Efficiency and cost effectiveness: PAGE-SSCP versus MDE and Phast gels for the identification of unknown beta thalassaemia mutations.

Background: Prenatal diagnosis for β thalassaemia has proved to be very effective in preventing the birth of an affected child and hence in controlling the disease. The success of prenatal diagnosis depends on the delineation of the underlying mutations in the population at risk. Each population carries a limited number of frequent defects (89–91%) and a variable number of rare alleles (4–5%), whereas 2–3% of alleles remain uncharacterised. To offer prenatal diagnosis when the parental mutation is unknown, the application of a non-specific detection method (such as single stranded conformational polymorphism (SSCP)) to localise the mutation, followed by direct sequencing of the amplified gene sequence, is required. With this objective in mind, this study was designed to devise the best protocol and system of SSCP for the rapid screening of unknown mutations in the β globin gene. Methods: To detect mutations in this disease, three different systems—Phast gels, MDE gels, and polyacrylamide gels—were used under varying conditions. Results: Polyacrylamide gels were found to be the most efficient, both in terms of resolution and cost. Conclusion: Polyacrylamide gels are the most rapid, efficient, reliable, and cost effective means for DNA mutation analysis of the β globin gene.