Deletion mapping and paternal origin of a Mexican AMELY negative male

The amelogenin represents the gender marker most widely used for human identification and biomedical purposes. However, some failures in sex-typing have been observed globally. In this study, we could approximate the population frequency of AMELY negative males in 1230 individuals from five states of Mexico (0.081%). For the sole AMELY negative male detected, we constructed a deletion map by means of 10 markers (7 STS and 3 Y-STRs). This allowed classifying the case into the most common category (Class I deletion), according to the nomenclature proposed by Jobling et al. (2007). Interestingly, the Mexican sample was R1a1(∗), a Y-chromosome haplogroup non-previously reported for AMELY negative cases. The geographic distribution of R1a1(∗), and the Y-STR haplotype similarity with a reported case from Slovenia, suggests an Eastern-Europe paternal origin for this case from Mexico. To our knowledge, this is the first report in Latin America that implies a low population frequency and European paternal origin of AMELY negative cases.