Browsing by Subject "single nucleotide polymorphisms"
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Item Automatable Virtual Array Screening System for Rapid Analysis of Mitochondrial DNA Polymorphism(2002-05-01) Campbell, Rowan Stewart; Arthur J. Eisenberg; Bruce Budowle; John PlanzCampbell, Rowan Stewart, Automatable Virtual Array Screening System For Rapid Analysis of Mitochondrial DNA Polymorphism. Doctor of Philosophy (Biomedical Sciences), May, 2002, 156 pp., 11 tables, 48 illustrations, bibliography, 96 titles. The goal of this research project was to develop alternative methods to traditional forensic mtDNA sequence analysis. Conventional forensic mtDNA analysis requires the direct sequencing of Hypervariable Region I and Hypervariable Region II in both the forward and reverse directions. This method is time consuming, labor intensive and expensive. Two methods for determining mtDNA haplotypes through the direct interrogation of Single Nucleotide Polymorphisms with HVI and HVII have been developed. A Sequence Specific Oligonucleotide Hybridization assay was developed on the Luminex 100™ flow cytometer, as well as a Single Base Extension assay developed for the ABI Prism® 310 Genetic Analyzer. The SNP typing of mtDNA sequences can provide a significant benefit in many forensic and human identification cases. The reassociation of mass disaster remains, mass grave analysis, and the screening of large numbers of crime scene samples are examples of their potential application. Their inclusion as a standard screening tool would be high beneficial since more extensive DNA analysis would be reserved for those samples that possess the greatest evidentiary value. In a blind study of 50 samples, the Sequence Specific Oligonucleotide Hybridization assay incorrectly identified the mtDNA haplotypes in 7 samples, whereas the Single Base Extension assay correctly identified each of the SNP positions interrogated. The SNaPshot™ primer extension assay was approximately 20-25 times more sensitive than the standard sequencing approach. This would suggest that this system could be a viable alternative to sequence analysis when samples are limited, as well as being more robust in detection and typing of heteroplasmic sites. A statistical evaluation of the SNP panels revealed that the genetic diversity estimated for the 50 Southwestern Hispanic samples tested was 0.9624 for the primer extension array and 0.9559 for the hybridization-based array. The probability of two randomly selected individuals from a population group having the same mtDNA haplotype was 0.0568 for the Single Base Extension assay and 0.0632 for the Sequence Specific Oligonucleotide Hybridization assay. A forensic mtDNA SNP array consisting of the positions evaluated in this study could provide a reasonable alternative to the full sequencing of the HVI and HVII regions.Item Highly Informative Short Tandem Repeat Markers for Enhanced DNA Mixture Deconvolution(2018-08-01) Novroski, Nicole M. M.; Bruce Budowle; Robert C. Barber; Bobby L. LaRueDNA typing in forensic genetics relies on amplification of short tandem repeat (STR) markers using the polymerase chain reaction (PCR), subsequently allele sizes are determined for each locus, using capillary electrophoresis (CE) and fluorescent detection. The resulting profiles are compared to reference sample profiles or to query existing profiles, such as those stored in the FBI Combined DNA Index System, to develop investigative leads to help solve crimes. The success of commercial STR kits to facilitate analysis of challenging samples has led to a demand to analyze increasingly complex DNA mixtures. Low quantity/low quality DNA samples have become commonplace in casework, but the interpretation of the resultant DNA profiles continues to remain challenging. Massively parallel sequencing (MPS) for typing forensically-relevant STR loci has dramatically enhanced the ability to identify allele diversity due to sequence variation within STR repeat and flanking regions. Sequence variation within the currently utilized STR loci for forensic genetic analysis is quite large. However, recent studies have demonstrated that some of the current core CODIS loci are devoid of repeat and/or flanking region sequence variation, minimizing the relative information via MPS for these STRs. Thus, novel STRs with increased sequence variation should be sought to facilitate mixture deconvolution. The primary goal of this research was to identify and characterize STR genetic variation, which in turn would allow for the development of a novel panel of highly polymorphic STR markers (referred to as the STR DECoDE panel; STR DNA EnhanCed DEconvolution panel) that is capable of deconvolving simple to complex DNA mixture samples better than current systems. A list of candidate STRs was generated by mining the 1000 Genomes Project using the criteria of 1) a repeat size of at least 4 nucleotides; 2) a minimum of 80% locus heterozygosity; and 3) generally an allele length spread of 10 nominal alleles or less. A preliminary panel of 248 candidate markers was designed, and a bioinformatics pipeline for MPS was created and implemented to assess the analytical performance and biological properties of each STR. The STR DECoDE panel is comprised of 73 of the 248 STRs that displayed the highest heterozygosity. This panel was compared to the current core CODIS loci regarding an ability to resolve in silico two-person mixtures from 443 population samples comprising three US populations. Additionally, each of the 73 loci was extensively characterized for its underlying genetic variation, and population genetic analyses were performed. The results of this dissertation research indicate that the STR DECoDE panel improves upon current mixture deconvolution efforts by employing markers that allow for better allele resolution of component contributors in a mixed DNA sample. The DECoDE panel loci offer a substantial degree of diversity compared with the current core CODIS STR loci used for forensic identity typing. In turn, use of this panel could facilitate complex downstream statistical modeling (probabilistic genotyping) and subjective interpretation that are currently utilized for analysis of DNA mixture samples in forensic laboratories. Finally, integration of DECoDE STR loci into current multiplexes will allow the field of forensic genetic investigation to increase the number of resolved genotypes in mixed samples being compared to reference and suspect profiles, and expand the DNA database by increasing the number of samples uploaded. The benefit to society from this revolutionary application will be an increase in the number of investigative leads and the overall resolution of more crimes.Item skater: an R package for SNP-based kinship analysis, testing, and evaluation(F1000 Research Ltd., 2022-01-07) Turner, Stephen D.; Nagraj, V. P.; Scholz, Matthew; Jessa, Shakeel; Acevedo, Carlos; Ge, Jianye; Woerner, August E.; Budowle, BruceMotivation: SNP-based kinship analysis with genome-wide relationship estimation and IBD segment analysis methods produces results that often require further downstream process- ing and manipulation. A dedicated software package that consistently and intuitively imple- ments this analysis functionality is needed. Results: Here we present the skater R package for SNP-based kinship analysis, testing, and evaluation with R. The skater package contains a suite of well-documented tools for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing IBD segment data. Availability: The skater package is implemented as an R package and is released under the MIT license at https://github.com/signaturescience/skater. Documentation is available at https://signaturescience.github.io/skater.