UC Davis

An allele frequency database can be used to determine how common or rare an allele or a combination of alleles is. Allele frequencies can be used to determine random match probabilities in forensic cases, paternity testing, mass disasters, cold cases and missing persons investigations. The purpose of this study is to create a population database that represents the 6.7 million people estimated to be living in El Salvador. We determined the allele frequencies of the 21 loci of the GlobalFiler™ PCR Amplification Kit for the El Salvador population. The DNA samples were collected by Pro-Busqueda, a non-profit organization in El Salvador from unrelated volunteers to be representative of the country. We received 762 DNA samples, extracted DNA from 502 samples, quantified, amplified and separated DNA fragments by size and determined the alleles from 360 samples, genotyped and generated DNA profiles for 317 samples. We used STRAF, an online tool to calculate allele frequencies, test loci for Hardy-Weinberg equilibrium and linkage disequilibrium, determine if there is population substructure, as well as calculate relevant forensic parameters such as the power of discrimination (PD or 1-PM), match probability (PM), polymorphism information content (PIC), the power of exclusion (PE) and typical parental index (TPI). We determined the 21 autosomal Globalfiler™ loci used for the database are in Hardy-Weinberg equilibrium and, therefore, can be used for genotyping probabilities. The loci are also in linkage equilibrium, are independent from one another and therefore the product rule can be used to calculate random match probabilities and likelihood ratios. We used GenePop v 4.7.5 to perform a Fisher’s Exact G-Test for population differentiation within the country. After validating the allele frequency database, we compared it to the United States Hispanic allele frequency database. We determined that the El Salvador and the United States Hispanic databases were significantly different from one another and cannot be used interchangeably. The allele frequency database generated from this study will the first to contain allele frequencies from 13 of the 14 departments in the country. This allele database will be a useful tool in helping identify and reunite victims of the country’s civil war with family members.