Sex Determination from Fragmented and Degenerated DNA by Amplified Product-Length Polymorphism Bidirectional SNP Analysis of Amelogenin and SRY Genes

Rapid and Reagent-Free Analysis of Dried Blood Spot by Paper Spray Mass Spectrometry Reveals Sex: Implications in Forensic Investigations

Identifying sex from an unknown dried blood spot (DBS), especially when the corpse remains undiscovered, often provides valuable evidence in forensic casework. While DNA-based sex determination is a reliable method in forensic settings, it requires expensive reagents and is time-consuming. To develop a rapid reagent-free blood test for sex, we employed paper spray ionization mass spectrometry (PSI-MS) to capture sex-discriminatory lipid profiles from 200 DBS samples comprising 100 males and 100 females. We conducted a supervised machine learning (ML) analysis on all detected lipid signals to hunt biomarkers of sex within the data set. This analysis unveiled significant differences in specific sphingomyelin and phospholipid species levels between male and female DBS samples. Using the parsimonious set of 60 lipid signals, we constructed a classifier that achieved 100% overall accuracy in predicting sex from DBS on paper. Additionally, we assessed three-day-old air-exposed DBS on glass and granite surfaces, simulating the typical blood samples available for forensic investigations. Consequently, we achieved ∼92% overall sex prediction accuracy from the holdout test data set of DBS on glass and granite surfaces. As a highly sensitive detection tool, PSI-MS combined with ML has the potential to revolutionize forensic methods by rapidly analyzing blood molecules encoding personal information.

Application of natural sciences methodology in archaeological study of Iron Age burials in Latvia: pilot study

Natural sciences provide several modern methodologies that could be successfully applied in archaeological studies. In this pilot study, archaeological human remains from two Iron Age cemeteries (7th-twelfth centuries AD), Lejasbitēni and Čunkāni-Dreņģeri, which are located in different regions of Latvia, were studied. We applied ancient DNA (aDNA) and tooth enamel peptide analysis to determine the biological sex of the individuals. In addition, aDNA analysis was used to perform mtDNA haplogroup analysis. In most cases, the results of aDNA analysis regarding the biological sex of individuals coincided with the gender assigned based on grave orientation and grave goods. The results of sex determination using peptide analysis in all four individuals for whom data were available matched the possible gender. Of the 17 samples that had sufficient DNA for sequencing, seven samples had enough reads to perform mtDNA haplogroup analysis. The H2a2a, I4a1, H2a2a1, and H16c mtDNA haplogroups were identified in the individuals from the Lejasbitēni cemetery, while the T2b and K1a + 150 mtDNA haplogroups were identified in the individuals from the Čunkāni-Dreņģeri cemetery. Overall, the obtained results demonstrated the feasibility of applying aDNA and tooth enamel peptide analysis for biological sex determination within archaeological studies. The availability of human aDNA data will be highly useful for investigating the demographic history and social structures in Iron Age Latvia.

Highly sensitive sex determination method using the exon 1 region of the amelogenin gene

Sex determination is a crucial factor in the identification of unidentified human remains. Sex determination by DNA analysis is particularly useful because it can be applied to samples for which morphological characteristics are unavailable. Because samples handled in forensic DNA typing are easily degraded by environmental factors and microorganisms, there is a need for a method that can accurately determine sex even in highly decayed samples. Previous studies mainly used sex differences in an intron of the amelogenin gene. However, this region is highly polymorphic, and there are cases where accurate sexing cannot be performed because of genetic mutations in the target region. Thus, for reliable sex determination, it is desirable to select loci with as few non-sexual polymorphisms as possible. In this study, we focused on the exon 1 region of the amelogenin gene, which has very little polymorphism other than sex differences. We developed a primer set for sex determination and compared it with the GlobalFiler™ PCR Amplification Kit (GF), which is widely used for forensic DNA typing. The results showed that the amount of DNA required for accurate sex determination was 25 pg for both methods, achieving equivalent sensitivity. Next, we compared the two methods using ancient human skeletons and found that the present method with its shorter amplicon was considerably superior to GF. The present method is simple, rapid, inexpensive, and suitable for analyzing highly degraded samples. Therefore, this method is expected to contribute to forensic sciences and physical anthropology.

Sequence variations, flanking region mutations, and allele frequency at 31 autosomal STRs in the central Indian population by next generation sequencing (NGS)

Capillary electrophoresis-based analysis does not reflect the exact allele number variation at the STR loci due to the non-availability of the data on sequence variation in the repeat region and the SNPs in flanking regions. Herein, this study reports the length-based and sequence-based allelic data of 138 central Indian individuals at 31 autosomal STR loci by NGS. The sequence data at each allele was compared to the reference hg19 sequence. The length-based allelic results were found in concordance with the CE-based results. 20 out of 31 autosomal STR loci showed an increase in the number of alleles by the presence of sequence variation and/or SNPs in the flanking regions. The highest gain in the heterozygosity and allele numbers was observed in D5S2800, D1S1656, D16S539, D5S818, and vWA. rs25768 (A/G) at D5S818 was found to be the most frequent SNP in the studied population. Allele no. 15 of D3S1358, allele no. 19 of D2S1338, and allele no. 22 of D12S391 showed 5 isoalleles each with the same size and with different intervening sequences. Length-based determination of the alleles showed Penta E to be the most useful marker in the central Indian population among 31 STRs studied; however, sequence-based analysis advocated D2S1338 to be the most useful marker in terms of various forensic parameters. Population genetics analysis showed a shared genetic ancestry of the studied population with other Indian populations. This first-ever study to the best of our knowledge on sequence-based STR analysis in the central Indian population is expected to prove the use of NGS in forensic case-work and in forensic DNA laboratories.

Study of Sexual Dimorphism in Metatarsal Bones: Geometric and Inertial Analysis of the Three-Dimensional Reconstructed Models

The aim of the present paper is to determine the sex of the individual using three-dimensional geometric and inertial analyses of metatarsal bones. Metatarsals of 60 adult Chinese subjects of both sexes were scanned using Aquilion One 320 Slice CT Scanner. The three-dimensional models of the metatarsals were reconstructed, and thereafter, a novel software using the center of mass set as the origin and the three principal axes of inertia was employed for model alignment. Eight geometric and inertial variables were assessed: the bone length, bone width, bone height, surface-area-to-volume ratio, bone density, and principal moments of inertia around the x, y, and z axes. Furthermore, the discriminant functions were established using stepwise discriminant function analysis. A cross-validation procedure was performed to evaluate the discriminant accuracy of functions. The results indicated that inertial variables exhibit significant sexual dimorphism, especially principal moments of inertia around the z axis. The highest dimorphic values were found in the surface-area-to-volume ratio, principal moments of inertia around the z axis, and bone height. The accuracy rate of the discriminant functions for sex determination ranged from 88.3% to 98.3% (88.3%-98.3% cross-validated). The highest accuracy of function was established based on the third metatarsal bone. This study showed for the first time that the principal moment of inertia of the human bone may be successfully implemented for sex estimation. In conclusion, the sex of the individual can be accurately estimated using a combination of geometric and inertial variables of the metatarsal bones. The accuracy should be further confirmed in a larger sample size and be tested or independently developed for distinct population/age groups before the functions are widely applied in unidentified skeletons in forensic and bioarcheological contexts.

Molecular analysis for sex determination in forensic dentistry: a systematic review

Background

Sex determination can be useful in forensic casework, such as in mass disasters, transportation accidents, and cases of a missing person or sexual assault. The remnants of the body can be traced by DNA of the victim, using samples from various sources such as teeth, oral epithelial tissue, and saliva.

Main body

The review aimed to describe research in forensic dentistry with DNA source from the oral region and methods of the applied DNA analysis. A search in PubMed, Google Scholar, and Scopus electronic databases from 2009 to 2019 was conducted to include studies according to PRISMA guidelines. Ten studies were eligible for the review. Genetic markers originated from dentin, dental pulp, saliva, or epithelial cells from buccal tissue and prosthesis. The applied DNA analysis methods were PCR, real-time PCR, and nested PCR.

Conclusions

The published articles mostly showed successful DNA extraction and sex determination, but the rate of success declined as the sample source underwent manipulation to mimic the forensic conditions. Amelogenin, SRY, and DYS14 were reliable indicators for sex determination. Molecular analysis has proved to be efficient and accurate, but the daily forensic practice must select the most appropriate method according to the available body remnants.