Characterization of a novel D1S80 pseudoallele

During a D1S80 population study conducted for databasing purposes in the Ne w York City Ashkenazi Jewish population, eight out of 96 samples were typed with a band corresponding to the position of a #15 allele. In seven of the eight samples, three bands appeared. Further investigation was needed to e xplain the high frequency of an allele considered so rare that it is not in cluded in the commercially provided allelic ladder. After extraction of the putative D1S80 15-repeat amplicon band from the 6% polyacrylamide genotypi ng gel, the amplicon bands were reamplified with D1S80 primers. After retyp ing as putative 15 alleles, these samples underwent Southern hybridization with a D1S80 locus-specific probe followed by DNA sequence analysis. Sequen ce analysis revealed that these bands did not arise from true D1S80 15 alle les. However, the PCR product was of a size that fell within the allelic la dder region corresponding to the 15 band and contained end sequences with s trong homology to the D1S80 primers. An alignment search of the sequenced p roduct revealed that a portion of the amplicons contained 72% identity to a known gene. These results emphasize the importance of sequencing analysis when questions arise about the authenticity of an allele.