Browsing by Subject "forensic genetics"
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Item A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures(MDPI, 2021-01-20) Smart, Utpal; Cihlar, Jennifer Churchill; Mandape, Sammed N.; Muenzler, Melissa; King, Jonathan L.; Budowle, Bruce; Woerner, August E.Despite the benefits of quantitative data generated by massively parallel sequencing, resolving mitotypes from mixtures occurring in certain ratios remains challenging. In this study, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated. The method was first tested on 270 in silico two-person mixtures varying in mixture proportions. An assortment of external reference panels containing information on haplotypic variation (from similar and different haplogroups) was leveraged to assess the effect of panel composition on phasing accuracy. Building on these simulations, mitochondrial genomes from the Human Mitochondrial DataBase were sourced to populate the panels and key parameter values were identified by deconvolving an additional 7290 in silico two-person mixtures. Finally, employing an optimized reference panel and phasing parameters, the approach was validated with in vitro two-person mixtures with differing proportions. Deconvolution was most accurate when the haplotypes in the mixture were similar to haplotypes present in the reference panel and when the mixture ratios were neither highly imbalanced nor subequal (e.g., 4:1). Overall, errors in haplotype estimation were largely bounded by the accuracy of the mixture's genotype results. The proposed framework is the first available approach that automates the reconstruction of complete individual mitotypes from mixtures, even in ratios that have traditionally been considered problematic.Item Expert Systems for High Throughput Analysis of Single Source Samples: A Comparison of GeneMarker® HID v1.71 and GeneMapper® ID v3.2 and Validation of GeneMapper® ID v3.2(2009-05-01) Phillips, Nicole R.; Planz, John V.The NIJ Convicted Offender DNA Backlog Reduction Program has helped laboratories in the U.S. to enhance throughput of single source sample processing technologies and methods with the adoption of robotics, single amplification kits and multicapillary instruments. With these advances, the bottleneck in forensic laboratories today is data analysis. Commercially available expert systems offer automated sizing and analysis, expediting the process of DNA data analysis. The University of North Texas Center for Human Identification Research & Development Laboratory has been contracted for several population database construction projects, requiring a high throughput approach for genetic processing of the single source samples. Summarized in this report are the comparison of two expert systems and the internal validation of a GeneMapper® ID v3.2 (Applied Biosystems, Foster City, CA) as an expert system. GeneMarker® HID v1.71 (SoftGenetics, State College, PA) and GeneMapper® ID v3.2 are the two expert systems chosen for the initial evaluation. The features, user interface, and performance of each software program were compared. GeneMarker HID and GeneMapper ID performed similarly, making accurate allele calls and appropriately directing the analyst's attention to data that do not meet defined thresholds. The decision was made to internally validate GeneMapper ID as an expert system for STR data analysis of single source samples. The expert system was successfully optimized for the analysis of samples amplified with Identifiler® and Yfiler® PCR Amplification Kits (Applied Biosystems)and analyzed on the 3130xl Genetic Analyzer (Applied Biosystems).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 Human Hair Shaft Volume and Mitochondrial DNA Recovery(2007-08-01) Kreikemeier, Melissa A.; Arthur Eisenberg; Joseph Warren; John PlanzKreikemeier, Melissa A., Human Hair Shaft Volume and Mitochondrial DNA Recovery. Master’s of Science (Biomedical Science, Emphasis in Forensic Genetics) August, 2007, 54 pp., 6 tables, 26 figures, References, 45 titles. The goal of this study was to determine if there was a relationship between hair volume and amount of amplified mtDNA for all head hair samples, as well as among the three major ethnic groups, different hair colors, and different donors. This relationship could be used to determine how much of a hair sample is needed for extraction so that enough mtDNA PCR product is obtained, while preserving forensic hair samples and avoiding unnecessary consumption of evidence. Amplification success rates were also calculated for each of these categories to determine if the findings coincided with previously published literature.