The interpretation of SSCP results is simple. What one is looking for is a variation in the SSCP banding patterns among different samples. The variation can be a band shift or some additional bands. Depending on such factors as gel composition and electrophoresis temperature, the variation can be very conspicuous in some cases, but subtle in other cases.
Subtle changes in banding patterns may be difficult to recognize if the bands are very broad as in the case of sample overloading, which should thus be avoided. Clean and specific PCR products are also a prerequisite for easy interpretation of banding patterns. Representative samples with distinctive SSCP patterns can then be sequenced to define the underlying sequence variations. In this way, initially unknown sequence variations can be identified and defined.
Alternatively, known sequence variations can be correlated with specific banding patterns if SSCP is used as a diagnostic method. If the DNA samples are from diploid organisms like human beings, then the banding patterns are additive. In other words, if one type of homozygote (e.g., A/A) has a particular pattern and another type of homozygote (e.g., G/G) has another pattern, then the heterozygote (A/G) has a banding pattern that is the summation of these two patterns.
However, this additive property is not applicable to the analysis of the X chromosome in human males, DNA from mitochondria or chloroplasts (except in heteroplasmy), and DNA from bacteria (haploid organisms).