This Forensic Anthropological tool can three functions; two general functions: the ability to enter genotypes of an individual at multiple SNPs and calculate likelihoods of that multisite genotype in each of several populations, and an eye color prediction function specific to a PISNP panel. These functions are possible for three types of SNP panels, IISNPs, AISNPs, and PISNPs.
1) For Individual Identification SNPs (IISNPs) this implementation provides examples and the ability to calculate match probabilities for user-specified genotypes. Two different published panels of IISNPs can be used to determine the probability of the user-specified genotype in each of several populations that have allele frequencies available for all SNPs in the panel.
2) For Ancestry Inference SNPs (AISNPs) this implementation provides examples and ability to calculate relative likelihoods of ancestry from different populations for user-specified genotypes. Two published AISNP panel can be used as well as a provisional panel of 39 SNPs assembled specifically to test this functionality.
3) For Phenotype Informative SNPs (PISNPs) this implementation provides ability to predict eye color for user-specified genotypes. One published PISNP panel can be used to test the eye color prediction functionality which is based on a published formula.
The interpretation of results likelihoods are calculated by maximum likelihood estimates because they are based on the maximum likelihood estimates for allele frequencies for independent loci. However, those allele frequency estimates have associated standard errors that vary inversely as the sample sizes. Thus, there are greater uncertainties for the likelihoods calculated for populations with small sample sizes. One of the results is that rankings among populations with very similar skeletal system structures and formations.
The images above are screenshots of the results of skeletal DNA traits that were compiled from the previous blog posts based on the first case. It is clear that he is a part of the Homo sapiens sapiens humanoid ladder and is a male between the ages of 39.48-39.49 (theoretically 39 years-old). What these images represent is that many of the ancestral backgrounds share common DNA genomes, however, one ancestral background will stand out from the rest. In this case, however, the young male that I was trying to identify contains Mesoamerican characteristics based on the Populations/Samples and genetic detail. This suggests that the young male originated from South of the United States where Mesoamerica is located as well as overlapping over to the country of Mexico and Belize.
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