Primer Extension Preamplification (PEP) of Single Cells: Efficiency and Bias
Single-cell PCR (polymerase chain reaction) is a powerful method for determining the genetic properties of an individual cell.1 However, since only one copy of the genome is present in a single cell, the number of genetic analyses that can be performed is significantly limited. Therefore, strategies have been developed to amplify the whole genomic content of single or small pools of cells prior to the analysis of specific loci.1 One of these methods is called primer extension preamplification (PEP). It increases the amount of template DNA by unspecifically amplifying the whole genome using random primers in a PCR reaction.2 Since its inception, the PEP technique has been used for the analysis of single spermatozoa,2 single or few blastomeres,3 and tumor cells,4 (as well as fetal cells which have been enriched from the maternal circulation)5 and in conjunction with comparative genomic hybridization (see Chapter 34 by Dagan Wells and Mercedes Garcia Bermudez). However, whole genome amplification by PEP is not without pitfalls, the most important being allelic loss.6 Consequently, this method is rarely used for clinical applications.