PCR for the detection of minority DNA populations

Although the polymerase chain reaction (PCR) is generally believed to be capable of detecting a single target DNA molecule, it is important to note that there are essentially two different types of "low copy number PCR." The first type involves the amplification of an isolated DNA target, such as single sperm analysis (1) and preimplantation embryo diagnosis (2) (see Chapter 20). In these examples the PCR target is surrounded by PCR buffer and there is no background DNA to interfere with the reaction. In the second category, the DNA target is surrounded by an excess of background DNA molecules. This is a common situation in many clinical scenarios from many different research and diagnostic discipilines, such as the molecular monitoring following bone marrow transplantation (see Chapter 15) and noninvasive prenatal diagnosis (see Chapters 21 and 22). This chapter reviews the theoretical and practical considerations of minority DNA population detection by PCR.