SNP Genotyping of Native DNA using Oxford Nanopore MinION Sequencing

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dc.contributor.advisorPlanz, John V.
dc.contributor.committeeMemberZascavage, Roxanne R.
dc.contributor.committeeMemberPhillips, Nicole R.
dc.contributor.committeeMemberYang, Shaohua
dc.creatorLudwick, Whitney N.
dc.date.accessioned2019-10-01T20:39:33Z
dc.date.available2019-10-01T20:39:33Z
dc.date.issued2018-05
dc.description.abstractShort tandem repeats (STRs) are the primary system of genetic variation used for human identity testing in forensics; however, STR typing relies on the use of time- consuming polymerase chain reaction and expensive laboratory equipment. The use of single nucleotide polymorphisms (SNPs) in forensics have several advantages over STRs. In this study, a panel of Identity SNPs were interrogated and typed from native genomic DNA sequencing libraries using the Oxford Nanopore Technologies (ONT) MinION sequencer. We determined that SNPs could be effectively captured using existing software. Four different methods of alignment were investigated, and we found that aligning sequence data to the human genomic sequence (hg19) provided partial profiles, while aligning data to a merged reference profile resulted in more complete profiles. As ONT?s platform continues to improve, SNP genotyping using the MinION may be used to generate complete SNP profiles with the sufficient depth of coverage for reliable genotype determination.
dc.format.mimetypeapplication/pdf
dc.identifier.urihttps://hdl.handle.net/20.500.12503/29694
dc.language.isoen
dc.subject.meshForensic Genetics
dc.subject.meshSequence Analysis, DNA, instrumentation
dc.subject.meshPolymorphism, Single Nucleotide
dc.subject.meshNanopores
dc.subject.meshGenotyping Techniques
dc.titleSNP Genotyping of Native DNA using Oxford Nanopore MinION Sequencing
dc.typeThesis
dc.type.materialtext
thesis.degree.departmentGraduate School of Biomedical Sciences
thesis.degree.disciplineForensic Genetics
thesis.degree.grantorUniversity of North Texas Health Science Center at Fort Worth
thesis.degree.nameMaster of Science

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