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Age Estimation Using DNA Extracted from Human Saliva As a Diagnostic Measure in Forensic Odontology

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Age Estimation Using DNA Extracted from Human Saliva As a Diagnostic Measure in Forensic Odontology Journal of Research in Medical and Dental Science Medic in al h an 2021, Volume 9, Issue 2, Page No: 132-139 c d r a D e Copyright CC BY-NC 4.0 s e n e t R a Available Online at: www.jrmds.in f l o S c l i eISSN No. 2347-2367: pISSN No. 2347-2545 a e n n r c u e o J JRMDS Age Estimation Using DNA Extracted from Human Saliva as a Diagnostic Measure in Forensic Odontology Keerthana T, Sindhu Ramesh* Department of Conservative Dentistry and Endodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India ABSTRACT Forensic age estimation can be used to gain information relevant to criminal and anthropological investigations. Forensic dentistry involves the processing, review, evaluation and presentation of dental evidence with the purpose of contributing scientific and objective data in legal processes. This study aims in estimating age of a person using DNA extracted from human saliva and to assess this methodology as a potential diagnostic measure in forensic odontology. Salivary samples were collected from 45 blinded participants aged 18 to 70 years with a DNA self-collection kit and stored at room temperature. DNA was extracted from the salivary samples using a separate kit and it was subjected to age estimation process by constructing an age predictive model. A constructed age predictive model of saliva has 6 selected CpG sites (5’—C---phosphate—G---3’) in genome-enabled age prediction with high accuracy. Univariate linear regression analysis was performed to test the association between age and gender.(p value<0.05). DNA methylation profiling of saliva was performed to identify age associated CpG markers. A model composed of 6 selected CpG sites enabled age prediction in saliva with high accuracy and this multiplex system can be integrated into the routine forensic laboratory workflow after further validation tests with various casework samples. Key words: Saliva, DNA, epigenetic age marker, Methylation, CpG sites HOW TO CITE THIS ARTICLE: Keerthana T, Sindhu Ramesh, Age Estimation Using DNA Extracted from Human Saliva as a Diagnostic Measure in Forensic Odontology, J Res Med Dent Sci, 2021, 9 (2): 132-139. Corresponding author: Sindhu Ramesh scene. Based on salivary samples, epigenetic age e-mail: [email protected] predictive models were formed to predict the Received: 23/09/2020 age of a suspected person in the crime scene. Accepted: 01/02/2021 DNA phenotyping refers to infer the appearance of an unknown sample donor from DNA [16]. INTRODUCTION Individual age estimation is a major key factor from the evidence does not match with anyone, in forensic science analysis which can provide forensicWhen there DNA is phenotyping no suspect to is match expected or DNA to provide profile very useful information applicable to crime an investigate lead that can facilitate a traced investigations. Age estimation in forensic science search for an unknown suspect by narrowing the was initially based on various morphological search range. The most well studied externally approaches or radiographic investigations visible characteristics are those associated with [1]. Later, molecular approaches came into the pigmentation such as skin color, eye color, practice for age estimation [2,3]. DNA based and hair color [7,8]. But age is noteworthy methodologies initially were technique sensitive because it can be used regardless of ethnicity to and had lack of accuracy. But, epigenetic predict an individual’s appearance. signature of DNA methylation had overcome To predict an individual’s age from DNA, these disadvantages. Most forensic age predictor molecular methods based on the detection of models have been developed based on blood telomere shortening and mitochondrial DNA DNA samples, because it is the most encountered deletion have been suggested [9,10]. DNA methylation based age prediction can be applied tissues are now being explored [4,5]. Saliva is the fluid in the crime scene. But now, additional in several researches reporting age associated to various tissues, body fluids which has resulted next frequently encountered fluid in the crime Journal of Research in Medical and Dental Science | Vol. 9 | Issue 2 | February 2021 132 Keerthana T, et al. J Res Med Dent Sci, 2021, 9 (2):132-139 DNA markers and age predictive models [11,12]. Sample size DNA methylation based biomarkers often Salivary samples were collected from 45 referred to as epigenetic age or ‘epigenetic clock’ volunteers among which 23 were males, and 22 as they are robust estimators of chronological were females in the age group between 18 to 60 age of an individual [13,14]. This estimate is years. The salivary samples were collected using consistent across many biological specimens a DNA self-collection kit and stored at room such as blood, brain, breast, kidney, liver, lung, temperature. saliva and cell types including CD4+ T cells, Procedure monocytes, glial cells and neurons [15,16]. The steps involved are Epigenetic age is associated with age related health outcomes above and beyond chronological Sample collection. age. Thus, epigenetic age captures some sort of biological age and the resulting susceptibility to saliva. the disease and multiple health outcomes. Genome wide DNA methylation profiling of Further, these age predictive models would not Construction of age predictive model for saliva. be practical to implement in routine forensic Targeted bisulfite sequencing. laboratories that usually deal with very limited Sample collection amounts of DNA. Therefore, models composed of After the collection process, DNA was segregated a small number of highly predictive CpG markers from the stored salivary samples ranging from 150 to 200 microliters of saliva using DNA mini been reported to produce reasonable prediction accuracyin a certain on type several of body different fluid analysisor tissue platforms. that have The protocol followed before collecting saliva Usually salivary samples have a heterogeneous kit and then quantified. was to wait one hour after eating a meal before cell composition that includes both buccal collecting saliva. Patients were asked to rinse epithelial cells and leukocytes [8,17,18]. This their mouths thoroughly to remove any food study aims at generating genome wide DNA particles or other contaminants. After 5 to 10 minutes the salivary samples were collected. and assessing those age predictive models can Collecting saliva soon after rinsing may reduce bemethylation suitable for profiles predicting using the bisulfite range of sequencing suspected the amount of DNA extraction and may also individuals. This study also emphasizes whether affect the biomarker analysis [19,20]. using salivary DNA samples can be a potential diagnostic aid with certain prediction accuracy Salivary DNA self-collection kit provided the in forensic practice. convenience of integrated ambient temperature stabilization, sample transport, and sample MATERIALS AND METHODS preparation. The device is available in several formats [21,22]. In this study, tube format was Study design used, for that whole saliva should be delivered Single blinded in vivo study. directly into the device by placing the kit against Ethical clearance the lower border and spitting into the funnel Ethical permission and approval for the project shaped end. was obtained from the Institutional Review Board The DNA in saliva originates from cells that are of Saveetha Institute of Medical and Technical shed from the inner linings of the mouth and from Sciences, Chennai, India. (SBA/2019/23/05). Study criteria samples was done by polymerase chain reaction. white blood cells [23,24]. The quantification of Salivary samples were collected from 45 volunteers aged 18 to 70 years with a DNA self- instructions, a mix solution of 10 microliters For quantification, as per manufacturer’s collection kit and stored at room temperature of powerquant* mastermix; 7 microlitres of and sent to the lab. DNA was extracted from the salivary samples using a separate kit and amplification grade (water); 1 microliter of it was subjected to age estimation process by was made on 7500 real time PCR cycles. power-quant* primer mix. The quantification constructing an age predictive model. Genome wide DNA methylation profiling of saliva Journal of Research in Medical and Dental Science | Vol. 9 | Issue 2 | February 2021 133 Keerthana T, et al. J Res Med Dent Sci, 2021, 9 (2):132-139 Microarray hybridization was performed. 1 to 3 of AmpliTaq Gold 1 DNA Polymerase (Applied using a DNA methylation kit according to the Biosystems),containing 1 to2mL 2mL of bisulfite-convertedGold ST*R 10 Buffer DNA, 2 micrograms of DNA was bisulfite converted (Promega, Madison, WI, USA), and 0.2–3.0mM DNA was then incubated at 37 degrees for 24 manufacturer's instructions. Bisulfite converted and hybridized to a hybridization oven at 48 of each primer.Bisulfite-converted DNA was degreeshours. The for amplified12 to 18 hours. DNA was then fragmented obtained by modification of 500 ng of genomic ngDNA of usinggenomic the DNAEpiTect1 with theFast Imprint DNA Bisulfite 1 DNA Following hybridization, single base extension Kit (Qiagen) or by modification of less than 10 of hybridized DNA was performed using hapten protocols. Modification Kit according to the manufacturers’ PCR cycling was conducted using a VeritiTM antibodiesmodified nucleotides in several steps[25,26]. to amplifyStaining the was signal, then 96-Well Thermal Cycler under the following theperformed arrays were by washed.adding fluorescently labeled conditions: 95°C for 11 min; 34 cycles of 94°C Data collection for 20 s,56°C for 60 s, and 72°C for 30 s; and a Then, univariate linear regression analysis was performed to test the association between beta 1mLfinal extensionof ExoSAP-ITTM at 72°C byfor incubation7 min. Then, at 37°C5mL score and age separately for each CpG site. The foraliquots 45 min, of followedPCR products by heat were inactivation purified atwith 80 C for 15 min.
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