Development of DNA Methylation Markers to Infer Age, Smoking Status and Body Fluid Types for Forensic Application

Authors

Hussain J.H. AlghanimFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Chemistry

First Advisor's Name

Dr. Bruce McCord

First Advisor's Committee Title

Committee chair

Second Advisor's Name

Dr. Watson Lees

Second Advisor's Committee Title

Committee member

Third Advisor's Name

Dr. Yuan Liu

Third Advisor's Committee Title

Committee member

Fourth Advisor's Name

Dr. Yuk-Ching Tse-Dinh

Fourth Advisor's Committee Title

Committee member

Fifth Advisor's Name

Dr. Wensong Wu

Fifth Advisor's Committee Title

Committee member

Keywords

Forensic, Age estimation, Tobacco smoking, Body fluid identification, Epigenetics, DNA methylation, Pyrosequencing, HRM analysis

Date of Defense

7-19-2019

Abstract

In forensic investigations, biological evidences have great potential to place a suspect at the scene of a crime. However, in many cases suspect(s) usually can’t be identified with any local or national databases. In such challenging cases, police need a tool that can provide investigative leads. Thus, different genetic biomarkers including DNA methylation markers have been developed for different phenotypic traits to serve as source of intelligence information to investigators in cases of unknown DNA profiles. In this project, novel sets of DNA methylation markers were developed for the forensic estimation of human age, determining the smoking status and body fluid identification.

First, single- and dual-locus age predictors for saliva and blood were developed from CpG sites in KLF14 and SCGN based on pyrosequencing data and using a multivariate linear regression analysis. In saliva, single-locus model in particular was efficient for younger subjects (³40 years) correctly predicting age of 78.9% of the samples with a MAD of 5.1 years in the validation set. Second, a quick and cost effective 4-CpG pyrosequencing assay was built to infer smoking habit using multinomial logistic regression model (MLR). In blood, the model correctly predicted 90.0% of current smokers, 66.7% of former smokers, and 84.9% of never smokers. In addition, the MLR model correctly predicted 86.9% of current smokers, 54.5% of former smokers, and 77.8% of never smokers in saliva. Finally, new set of tissue specific differentially methylated region (tDMRs) were identified for forensic discrimination of body fluids. NMUR2 and UBE2U markers were found to be specific for semen and the two assays developed can be employed using both pyrosequencing or High resolution melt (HRM) analysis. In addition, the developed AHRR marker can discriminate blood stains from other body fluids. These three piece of information may be very valuable source of investigative leads aiming to trace unknown perpetrators who could not be identified using the conventional autosomal DNA typing.

Identifier

FIDC008888

Previously Published In

Alghanim, H., Antunes, J., Silva, D. S. B. S., Alho, C. S., Balamurugan, K., & McCord, B. (2017). Detection and evaluation of DNA methylation markers found at SCGN and KLF14 loci to estimate human age. Forensic Science International: Genetics, 31, 81-88.‏

Alghanim, H., Wu, W., & McCord, B. (2018). DNA methylation assay based on pyrosequencing for determination of smoking status. Electrophoresis, 39(21), 2806-2814.‏

Recommended Citation

Alghanim, Hussain J.H., "Development of DNA Methylation Markers to Infer Age, Smoking Status and Body Fluid Types for Forensic Application" (2019). FIU Electronic Theses and Dissertations. 4367.
https://digitalcommons.fiu.edu/etd/4367