DNA analysis of family members with deletion in Yp11.2 region containing amelogenin locus

For personal identification of two male bodies discovered at the scene of a fire, autosomal and Y chromosomal STR of the two cadavers and of two living male relatives were genotyped. The four males were incorrectly typed as female due to the lack of the amelogenin Y homolog, whereas all loci of Y-STR except for DYS458 were successfully genotyped. Because PCR of Y-specific amelogenin (AMELY) and DYS458 loci failed to amplify target products when using additional primer sets, it was concluded that deletion in the Yp11.2 region containing the loci of AMELY and of DYS458 on the Y chromosome, rather than mutation in the annealing region of the primer sets, had occurred. Investigation using Y-specific markers showed the deletion extending approximately 2.56 Mb in the Yp11.2 region. The variety of deletion sizes and Y-STR haplotypes among AMELY negative males presented to date suggests that the mutation of the Yp11.2 region occurs independently in different ethnic groups. A study on the frequency of the AMELY deletion in the Japanese population would be helpful for future criminal investigation.