Single-cell whole genome amplification (WGA) PCR is an application of PCR technology that amplifies the nucleic acid in a single cell rather than in a tissue sample or a pool of homogenous cells. While single-cell amplification has been recognized almost as long as PCR technology itself, it was not considered a very efficient technique due to technical limitations such as the lack of available primers and efficient cell-lysing techniques, which only allowed a small quantity of cell DNA to be amplified. However, advances in primer technologies and lysing techniques have led to more reliable and accurate whole cell genome amplification.

Isolation is the first step in single-cell WGA and can be accomplished by numerous established cell-sorting methods, including cytometry. The two most widely used WGA methods are primer extension PCR (PEP) and degenerative oligonucleotide primer (DOP). PEP was one of the first WGA methods developed and uses a high number of PCR cycles at low temperatures. Although much of a genome can be probed and amplified by this method, some segments of the DNA, especially those with repeating sequences, tend to be excluded. DOP is a more established technique. As its name suggests, it uses degenerative oligonucleotide primers and Taq polymerases to bind at low temperatures, followed by cycles with high annealing temperatures.

Applications for single-cell WGA range from drug discovery, to cancer research, to diagnostics. Prenatal research and diagnostic screening are among the most common applications. Screening for a variety of developmental and neurological genetic disorders is heavily dependent on single-cell WGA.

In general, single-cell WGA experiments are performed with an RT-PCR utilizing specific WGA PCR kits. Sigma-Aldrich (in association with Rubicon Genomics), QIAGEN NV and GE Healthcare are the major providers of these kits. GenomePlex WGA4 kits from Sigma-Aldrich are among the few kits on the market specifically designed for single-cell WGA. Most other kits can be used for either single cells or, more commonly, pools of cells. QIAGEN manufactures the REPLI-g kits for WGA. In addition to the REPLI-g mini kits, QIAGEN also offers the REPLI-g mitochondrial DNA kit to be used with human mitochondrial DNA, and the REPLI-g screening kit designed for high-throughput applications. GenomiPhi, made by GE Healthcare, is another WGA kit, which uses strand displacement amplification and Phi29 bacteriophage to amplify single or double-stranded linear DNA.

The single-cell WGA market is expected to grow in the low double digits in the next few years. In addition to kit sales, many contract and independent research organizations, along with kit manufacturers, have started to provide WGA services, whose customers include pharma, biotech, government, and clinical and hospital laboratories, among others.