Capillary electrophoresis (CE) is an effective tool for the separation of a variety of compounds and materials and is used in the medical and scientific communities.⁰¹ CE is also widely used in the forensic science community in areas such as gunshot residue analysis, explosive analysis, drug analysis, and pen inks analysis.⁰² The focus of this module is routine forensic DNA analysis by CE, which was first introduced in the mid 1990's. It is important to realize that CE is now a well-validated procedure that meets the requirements of Frye, Daubert, and the Quality Assurance Standards for Forensic DNA Analysis.

A comparison of some features of capillary and slab-gel electrophoresis is presented in the table below.

CE methods can provide quantitative information. For example, forensic analysis of illicit drugs can employ CE methods to determine the quantity of a controlled substance in a sample. The use of CE in forensic DNA analysis provides some quantitative information on the components of an amplified DNA mixture. This does not necessarily represent quantitative differences in the original example because preferential amplification during the PCR process can affect the proportions of detectable DNA.

One major disadvantage of CE is the throughput. Electric fields used with CE instruments are considerably higher (~300V/cm) than those used for slab gel-based instruments (~10V/cm), resulting in faster run times. However, the single-capillary ABI Prism^® 310 Genetic Analyzer can analyze only one sample at a time. In contrast, many slab-gel methods allow numerous samples to electrophorese simultaneously, allowing greater throughput even though the electrophoresis time is approximately twice as long as that in CE.

The development of capillary array electrophoresis (CAE) instruments, which allow for multiple samples to be run in parallel, resulted in throughput capabilities equal to or surpassing that of slab-gel methods.

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