Novel Applications for Forensic DNA Analysis, the Human Genome and Beyond

Authors

Mirna Salim Ghemrawi, Florida International UniversityFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Biochemistry

First Advisor's Name

Bruce McCord

First Advisor's Committee Title

Committee Chair

Second Advisor's Name

Jeffrey Wells

Second Advisor's Committee Title

Committee member

Third Advisor's Name

Brian Young

Third Advisor's Committee Title

Committee member

Fourth Advisor's Name

Sara Casado Zapico

Fourth Advisor's Committee Title

Committee member

Fifth Advisor's Name

Steven Lee

Fifth Advisor's Committee Title

Committee member

Keywords

Forensic DNA, Epigenetics, Species Identification, Body Fluid Identification, Genital Microbial Identification

Date of Defense

10-27-2022

Abstract

In forensic casework, biological exhibits and unknown remains are sampled, extracted, and identified using PCR amplification of short tandem repeats. This procedure, known as DNA typing, is the gold standard in forensic identification. However, there are situations where DNA typing does not provide sufficient information to clarify the facts of the crime. For example, innocent transfer of biological materials may occur in situations where the suspect is known to the victim. In these situations, identifying the type of body fluid, blood- indicating foul play vs. skin, an innocent transfer can be critical. In other situations, non-human species, including pets and livestock, may also contribute to the evidence in question. Thus, it can be important to identify the species and body fluid type as well as to deconvolute possible mixtures of these types of samples. Lastly, in cases of sexual assault where no foreign male DNA is present, other microorganisms, including bacteria, may be present and transferred after contact. Thus, this dissertation is divided into three segments: first, an investigation of complex body fluids, particularly saliva and menstrual blood, was performed. DNA loci viii that vary in relative methylation depending on cell type were utilized, such as FAM43A, SOX2OT, SLC12A8, and BCAS4. Different collection methods and fluid depositions were examined, including buccal, lip, spit, and tongue, compared to nasal secretions and other non-oral fluids. For menstrual blood, the methylation status of two different loci, SLC26A10 and MDFI, were examined in a longitudinal study. Second, for species identification, a pyrosequencing-based assay was developed and validated according to the Scientific Working Group on DNA Analysis Methods (SWGDAM). Thirty-two different species were examined. A nanoplate-based digital PCR multiplex was also developed for mixture deconvolution of commonly found species, including Homo sapiens, Canine, Feline, Bovine, Swine, Pisces, and Gallus. Lastly, an investigation of the human genital microbiome was performed on penile and vaginal swabs to locate potential bacterial signatures that could be used to prove the act of sexual contact. Overall, the goal of this dissertation has been to access fundamental discoveries which permit the development of novel tools for forensic analysis. These tools exploit DNA analysis beyond traditional hereditary genetic markers to provide investigative leads in forensic casework. The development and validation of these novel methods bring additional tools to the forensic community and serve the public by providing useful information to the trier of fact.

Identifier

FIDC010864

ORCID

0000-0002-9584-7073

Previously Published In

• Ghemrawi, M., Fischinger, F., Duncan, G., Dukes, M. J., Guilliano, M., & McCord, B. (2021). Developmental validation of SpeID: A pyrosequencing-based assay for species identification. Forensic Science International: Genetics, 55, 102560.
• Ghemrawi, M., Tejero, N. F., Duncan, G., & McCord, B. (2022). Pyrosequencing: Current forensic methodology and future applications—a review. Electrophoresis.
• Ghemrawi, M., Torres, A. R., Duncan, G., Colwell, R., Dadlani, M., & McCord, B. (2021). The genital microbiome and its potential for detecting sexual assault. Forensic science international: genetics, 51, 102432.
• Ghemrawi, M., & McCord, B. (2022). Development of a nanoplate-based digital PCR assay for species identification with mixture deconvolution. Forensic Science International: Genetics Supplement Series.

Recommended Citation

Ghemrawi, Mirna Salim, "Novel Applications for Forensic DNA Analysis, the Human Genome and Beyond" (2022). FIU Electronic Theses and Dissertations. 5214.
https://digitalcommons.fiu.edu/etd/5214