In Chapter 12, we discussed the advantages of capillary electrophoresis due to its capability for automated injection, separation, and detection of samples. However, one of the major disadvantages of single capillary instruments is that sample throughput is limited because samples are processed sequentially rather than in parallel as on a gel. Parallel CE separations may be performed though by placing a number of capillaries next to each other to form a capillary array electrophoresis (CAE) system. Each capillary in the array then would be analogous to a lane of a gel, although without the problems of lane tracking on the gel.
In 1999, two capillary 96-array electrophoresis systems became commercially available: the ABI 3700 from Applied Biosystems (Foster City, CA) and the MegaBACE from Molecular Dynamics/Amersham Pharmacia Biotech (Sunnyvale, CA). These instruments were developed to meet the large-scale sequencing needs of the Human Genome Project. Both the ABI 3700 and MegaBACE instruments have 96 capillaries in parallel and are capable of sequencing more than 500 nucleotides in each capillary every two or three hours. These CAE instruments are capable of analyzing more than 1000 samples every 24 hours and have been applied to high-throughput processing of forensic DNA database samples. The literature contains several published reports demonstrating effective STR typing with capillary array electrophoresis instruments (Wang et al. 1995, Mansfield et al. 1996, 1998, Gill et al. 2001, Sgueglia et al. 2003).
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