Browsing by Subject "forensics"
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Item A Problem in Greek Ethics(1908-01-01) Symonds, JohnItem Allele Characterization of Ten Short Tandem Repeat Loci of North American Bears (Ursids) Using Next-Generation Sequencing(2014-05-01) Kreutzer, Mckensie; John PlanzAn identification method that provides higher genetic resolution than capillary electrophoresis (CE) is needed for isolated bear populations that possess low genetic diversity. Amplification conditions were optimized for ten bear STR loci. Amplicons were used to develop a library for next-generation sequencing (NGS) on the Ion Torrent™ PGM™ Sequencer. Through ligation of DNA barcode adaptors, seven black bear (Ursus americanus) samples were sequenced together. Sequencing reads were aligned to a virtual ladder and analyzed in NextGENe® software. Allele concordance was shown between CE and NGS. Variants within alleles (SNPs and INDELs) showed that NGS provided higher genetic resolution. These results have implications for improving individual identification and population assignment in wildlife forensics and conservation for populations with low genetic diversity.Item Amplification of Mitochondrial DNA Regions HVI and HVII in its Entirety and Reducing Cycle Sequencing(2004-08-01) Ariyo, Bolanle; Joseph Warren; John Planz; Arthur EisenbergAriyo, Bolanle. Amplification of Mitochondrial DNA Regions HVI and HVII in its Entirety and Reducing Cycle Sequencing Reactions. Master of Science (Forensic Genetics), August 2004, 46 pages, 10 figures, 7 tables, 18 references. Mitochondrial DNA is widely used in the forensic community because of its high copy number in cells, location, and mode of inheritance. Yet this method of analysis is expensive, time consuming, and labor intensive, therefore labs should take steps to improve the procedure of mtDNA analysis. This study is performed to validate the use of amplifying HVI and HVII region in its entirety (2 primer sets) for use in reference samples. Amplification performed using primers F15989-R16410 (HVI) and F73-R340 (HVII). The current method of amplification is 4 primer sets at full cycle sequencing reactions. The cost of Cycle Sequencing Kit is also expensive, therefore performing half and quarter reactions would be beneficial in reducing the amount of kit consumed. To validate the use of reducing cycle sequencing reactions, half and quarter cycle reactions were performed using 2 and 4 primer sets. Results demonstrate that sequence data for reducing cycle sequence data is consistent with the sequence data using the current method. Results also show that sequence data obtained using two primer sets was consistent with sequence data amplified by the current method with the exception of two samples at length heteroplasmy polyctosine regions.Item Analysis of HemaSpot[TM]-HF and HemaSpot[TM]-HD Sampling Kits Using Trace DNA(2019-05) McGehee, Rachel L.; Warren, Joseph E.; Planz, John V.; Schiro, GeorgeSpot On Sciences, Inc. has recently developed a new device, the HemaSpot[TM], which allows for samples to be stored safely at ambient temperatures. The UNTHSC FGEN program was contacted to conduct a research study to determine its feasibility for use as collection and storage media with trace samples. Extractions of 108 samples were conducted with QIAGEN[R] QIAamp DNA Investigator Kits, a 3130xL Genetic Analyzer, and GeneMapper[R] ID-X software. A hypersensitivity study worked with sub-optimal amounts of control DNA in order to observe the quality and variation of the generated profiles. The trace study swabbed items found at typical crime scenes and determined the device's ability to generate readable profiles. Results uncovered that all samples either contained large portions of allelic dropout or contamination. Relatively similar partial profiles were produced for both cartridge types in the hypersensitivity study. In addition, readable trace profiles were compared to one another to conclude that the HemaSpot[TM]-HD had the most success, however this may have been the cause of limited size and sample variation. Both products should be tested further.Item Dr. Joseph Warren(2013-08-02)Item Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples(Frontiers Media S.A., 2022-06-30) Turner, Stephen D.; Nagraj, V. P.; Scholz, Matthew; Jessa, Shakeel; Acevedo, Carlos; Ge, Jianye; Woerner, August E.; Budowle, BruceTechnological advances in sequencing and single nucleotide polymorphism (SNP) genotyping microarray technology have facilitated advances in forensic analysis beyond short tandem repeat (STR) profiling, enabling the identification of unknown DNA samples and distant relationships. Forensic genetic genealogy (FGG) has facilitated the identification of distant relatives of both unidentified remains and unknown donors of crime scene DNA, invigorating the use of biological samples to resolve open cases. Forensic samples are often degraded or contain only trace amounts of DNA. In this study, the accuracy of genome-wide relatedness methods and identity by descent (IBD) segment approaches was evaluated in the presence of challenges commonly encountered with forensic data: missing data and genotyping error. Pedigree whole-genome simulations were used to estimate the genotypes of thousands of individuals with known relationships using multiple populations with different biogeographic ancestral origins. Simulations were also performed with varying error rates and types. Using these data, the performance of different methods for quantifying relatedness was benchmarked across these scenarios. When the genotyping error was low (<1%), IBD segment methods outperformed genome-wide relatedness methods for close relationships and are more accurate at distant relationship inference. However, with an increasing genotyping error (1-5%), methods that do not rely on IBD segment detection are more robust and outperform IBD segment methods. The reduced call rate had little impact on either class of methods. These results have implications for the use of dense SNP data in forensic genomics for distant kinship analysis and FGG, especially when the sample quality is low.Item Evaluation of the AmpFlSTR® MiniFiler Typing Kit: Mixture Studies and Non-Probative Sample Studies(2009-05-01) Feller, Elizabeth A.; Planz, John V.This project was aimed to assemble and assess data from internal validations of AmpFlSTR® MiniFilerTM PCR Amplification Kit by forensic laboratories across the United States. After compilation, data was evaluated for quality of testing, results, and concordance within and between participating laboratories. It was concluded that MiniFilerTM can successfully amplify DNA from multiple sources in mixtures of neat and degraded samples, as well as enhance DNA profiles obtained for several types of samples with suspected PCR inhibition or degradation. The data was collected into a final report with discussions and conclusions to the findings for submission to the National DNA Indexing System (NDIS) Approval Board for authorization to use forensic DNA genotypes generated using MiniFilerTM in national DNA databases.Item Extraction and STR Amplification of HAEIII Restriction Cut, Membrane Bound Human DNA(2005-07-01) Andrews, John S.; Joseph Warren; Arthur Eisenberg; John PlanzThe use of DNA in forensics has become widely accepted since its introduction into the field in 1985 with Restriction Fragment Length Polymorphisms (RFLP) by Alec Jeffreys (1). RFLP techniques were utilized in the forensic DNA community until the mid 1990s when less labor-intensive PCR-STR techniques became available. During the transition from RFLP technology to PCR based STR technology a method for comparing RFLP profiles to that of STR profiles was not developed. Currently there have been no published studies where STR profiles have been obtained from membrane-bound, restriction cut human DNA. The only way to compare RFLP profiles to STR profiles would be to obtain STR profiles from the bound restriction cut DNA left on the nylon membranes. Since the shift in technology from RFLP to PCR-STR most labs, including the FBI, have stopped RFLP analysis as of the year 2000 (4). Today many unsolved cases exist that utilized RFLP technology. Due to the nature of RFLP analysis many times all of the biological sample must be consumed in order to obtain an RFLP profile. When this occurs, there is no longer biological sample left for future testing. In these instances the only DNA left from the case is restriction cut and bound to nylon RFLP membranes. The only chance of determining the STR profile of the source of the biological sample found at the crime scene would be to remove the membrane bound DNA and obtain an STR profile. The experimental hypothesis of this study is that DNA can be recovered from nylon membranes and interpretable STR results can be obtained. The use of multiple STRs are highly discriminatory being able to generate rare DNA profiles possessing a discriminatory power of in many times that of the earth’s population. Due to this discrimination power, profiles are able to individualize the source of a biological sample and aid in criminal investigations. If STR profiles could be obtained from old RFLP membranes numerous cold cases could be reopened and reinvestigated. The STR profiles obtained from the RFLP membranes could be placed into the Combined DNA Indexing System (CODIS). CODIS blends forensic science and computing software into a tool for solving violent crimes. Through CODIS, STR profiles can be entered into the database and searched against possible suspects at the local, state, and national level. Obtaining STR profiles from RFLP membranes would allow for the comparison of these profiles to those found in CODIS for a possible suspect. This project will employ methods to try and obtain an STR profile from Hae III restriction cut DNA bound to Magna Graph membranes. Attempts will be made to obtain STR profiles through direct amplification off of the membrane with PowerPlex 16 and separation on the Avant 3100 equipped with GeneMapper ID. Methods will also be utilized to remove the bound DNA from the membrane prior to amplification and separation. Removal of the bound DNA from the membrane will involve physical means, as well as, the use of various extraction chemicals. If a technique is found successful at removing DNA from Magna Graph membranes, then the technique will be applied to true RFLP membranes donated by the UNTHSC.Item Human Blood versus Two Commercially Available Blood Substitutes: A Comparative Analysis(2016-05-01) Murphy, Katharine M.; Warren, Joseph E.; Planz, John V.; Courtney, MaxThe experiments included in this research were conducted in order to compare expired human blood and two commercially available synthetic blood spatter products (Arrowhead Forensics Spatter Blood and Evident® Crime Scene Products Spatter Training Blood) in appearance and fluid dynamics in order to compare similarities and differences between the three substances. For training purposes, synthetic blood substitutes are preferred due to increased safety and reduced costs. Experiments conducted included point of origin calculations at three distances and overall appearance of spatter on wood, tile, denim, and concrete at three distances. It was determined that point of origin calculations at one of three distances was significantly different, but all other distances and experiments were comparable among the three substances.Item Medical Chaos and Crime(Mitchell Kennerley, 1910-01-01) Barnesby, NormanItem North Texas Health & Science - 2011, Issue 1(University of North Texas Health Science Center at Fort Worth, 2011-01-01)Item Population Variances in the Whole Mitochondrial Genome Impacting Capture for Human Identification(2015-05-01) Skandalis, Lisa A.; Bruce Budowle; Michael Allen; Robert C. BarberThe mitochondrial genome (mtGenome) holds a wealth of information that can be used for human identification purposes. Sequencing and analyzing the entire mtGenome can help to obtain more of this information. However, library preparation steps prior to sequencing could be problematic when dealing with compromised or degraded samples. A capture/hybridization assay targeted to the entire mtGenome can enrich for the target DNA without PCR or chemically altering the DNA. The melting temperatures (Tm) of two different length fragments for an African American and Caucasian individual were mapped across the length of the genome to study any variation that might occur. While population-specific Tm differences seem to be almost negligible, there is wide intra-individual Tm variation, ranging from about 11-31°C. To overcome the issue of an assay run at a single set of temperature parameters, two separate reactions optimized for higher and lower Tm values could prove to be more efficient.Item Selection of an Ancestry-Informative Marker (AIM) Panel of INDELs(2015-05-01) Thompson, Lindsey M.; LaRue, Bobby L.; Hodge, Lisa M.; Oglesby, MichaelShort Tandem Repeat (STR) loci are commonly used for forensic identification purposes. Most commercially available STR kits yield amplified fragments with lengths between 100 and 600 base pairs (bp). However, the genomic DNA of forensic samples can be highly degraded, yielding incomplete STR profiles. Small insertion/deletion polymorphisms (INDELs) in the intergenic regions of the genome, are viable options for typing degraded samples. Furthermore, when there are no suspects for comparison, ancestry-informative markers (AIMs) are useful for developing investigative leads. This project tested the hypothesis that using publicly available genome data, a panel of AIM-INDELs can be selected for the purposes of distinguishing the Caucasian, East Asian and African population groups. To test this hypothesis, the data from the 1000 Genomes Project were mined to select a panel of AIMs that can be used for the purposes of providing ancestry information as an investigative lead to law enforcement.Item Validation of the ParaDNA[R] Screening System with touch DNA using mock evidence samples(2018-05) West, Whitney R.; Allen, Michael S.; Warren, Joseph E.; Staub, Rick W.; Schreihofer, Ann M.Short tandem repeat, or STR, analysis is expensive and often creates a waiting game for law enforcement agencies to receive these results due to high demand and the current backlog at forensic laboratories. ParaDNA[R] by LGC utilizes HyBeacon Probe technology to rapidly analyze DNA and provide a percentage value of the amount of DNA present, as well as 2-5 loci, depending on whether the Screening System or Intelligence System is being used. Currently, this technology is novel and is intended for sample screening and prioritizing purposes for the Plano Police Department. This validation study has shown that the ParaDNA[R] Screening System can obtain genetic data from touch DNA and trace DNA samples by using both direct and indirect sampling methods. The results from this validation have further indicated that if the Screening System provides a score higher than 60%, these samples should be prioritized and sent to forensic laboratories for full STR analysis.