Browsing by Subject "haplotype"
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Item Haplotype for Promega's Powerplex®Y System for Southwestern Hispanic and Asian Populations(2004-05-01) Silvis, Renee; John Planz; Arthur Eisenberg; Joseph WarrenThis project had two objectives. The primary one was to establish the haplotype frequency data for the Asian and Southwestern Hispanic populations. This involved developing Y-STR profiles for the entire sample set, establishing haplotype frequencies from the data’s allele frequencies for each of the loci interrogated. This information was then used to calculate the Power of Discrimination for the PowerPlex Y System. The secondary objective was to calculate a mutation rate for this particular Y-STR panel by analyzing established father-son pairs (each pair being one meiosis) and counting the number of differences between the pairs, noting which loci the mutations occurred in.Item Polymorphism of Y-STR haplotypes is governed by patrilineal ancestry combined with effects of male migration(2015-12-01) Nolan, Michael R.; Ranajit Chakraborty; John V. PlanzThis study examined geographic origins of Y-haplogroups and effects of migration using Y-STR haplotype databases compiled from the literature. Accuracy of haplogroup prediction was analyzed by varying the number of loci in haplotype definitions and by including rapidly mutating Y-STRs. Lastly, haplogroup diversities of populations were analyzed with respect to evolutionary history/size of populations and effects of admixture. These analyses demonstrated: a) haplotype definitions with more loci increased haplogroup prediction accuracy; b) older populations did not negatively impact haplogroup prediction; c) including rapidly mutating loci as part of the haplotype-definition had minimal impact on haplogroup prediction and inferring population clustering, but had moderate impact on Network analysis; and d) haplogroup diversities increased with male admixture.Item USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences(BioMed Central Ltd., 2022-11-20) Wang, Xuewen; Budowle, Bruce; Ge, JianyeBACKGROUND: Tandem repeats (TR), highly variable genomic variants, are widely used in individual identification, disease diagnostics, and evolutionary studies. The recent advances in sequencing technologies and bioinformatic tools facilitate calling TR haplotypes genome widely. Both length-based and sequence-based TR alleles are used in different applications. However, sequence-based TR alleles could provide the highest precision in characterizing TR haplotypes. The need to identify the differences at the single nucleotide level between or among TR haplotypes with an easy-use bioinformatic tool is essential. RESULTS: In this study, we developed a Universal STR Allele Toolkit (USAT) for TR haplotype analysis, which takes TR haplotype output from existing tools to perform allele size conversion, sequence comparison of haplotypes, figure plotting, comparison for allele distribution, and interactive visualization. An exemplary application of USAT for analysis of the CODIS core STR loci for DNA forensics with benchmarking human individuals demonstrated the capabilities of USAT. USAT has user-friendly graphic interfaces and runs fast in major computing operating systems with parallel computing enabled. CONCLUSION: USAT is a user-friendly bioinformatics software for interpretation, visualization, and comparisons of TRs.