Automated genotyping for accurate assignment of the (AT)(x)N-z(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 c ontrol region is the (AT)(x)N-z(AT)(y) motif, which comprises two short tan dem repeats of dinucleotide (AT) interrupted by a short variable DNA sequen ce (N-z). 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 genot yping with direct sequence analysis to demonstrate that it is possible to o vercome this problem; the approach should be applicable for the investigati on of other sequence repeats of this nature.