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Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905

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The development of technically simple and reliable methods to detect sequence variations in specific genes is becoming more important as the number of genes associated with specific diseases grows. DNA sequencing is considered the "gold standard" for characterization of specific nucleotide alteration(s) that lead to genetic disease. Although sequencing was long considered too cumbersome, expensive, and operator-dependent for use in the clinical laboratory, a combination of clinical need and improved technology has brought automated DNA sequencing into routine clinical use. Sequencing technology is now firmly entrenched in the clinical molecular diagnostics laboratory, but it remains too expensive and time-consuming for all of the laboratory’s mutation-detection needs. Several PCR-based mutation-detection strategies can be used to identify both characterized and uncharacterized mutations and sequence variations.

The degree of allelic heterogeneity, or the number of different disease-causing mutations in a single gene, influences the method used for mutation detection. For diseases that exhibit no or limited heterogeneity (such as sickle cell anemia or factor V Leiden), assay systems designed to detect specific mutations are appropriate. These types of strategies are also appropriate for disorders in which allelic heterogeneity is high but only a limited set of mutations are typically analyzed, such as cystic fibrosis. For disorders in which the mutational spectrum is wide (e.g., mismatch-repair genes in hereditary nonpolyposis colon cancer), a scanning method is needed. A scanning method is also appropriate for analysis of newly identified disease genes for which there is little or no information regarding the number of disease-causing mutations.

A wide array of methods and technologies have been proposed for detection of specific mutations, and many of them are in use in clinical and research laboratories worldwide. Examples of the various technologies for specific-mutation analysis include restriction enzyme digestion of PCR-amplified DNA, with or without the introduction of differential . . . [Full Text of this Article]