Browsing by Subject "forensic"
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Item A Novel Multiplex Assay for an Ancestry-Informative Marker (AIM) Panel of INDELs(2016-05-01) Sturm, Sarah A.; LaRue, Bobby L.; Budowle, Bruce; Krishnamoorthy, Raghu R.The current standard for forensic laboratories in criminal casework is to use Short Tandem Repeat (STR) markers to develop an evidentiary profile. Commercially available STR amplification kits yield amplicons 100 to 500 base pairs (bp) in length. Commonly, forensic DNA samples are highly degraded to approximately 180-200 bps in length, resulting in incomplete STR profiles. Therefore, markers that can be generated with smaller amplicons may be better suited for degraded DNA samples. Additionally, there are cases where no STR match was obtained through a DNA database search and thus no investigative lead is obtained. The bioancestry of a sample donor could aid law enforcement in such cases. A class of markers that could provide investigative value from degraded DNA samples is Ancestry-Informative Marker (AIM) Insertion/Deletions (INDELs). INDELs are polymorphisms that can be amplified from degraded samples due to their smaller amplicon size. AIMs have the ability provide bioancestry information. This project tested the hypothesis that a multiplex PCR-based assay of INDELs can be developed, and subsequently be analyzed by capillary electrophoresis for population identity testing applications. The use of this assay would require no additional tools or machinery than what already is in standard forensic laboratories. To test this hypothesis, a previously developed panel of AIM-INDEL markers was used to develop this multiplex assay.Item A Validation of STRmix™ for Forensic Casework(2017-05-01) Conway, Allison; Budowle, Bruce; Warren, Joseph E.; Gwirtz, Patricia A.The interpretation of complex DNA profiles has been a controversial issue in forensic biology. The current methods of interpretation are limited in scope and do not make full use of the data. Efforts have been made to develop software which can incorporate more data and process more calculations than were previously possible. One such program, STRmix™ (Institute of Environmental Science and Research, Porirua, New Zealand), uses a Markov Chain Monte Carlo (MCMC) principle to simulate many different possible profiles and determine the probability of observing a profile in the evidence. A validation of this software is necessary to indicate which situations are appropriate for analysis and define existing limitations.Item Bone Marrow Engraftment Monitoring Using Mixture Deconvolution Software Designed for Forensic Casework.(2009-08-01) Newman, Alexandra; Warren, JosephFollowing a bone marrow transplant, patients are monitored closely for evidence of graft rejection or recurrence of the original disease. Bone marrow transplantation creates a donor-recipient cellular chimerism in the patient, which can be quantitively measured through short tandem repeat (STR) analysis of peripheral whole blood to determine the percent chimerism of the sample. Increasing recipient chimerism is an indication of graft rejection or relapse. Software programs designed to analyze forensic mixture samples have the potential to be useful in analyzing post-transplant mixed chimeric samples. Post-transplant samples were analyzed using three mixture deconvolution software programs. The programs were fast, accurate and consistent in determining the mixing proportions of the samples and the three programs gave concordant results.Item Evaluation of Y-STR Data Using a Duplex Gender Real-Time PCR Assay on an ABI Prism 7000 SDS Followed by Amplification with Applied Biosystems AmpFLSTR Yfiler PCR Amplification Kit(2007-08-01) Miller, Jennifer J.; John Planz; Arthur Eisenberg; Joseph WarrenQuantification is the process of determining the concentration of DNA in a sample and plays an extremely important role in the processes of amplification and STR typing. A method of quantification is mandated for a laboratory conducting forensic DNA analysis by National Standard 9.3 (1). Furthermore, anytime a forensic laboratory chooses to implement a new or novel methodology for any step in DNA analysis, a laboratory must conduct an internal validation to ensure the quality of method and any results generated on the equipment used within that laboratory are reliable, reproducible, and accurate before the method is utilized for casework analysis (1). Prior to an internal validation, the method or technology must undergo a developmental validation by the developer or manufacturer to determine conditions or limitations of the method or technology on DNA analysis of forensic samples (2). A study has shown that Y-STR results can be obtained even when the quantification of samples yields a value of 0.00ng/μl (4). The issue of the absolute lowest limit of detection in the quantification process versus input DNA concentrations of the unknown samples to yield any valuable Y-STR typing data has not been addressed. A duplex gender assay developed by Nicklas and Buel (3) has a reported detection limit of 0.5pg for the Alu probe of the duplex assay and quantification will be evaluated on a different qPCR platform than originally reported and followed by amplification using Applied Biosystems’ AmpFLSTR Yfiler PCR Amplification Kit to assess quantification limits. The goal of this internship project was to complete a preliminary evaluation of the sensitivity of a quantification methodology on a different qPCR platform under different detection parameters utilizing Y-chromosome DNA in correlation to Y-STR typing results and evaluate the data qualitatively.Item Sequencing Long Amplicon Microsatellite Loci Using the Oxford Nanopore Technologies MinION[TM] Device(2019-05) Hall, Courtney L.; Planz, John V.; Zascavage, Roxanne R.; Phillips, Nicole R.; Menegaz, Rachel A.Forensic DNA typing utilizes highly variable short tandem repeat (STR) markers to differentiate individuals. Despite the power and reliability of current techniques, sequence-level variations are masked in the length-based profiles generated. Nanopore sequencing has the ability to provide long-read data, allowing for accurate alignment and identification of single nucleotide polymorphisms (SNPs) within and around microsatellite loci. To evaluate the applicability of nanopore sequencing to forensically-relevant autosomal and Y chromosome markers, selected STRs and their flanking regions (~800 bp) were amplified using custom primer sets, barcoded by sample, and sequenced on the MinION[TM] device. High quality sequencing data were obtained for all 24 samples at the 45 STRs interrogated using a customized data analysis pipeline. This project sets the foundation for future development of STRs for potential forensic applications as well as biomedically-relevant regions.Item The Evaluation of Different Collection Methods for the Optimum Recovery of DNA from Bloodstains on Various Surfaces(2013-05-01) Stricklin, Sarah N; Arthur EisenbergThis study compared the ability of cotton tip swabs and 4N6FLOQ™Swabs (Life Technologies, Carlsbad, CA) to collect dried bloodstains from various surfaces and recover the DNA transferred onto each swab. This study also examined whether swabs moistened with phosphate buffered saline (PBS) rather than distilled water (dH2O) provided any advantage in the recovery of DNA. The DNA yield; the quality of the Short Tandem Repeat (STR) profiles generated; and the ease of use were evaluated for the two swabs. The FLOQ™ swabs yielded the most DNA in the majority of the samples collected from each of the surfaces. There was no indication that PBS compared with dH2O provided any significant advantage in DNA yield and the quality of the STR profiles generated.