Browsing by Subject "Genetics, Population"
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Item Establishing an STR allele frequency database for the Paraguayan population(2018-05) Giuffrida, Stephanie M.; Planz, John V.; Warren, Joseph E.; Phillips, Nicole R.; Cunningham, J. ThomasThis project determined whether the loci included in the Athos PCR Directa para Identificacao Humana Amplification and AmpFlSTR[R] Identifiler[R] PCR Amplification Kits are suitable for establishment of an STR allele frequency database representative of the Paraguayan population. Allele frequencies for the 21 STR loci included in the Athos PCR Directa para Identificacao Humana Amplification Kit were calculated for 200 individuals in the Paraguayan population. Allele frequencies for the 15 STR loci included in the AmpFlSTR[R] Identifiler[R] PCR Amplification Kit were also calculated for 300 individuals in the Paraguayan population. Performance of these loci was determined by testing the population for Hardy-Weinberg Equilibrium, testing for Linkage Disequilibrium between the loci in the kits, and calculating Power of Discrimination, Power of Exclusion, and Mean Power of Exclusion. Comparability between the common loci included in the two PCR kits was also tested. Results of these tests determined that the Athos PCR Directa para Identificacao Humana Amplification and AmpFlSTR[R] Identifiler[R] PCR Amplification Kits are both suitable for use in an STR allele frequency database. Additionally, the common loci contained in the two PCR kits are comparable, and the populations can be combined to create one database.Item Genetic assessment reveals no population substructure and divergent regional and sex-specific histories in the Chachapoyas from northeast Peru(PLOS, 2020-12-31) Guevara, Evelyn K.; Palo, Jukka U.; Oversti, Sanni; King, Jonathan L.; Seidel, Maria; Stoljarova, Monika; Wendt, Frank R.; Bus, Magdalena M.; Guengerich, Anna; Church, Warren B.; Guillen, Sonia; Roewer, Lutz; Budowle, Bruce; Sajantila, AnttiMany native populations in South America have been severely impacted by two relatively recent historical events, the Inca and the Spanish conquest. However decisive these disruptive events may have been, the populations and their gene pools have been shaped markedly also by the history prior to the conquests. This study focuses mainly on the Chachapoya peoples that inhabit the montane forests on the eastern slopes of the northern Peruvian Andes, but also includes three distinct neighboring populations (the Jivaro, the Huancas and the Cajamarca). By assessing mitochondrial, Y-chromosomal and autosomal diversity in the region, we explore questions that have emerged from archaeological and historical studies of the regional culture (s). These studies have shown, among others, that Chachapoyas was a crossroads for Coast-Andes-Amazon interactions since very early times. In this study, we examine the following questions: 1) was there pre-Hispanic genetic population substructure in the Chachapoyas sample? 2) did the Spanish conquest cause a more severe population decline on Chachapoyan males than on females? 3) can we detect different patterns of European gene flow in the Chachapoyas region? and, 4) did the demographic history in the Chachapoyas resemble the one from the Andean area? Despite cultural differences within the Chachapoyas region as shown by archaeological and ethnohistorical research, genetic markers show no significant evidence for past or current population substructure, although an Amazonian gene flow dynamic in the northern part of this territory is suggested. The data also indicates a bottleneck c. 25 generations ago that was more severe among males than females, as well as divergent population histories for populations in the Andean and Amazonian regions. In line with previous studies, we observe high genetic diversity in the Chachapoyas, despite the documented dramatic population declines. The diverse topography and great biodiversity of the northeastern Peruvian montane forests are potential contributing agents in shaping and maintaining the high genetic diversity in the Chachapoyas region.Item Mutual Independence of Loci in databases of Multi-locus Genotypes: Application in Human Identification and Population Genetics(2020-12) Song, Bing; Planz, John V.; Woerner, August E.Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested for linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly software is necessary for testing and assessing the global linkage disequilibrium among mixed genetic data. This study describes a software package for testing the mutual independence of mixed genetic datasets. The new R package "mixIndependR" calculates basic genetic parameters like allele frequency, genotype frequency, heterozygosity, and Hardy-Weinberg equilibrium by mutual independence from population data, regardless of the type of markers, such as simple nucleotide polymorphisms, short tandem repeats, insertions and deletions, and any other genetic markers. A novel method of assessing the dependence of mixed genetic panels is developed in this study and functionally analyzed in the software package. By comparing the observed distribution of two common summary statistics (the number of heterozygous loci [K] and the number of share alleles [X]) with their expected distributions under the assumption of mutual independence, the overall independence is tested. The package "mixIndependR" is compatible to all categories of genetic markers and detects the overall non-random associations. Compared to pairwise disequilibrium, the approach described herein tends to have higher power, especially when the numbers of markers are large. With this package, more multi-functional genetic panels can be developed, like mixed panels with different kinds of markers. In population genetics, the package "mixIndependR" makes it possible to discover more about admixture, natural selection, genetic drift, and population demographics, as a more powerful method of detecting LD. Moreover, this new approach can optimize variants selection in disease studies and contribute to panel combination for treatments in multimorbidity. Application of this approach in real data is expected in the future, and this might bring a leap in the field of genetic technology. The R package "mixIndependR", is available on the Comprehensive R Archive Network (CRAN) at: https://cran.r-project.org/web/packages/mixIndependR/index.html