Optimization of capillary array electrophoresis single-strand conformation polymorphism analysis for routine molecular diagnostics.
ABSTRACT Mutation screening is widely used for molecular diagnostics of inherited disorders. Furthermore, it is anticipated that the present and future identification of genetic risk factors for complex disorders will increase the need for high-throughput mutation screening technologies. Capillary array electrophoresis (CAE) SSCP analysis is a low-cost, automated method with a high throughput and high reproducibility. Thus, the method fulfills many of the demands to be met for application in routine molecular diagnostics. However, the need for performing the electrophoresis at three temperatures between 18 degrees C and 35 degrees C for achievement of high sensitivity is a disadvantage of the method. Using a panel of 185 mutant samples, we have analyzed the effect of sample purification, sample medium and separation matrix on the sensitivity of CAE-SSCP analysis to optimize the method for molecular diagnostic use. We observed different effects from sample purification and sample medium at different electrophoresis temperatures, probably reflecting the complex interplay between sequence composition, electrophoresis conditions and sensitivity in SSCP analysis. The effect on assay sensitivity from three different polymers was tested using a single electrophoresis temperature of 27 degrees C. The data suggest that a sensitivity of 98-99% can be obtained using a 10% long chain poly-N,N-dimethylacrylamide polymer.
- SourceAvailable from: Per M Ueland[show abstract] [hide abstract]
ABSTRACT: We investigated the effects of temperature and pH on single strand-conformation polymorphism (SSCP) analyzed by capillary electrophoresis (CE) using short-chain linear polyacrylamide as the sieving medium. Nine different mutations (in factor V, cystathionine beta-synthase, and methylenetetrahydrofolate reductase genes), including both transitions and transversions, were investigated. We confirmed that low temperature in general increased the number of detectable single-strand conformations and thereby the sensitivity of the analysis. The pH effects of the separation matrix on the migration pattern, and thus the assay sensitivity, varied markedly between the different DNA fragments. Seven of nine single point mutations were detected at the ordinary pH of 8.3, whereas the CBS T833C mutation was discriminated at the extreme pH values of 9.0 and 6.4, and the CBS G797A mutation could not be detected at any pH value within the range 6.4--9.0. These data emphasize the importance of the pH of the separation matrix in detecting certain mutations by SSCP.Human Mutation 02/1999; 13(6):458-63. · 5.21 Impact Factor
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ABSTRACT: We developed mobility shift analysis of single-stranded DNAs on neutral polyacrylamide gel electrophoresis to detect DNA polymorphisms. This method follows digestion of genomic DNA with restriction endonucleases, denaturation in alkaline solution, and electrophoresis on a neutral polyacrylamide gel. After transfer to a nylon membrane, the mobility shift due to a nucleotide substitution of a single-stranded DNA fragment could be detected by hybridization with a nick-translated DNA fragment or more clearly with RNA copies synthesized on each strand of the DNA fragment as probes. As the mobility shift caused by nucleotide substitutions might be due to a conformational change of single-stranded DNAs, we designate the features of single-stranded DNAs as single-strand conformation polymorphisms (SSCPs). Like restriction fragment length polymorphisms (RFLPs), SSCPs were found to be allelic variants of true Mendelian traits, and therefore they should be useful genetic markers. Moreover, SSCP analysis has the advantage over RFLP analysis that it can detect DNA polymorphisms and point mutations at a variety of positions in DNA fragments. Since DNA polymorphisms have been estimated to occur every few hundred nucleotides in the human genome, SSCPs may provide many genetic markers.Proceedings of the National Academy of Sciences 05/1989; 86(8):2766-70. · 9.74 Impact Factor
Article: How sensitive is PCR-SSCP?[show abstract] [hide abstract]
ABSTRACT: Single-strand conformation polymorphism analysis (SSCP) is a rapid method for detection of minor sequence changes in polymerase chain reaction-amplified DNA. Since the first reported use of SSCP in 1989 (Orita et al., 1989), this technique has been used widely to detect mutations in oncogenes, tumor suppressor genes, and genes responsible for genetic diseases. Published mutations that have been detected using this technique include base substitutions, small insertions and deletions, and rearrangements. This technique has also been applied for the detection of DNA polymorphisms at various loci of the human genome (reviewed by Hayashi, 1991; Hayashi, 1993). However, many factors can influence the sensitivity of SSCP, and its optimization is highly empirical. In this review, we estimate the percentage of mutations that can be detected by this technique under various controlled conditions, and describe some critical elements affecting sensitivity.Human Mutation 02/1993; 2(5):338-46. · 5.21 Impact Factor