Discovery and identification of new D13S317 primer binding site mutations

During the course of conventional testing of CODIS standards at the Alabama Department of Forensic Sciences, a sample with a heterozygous null genotype at D13S317 was discovered using the PowerPlex® 1.1 kit (Promega, Madison, WI). The loss of both alleles was confirmed when the sample was amplified using PowerPlex® 1.2 primers and resulted in a 9, 10 genotype at this locus. To determine the cause of the silent alleles, the ADFS designed D13S317 primers which encompassed the PowerPlex 1.1 D13S317 primer binding sites and sequenced the region. Both alleles showed the presence of two substitutions (T → A and G → T) at positions 1 and 5 (5′ → 3′) of the reverse primer (positions 196 and 200 of the sequence in GenBank accession number G09017). Since the mutations were identical on both alleles, they may be assumed to be of ancestral origin.