Automatable Virtual Array Screening System for Rapid Analysis of Mitochondrial DNA Polymorphism

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dc.contributor.advisorArthur J. Eisenberg
dc.contributor.committeeMemberBruce Budowle
dc.contributor.committeeMemberJohn Planz
dc.creatorCampbell, Rowan Stewart
dc.date.accessioned2019-08-22T21:07:17Z
dc.date.available2019-08-22T21:07:17Z
dc.date.issued2002-05-01
dc.date.submitted2013-06-27T15:00:08-07:00
dc.description.abstractCampbell, 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.
dc.format.mimetypeapplication/pdf
dc.identifier.urihttps://hdl.handle.net/20.500.12503/29085
dc.language.isoen
dc.provenance.legacyDownloads1
dc.subjectEquipment and Supplies
dc.subjectGenetics
dc.subjectGenetics and Genomics
dc.subjectGenetic Structures
dc.subjectGenomics
dc.subjectInstrumentation
dc.subjectInvestigative Techniques
dc.subjectLife Sciences
dc.subjectMedical Genetics
dc.subjectMedicine and Health Sciences
dc.subjectMolecular Genetics
dc.subjectOther Genetics and Genomics
dc.subjectProbability
dc.subjectmtDNA sequence analysis
dc.subjectmitochondrial DNA polymorphism
dc.subjectrapid analysis
dc.subjectautomatable virtual array screening system
dc.subjectalternative methods
dc.subjectsequence specific oligonucleotide hybridization
dc.subjectsingle nucleotide polymorphisms
dc.subjectLuminex 100 flow cytometer
dc.subjectABI Prism 310 Genetic Analyzer
dc.subjectDNA analysis
dc.subjectSNaPshot primer extension assay
dc.subjectmtDNA haplotype
dc.subjectSNP array
dc.titleAutomatable Virtual Array Screening System for Rapid Analysis of Mitochondrial DNA Polymorphism
dc.typeDissertation
dc.type.materialtext
thesis.degree.departmentGraduate School of Biomedical Sciences
thesis.degree.disciplineBiomedical Sciences
thesis.degree.grantorUniversity of North Texas Health Science Center at Fort Worth
thesis.degree.nameDoctor of Philosophy

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