined based on comp rehensive analysis of representative Tamra-500 markers and BRCA1 fragments at different concentrations of sieving polymer and temperatures in the pres ence or absence of glycerol. The intrinsic features of DNA duplex structure s are discussed in detail to explain differences in the migration rates bet ween various types of duplexes. When combined SSCP/duplex analysis was carr ied out in single conditions, those found to be optimal for analysis of dup lexes, all 31 BRCA1 and BRCA2 mutations, polymorphisms and variants tested were detected. It is worth noting that the panel of analyzed sequence varia nts was enriched in base substitutions, which are usually more difficult to detect. The sensitivity of mutation detection in the SSCP portion alone wa s 90%, and that in the duplex portion was 81% in the single conditions of e lectrophoresis. As is also shown here, the proposed combined SSCP/duplex an alysis by CE has the potential of being applied to the analysis of pooled g enomic DNA samples, and to multiplex analysis of amplicons from different g ene fragments. These modifications may further reduce the costs of analysis , making the method attractive for large scale application in SNP scanning and screening.