Genetic diversity of Mexican-Mestizo populations using 114 INDEL polymorphisms

Abstract

We analyzed 154 unrelated individuals from four Mexican-Mestizo (admixed) populations with 114 INDEL loci; 68 of them have been proposed for forensic use and 46 constitute Ancestry informative markers (AIM-INDELs). Allele frequencies and genetic diversity were calculated for all these loci. The Hardy-Weinberg equilibrium was demonstrated for 113 loci, excepting the 360 locus (AIM-INDEL). Linkage disequilibrium (LD) test only showed departure for the HLD45/HLD64 combination among the 68 INDEL loci. Random match probability (RMP), power of discrimination (PD), and power of exclusion (PE) for the 68 INDELs are reported. The combined PD and PE were similar to those from STR systems: >0.999999999999999 and 0.999996089797308, respectively; whereas the RMP was <5.54×10−22. AMOVA and structure analyses showed moderated interpopulation differentiation, which support the establishment of a national DNA database for forensic casework interpretation in Mexico when using these 68 INDELs. The ancestral proportions assessed from 46 AIM-INDELs displayed differences mainly for the Native American (0.462–0.702) and European (0.487–0.254) ancestries, while the African was relatively homogeneous (0.028–0.052).