Determination of deleted regions from Yp11.2 of an amelogenin negative male

The use of short tandem repeat (STR) multiplexes with the incorporated gender marker amelogenin is now common practice in forensic laboratories. The amelogenin locus is encoded by two single copy genes located on Xp22.1-Xp22.3 (AMELX) and Yp11.2 (AMELY). There are differences in size and sequence between AMELX and AMELY that can be used for sex-typing tests. A sized-based difference for AMELX and AMELY is an integral part of most PCR multiplex kits that are used for DNA profiling. However, we experienced a case of a normal male being typed as female (dropout of the amelogenin Y allele) with AmpFlSTR Profiler kit, AmpFlSTR Identifiler kit and PowerPlex 16 System. Further testing with Y-STR loci using the AmpFlSTR Yfiler kit revealed an additional null at DYS458 locus in this amelogenin negative male. We examined the deleted regions using a total of 60 loci from Y-STRs, STSs (sequence tagged sites) and newly designed primer sets. Three deleted regions in Yp11.2 were seen in this sample. The sizes of these deletions were approximately 2.51 Mb, 25 kb and 834 b, respectively. The deletions did not belong to the five reported patterns in a collection of 45 deletion males from 12 populations described by Jobling et al.