A variety of gene arrangements can be detected using dsDNA binding dyes. Our laboratory has some experience in the detection of T-cell receptor (TCR) genes. During their passage through the thymus, T-cell precursors rearrange their TCR genes. This step requires the excision of segments of DNA, the ends of which are subsequently ligated to form small circles of episomal DNA (signal and coding) referred to as T-cell receptor excision circles (TREC). The sequences remaining after recombination provide the target for the PCR detection of TREC. The point of recombination in TREC dictates the position of the primers on either side. The sequence around these allows the primers to be designed with more or less flexibility within the Tm and amplicon length limits (Ponchel et al., 2003). Similar examples include Immunoglobulin gene rearrangements, translocations (chromosome 14/18 translocation t (14:18) (q32;q21)).
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