Multiple-allele single nucleotide polymorphisms (SNPs) are potentially useful for forensic DNA analysis
as they can provide more discrimination power than normal binary SNPs. In addition, the presence in a
profile of more than two alleles per marker provides a clearer indication of mixed DNA than assessments
of imbalanced signals in the peak pairs of binary SNPs. Using the 1000 Genomes Phase III human variant
data release of 2014 as the starting point, this study collated 961 tetra-allelic SNPs that pass minimum
sequence quality thresholds and where four separate nucleotide substitution alleles were detected.
Although most of these loci had three of the four alleles in combined frequencies of 2% or less, 160 had
high heterozygosities with 50 exceeding those of ‘ideal’ 0.5:0.5 binary SNPs. From this set of most
polymorphic tetra-allelic SNPs, we identified markers most informative for forensic purposes and
explored these loci in detail. Subsets of the most polymorphic tetra-allelic SNPs will make useful
additions to current panels of forensic identification SNPs and ancestry-informative SNPs. The 24 most
discriminatory tetra-allelic SNPs were estimated to detect more than two alleles in at least one marker
per profile in 99.9% of mixtures of African contributors. In European contributor mixtures 99.4% of
profiles would show multiple allele patterns, but this drops to 92.6% of East Asian contributor mixtures
due to reduced levels of polymorphism for the 24 SNPs in this population group