Date of Award

5-1-2013

Degree Type

Thesis

Degree Name

Master of Science

Field of Study

Forensic Genetics

Department

Graduate School of Biomedical Sciences

First Advisor

John V. Planz

Abstract

Mitochondrial DNA (mtDNA) sequencing is used in many applications of the scientific field including disease studies, migration/ancestry studies and forensic identification. Most mitochondrial sequencing thus far has been performed solely on the highly variable control region of the mitochondrial genome, but new technologies such as next generation sequencing platforms are facilitating an increase in whole mitochondrial genome sequencing. In migration studies, obtaining sequences of the entire mtDNA allows for utilization of the more conserved regions of the genome to develop haplotypes which can help in more accurate estimation of population affiliations of specific mtDNA haplotypes. In this study, a target-enriched full mitochondrial genome library was developed to be used for next generation sequencing technologies. The two 12-plex polymerase chain reaction (PCR) primer multiplexes used to develop this library were designed to be able to completely amplify the mtDNA of a set of Easter Island samples on WhatmanTM FTATM cards that a previously-developed nine primer multiplex reaction could not. It was hypothesized that the matrix of the cards prevented amplification of very long fragments (greater than approximately1000 bp). Successful amplification using the 12-plex reactions was accomplished using extracted DNA samples and direct amplification from the FTATM cards. Libraries of a pilot set of Easter Island samples were created so that sequences could be generated and genetic associations between the remote island population and its two closest geographic populations, Oceania and mainland Chile, could be determined. The multiplexes developed from this study could be used in the future for other samples that appear to be challenged due to either sample quality or their complex storage medium, in this case, FTATM cards.

Comments

Oatts, Sarah M., Development of a full mitochondrial genome specific target-enriched library for next generation sequencing applications. Master of Science (Forensic Genetics), May 2013, 65 pp., 4 tables, 13 figures, 27 references.

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