Forensic DNA phenotyping using Oxford Nanopore Sequencing system.

In forensic science, the demand for precision, consistency, and cost-effectiveness has driven the exploration of next-generation sequencing technologies. This study investigates the potential of Oxford Nanopore Sequencing (ONT) Technology for analyzing the HIrisPlex-S panel, a set of 41 single nucleotide polymorphism (SNP) markers used to predict eye, hair, and skin color. Using ONT sequencing, we assessed the accuracy and reliability of ONT-generated data by comparing it with conventional capillary electrophoresis (CE) in 18 samples. The Guppy v6.1 was used as a basecaller, and sample profiles were obtained using Burrows-Wheeler Aligner, Samtools, BCFtools, and Python. Comparing accuracy with CE, we found that 62% of SNPs in ONT-unligated samples were correctly genotyped, with 36% showing allele dropout, and 2% being incorrectly genotyped. In the ONT-ligated samples, 85% of SNPs were correctly genotyped, with 10% showing allele dropout, and 5% being incorrectly genotyped. Our findings indicate that ONT, particularly when combined with ligation, enhances genotyping accuracy and coverage, thereby reducing allele dropouts. However, challenges associated with the technology's error rates and the impact on genotyping accuracy are recognized. Phenotype predictions based on ONT data demonstrate varying degrees of success, with the technology showing high accuracy in several cases. Although ONT technology holds promise in forensic genetics, further optimization and quality control measures are essential to harness its full potential. This study contributes to the ongoing efforts to refine sequence read tuning and improve correction tools in the context of ONT technology's application in forensic genetics.

Epigenetic-based age prediction in blood samples: Model development.

Aging is a complex process influenced by genetic, epigenetic, and environmental factors that lead to tissue deterioration and frailty. Epigenetic mechanisms, such as DNA methylation, play a significant role in gene expression regulation and aging. This study presents a new age estimation model developed for the Turkish population using blood samples. Eight CpG sites in loci TOM1L1, ELOVL2, ASPA, FHL2, C1orf132, CCDC102B, cg07082267, and RASSF5 were selected based on their correlation with age. Methylation patterns of these sites were analyzed in blood samples from 100 volunteers, grouped into age categories (20-35, 36-55, and ≥56). Sensitivity analysis indicated a reliable performance with DNA inputs ≥1 ng. Statistical modeling, utilizing Multiple Linear Regression, underscores the reliability of the primary 6-CpG model, excluding cg07082267 and TOM1L1. This model demonstrates strong correlations with chronological age (r = 0.941) and explains 88% of the age variance with low error rates (MAE = 4.07, RMSE = 5.73 years). Validation procedures, including a training-test split and fivefold cross-validation, consistently confirm the model's accuracy and consistency. The study indicates minimal variation in error scores across age cohorts and no significant gender differences. The developed model showed strong predictive accuracy, with the ability to estimate age within certain prediction intervals. This study contributes to the age prediction by using DNA methylation patterns, which can have disparate applications, including forensic and clinical assessments.

Predicting Eye and Hair Color in a Turkish Population Using the HIrisPlex System.

Forensic DNA Phenotyping (FDP) can reveal the appearance of an unknown individual by predicting the ancestry, phenotype (i.e., hair, eye, skin color), and age from DNA obtained at the crime scene. The HIrisPlex system has been developed to simultaneously predict eye and hair color. However, the prediction accuracy of the system needs to be assessed for the tested population before implementing FDP in casework. In this study, we evaluated the performance of the HIrisPlex system on 149 individuals from the Turkish population. We applied the single-based extension (SNaPshot chemistry) method and used the HIrisPlex online tool to test the prediction of the eye and hair colors. The accuracy of the HIrisPlex system was assessed through the calculation of the area under the receiver characteristic operating curves (AUC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). The results showed that the proposed method successfully predicted the eye and hair color, especially for blue (100%) and brown (95.60%) eye and black (95.23) and brown (98.94) hair colors. As observed in previous studies, the system failed to predict intermediate eye color, representing 25% in our cohort. The majority of incorrect predictions were observed for blond hair color (40.7%). Previous HIrisPlex studies have also noted difficulties with these phenotypes. Our study shows that the HIrisPlex system can be applied to forensic casework in Turkey with careful interpretation of the data, particularly intermediate eye color and blond hair color.

Monitoring geographical differences in illicit drugs, alcohol, and tobacco consumption via wastewater-based epidemiology: Six major cities in Turkey.

A national wastewater-based epidemiology (WBE) monitoring campaign has been initiated to determine the trends in drug consumption in Turkey since 2019. This study aimed to present the wastewater monitoring results for four periods in 2019 for six major cities with 17 wastewater treatment plants. The study investigated heroin (HER), amphetamine (AMP), methamphetamine (METH), cocaine (COC), 3,4-methylenedioxymethamphetamine (MDMA), cannabis, alcohol, and tobacco to understand the temporal and geographical drug consumption trends. The results indicated a trend of regular cannabis use in all the cities. Considering geographical variations, the drug usage trends were not homogeneous within the country for any of the investigated drugs, except cannabis. HER consumption was predominant in Denizli (1042.48 mg/1000 inh/day), while Izmir and Antalya (154.10 and 79.56 mg/1000 inh/day, respectively) topped for COC consumption. Aydin had the highest consumption levels of AMP (90.03 mg/1000 inh/day) and METH (358.13 mg/1000 inh/day), while MDMA consumption was the highest in Samsun (157.64 mg/1000 inh/day). Tobacco consumption was high in Aydin (8791.69 mg/1000 inh/day) and Antalya (5375.17 mg/1000 inh/day), whereas alcohol consumption was higher in Bursa than in the other cities (53434.61 mL/1000 inh/day). There were no statistically significant differences in the weekend consumption levels of the investigated drugs among these six cities. Although this study included the results of 1 year of consumption monitoring, the data confirms internationally published information on the drug trafficking routes of conventional drugs in this region, especially the Heroin-Balkan route. Results from further sampling will enable accurate evaluation of global drug consumption and trafficking, in addition to alcohol and tobacco use.