The Study of Tissue-Specific DNA Methylation as a Method for the Epigenetic Discrimination of Forensic Samples

Authors

Joana AP AntunesFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Biochemistry

First Advisor's Name

Dr. Bruce McCord

First Advisor's Committee Title

Committee chair

Second Advisor's Name

Dr. Yuan Liu

Second Advisor's Committee Title

Committee member

Third Advisor's Name

Dr. DeEtta Mills

Third Advisor's Committee Title

Committee member

Fourth Advisor's Name

Dr. Kuppareddi Balamurugan

Fourth Advisor's Committee Title

Committee member

Fifth Advisor's Name

Dr. José Almirall

Fifth Advisor's Committee Title

Committee member

Sixth Advisor's Name

Dr. George Duncan

Sixth Advisor's Committee Title

Committee member

Keywords

epigenetics, forensic sciences, DNA, DNA methylation, pyrosequencing, high-resolution melt analysis, PCR, qPCR, body fluids

Date of Defense

11-21-2017

Abstract

In forensic sciences, the serological methods used to determine which body fluid was collected from the crime scene are merely presumptive or labor intensive since they rely on protein detection or on microscopic identification of cells. Given that certain forensic cases may need the precise identification of a body fluid to determine criminal contact, such is the example of a suspected sexual assault of a minor; certainty in the body fluid of origin may depict a precise picture of the events. The identification of loci that show differences in methylation according to the tissue of origin can aid forensic analysts in determining the origin of a DNA sample. The process of DNA methylation occurs naturally in the genome of living organisms and consists in the presence of a methyl group on the carbon 5 of a cytosine, which is typically followed by a guanine (CpG). Analyzing patterns of DNA methylation in body fluids collected from a crime scene is preferential to the analysis of proteins or mRNA since the same extracted DNA used for STR typing can be used for DNA methylation analysis. We have validated and identified loci able to discriminate blood, saliva, semen and vaginal epithelia. In the current study, we have also established the minimum amount of DNA able to provide reliable results using methodologies such as pyrosequencing and high-resolution melt (HRM) analysis for the different markers identified. Lastly, we performed an alternative bioinformatic analysis of data collected using an array that studied methylation in over 450,000 individual cytosines on the human genome. We were able to sort the locations that showed potentially higher methylation differences between body fluids and investigated over 100 of them using HRM analysis. The results of that study, allowed the identification of three new loci able to distinguish blood and two new loci able to distinguish saliva and vaginal epithelia, respectively. The use of DNA methylation patterns to aid forensic investigations started with a publication in 2010, therefore each small contribution such as this work may, similarly to what occured in the biochemistry field, result in the discovery of a method able to put the technology in the hands of forensic analysts.

Identifier

FIDC006582

ORCID

0000-0003-3614-3233

Creative Commons License

This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Recommended Citation

Antunes, Joana AP, "The Study of Tissue-Specific DNA Methylation as a Method for the Epigenetic Discrimination of Forensic Samples" (2017). FIU Electronic Theses and Dissertations. 3676.
https://digitalcommons.fiu.edu/etd/3676