Automated genotyping for accurate assignment of the (AT)xNz(AT)y motif within the beta-globin locus control region-hypersensitive site 2.

Within the core region of hypersensitive site 2 of the beta-globin locus control region is the (AT)xNz(AT)y motif, which comprises two short tandem repeats of dinucleotide (AT) interrupted by a short variable DNA sequence (Nz). The motif is usually investigated using direct sequence analysis of specifically amplified DNA, but without family studies, phase alignment of the two tandem repeats, occasionally confounded by a variable N sequence in between, can be erroneous. We combined the technique of automated genotyping with direct sequence analysis to demonstrate that it is possible to overcome this problem; the approach should be applicable for the investigation of other sequence repeats of this nature.