Browsing by Subject "Gene Frequency"
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Item Ancestry Informative Markers Tailored to Hispanic Populations(2020-05) Setser, Casandra H.; Cross, Deanna S.; Planz, John V.; Barber, Robert C.; Phillips, Nicole R.; Krishnamoorthy, Raghu R.Hispanic populations are highly heterogeneous despite being grouped together as a conglomerate population; this makes an accurate panel of ancestry informative markers (AIMs) especially important for human identification. In Chapter 2, the Genomic Origins and Admixture in Latinos (GOAL) dataset containing 494,886 SNPs was used for SNP ascertainment. Utilizing a country attributable variant of Wright's FST, 234 SNPs were selected for biogeographic ancestry (BGA) determination by tailoring each SNP to genetic differentiation of specific populations. Accuracy of BGA prediction was tested using multinomial logistic regression (MLR) and as few as 55 SNPs were robust to 90% for all populations studied. The panel of 234 SNPs was compressed by 65.8% to 80 SNPs by decreasing the influence of Honduras and the Dominican Republic SNPs with high country attributable mean FST values in favor of additional SNPs for Colombia, Cuba, and Puerto Rico; this balanced small panel size with classification accuracy. In Chapter 3, the Setser80 Hispanic AIMs panel was tested against the panels of 128 SNPs developed by the Seldin group and 55 SNPs developed by the Kidd group using STRUCTURE, PCA, a naive Bayesian classifier and MLR. In STRUCTURE, the Setser80 was able to distinguish Honduras, the Dominican Republic, and Colombia at K=4, where the Seldin and Kidd panels were optimized at K=3 and distinguished only Honduras and the Dominican Republic; similar results were obtained by PCA. The GOAL dataset was combined with the Admixed American super-population from the 1000 Genomes Project to test the panel on an expanded dataset of seven populations. Overall, the Setser80 had superior results to the Seldin and Kidd panels with 91.5% accuracy by naive Bayesian classifier and 93.2% by MLR. As an indication of its portability, the Setser80 had accuracies of >98% for Peru and >80% for Mexicans living in Los Angeles, which were not involved in SNP ascertainment. Given its accuracy and lack of overlap, the Setser80 may supplement existing panels for more granular Hispanic BGA determination. In Chapter 4, the application of allele frequencies to forensic genetics, genealogy, and clinical genetics are discussed as well as future directions and ethical considerations.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.