A microsatellite marker within the duplicated D16S79 locus has a null allele; significance for linkage mapping

The dinucleotide repeat 16AC66f3 was characterised from D16S79A within a duplicated section of 16p13.11, which is duplicated on all normal chromosome 16's. This marker has a common null allele caused by polymorphism within one of the primer sites. A redesigned primer overcame this problem; however, this allowed amplification of two dinucleotide repeats, at D16S79A and D16S79B, with an overlapping and uninterpretable distribution of alleles. Thus, the 16AC66F3 marker with a null allele is potentially useful for linkage mapping, as it avoids the ambiguity associated with the genotyping of homologous AC repeats at this duplicated locus. The distribution of additional D16S79 RFLPs flanking FRA16A is clarified.