Novel methods of molecular sex identification from skeletal tissue using the amelogenin gene

Visual identification for species and sex derived from bloodstain based on phosphate-mediated isothermal amplification colorimetric system

Species and sex confirmation of the biological specimen play a crucial role in crime investigation. However, the specimen found in the scene is always trace quantity, which is hard to be analyzed by current methods. Moreover, the time-consuming DNA extraction, sophisticated apparatus, and complex data processing make it difficult to satisfy the demand of speediness and convenience for point-of-care tests. In this study, we first exhibit a phosphate-based visual system for field-based species and sex identification derived from trace bloodstain. By introducing phosphate ion-based colorimetry into loop-mediated isothermal amplification (LAMP) for result interpretation, not only the bloodstain can be directly submitted to mitochondrial variant amplification owing to the enhanced amplification efficiency by pyrophosphate ion hydrolyzation, but also the colorimetric signal can be recognized by the naked eye for result output within 30 min through molybdophosphate generation. Aerosol contamination, the major conflict of LAMP, has been solved once and for all by integrating uracil-DNA glycosylase into this system that still holds on a constant temperature. As a demonstration, cytochrome b and Y-chromosomal amelogenin are employed to identify species and sex respectively, which has achieved a highly sensitive and specific distinguishability under a strong interferential background. Accurate results can be obtained from both the simulative degraded and dated specimen, which indicates that this novel system may serve as a promising tool in forensic practice.

Comparing Walker's (2008) skull trait sex estimation standard to proteomic sex estimation for a group of South Asian individuals

This research assesses the potential for misidentification of sex in individuals of South Asian ancestry using the Walker (2008) morphological skull sex estimation standard [1]. Chromosomal sex was assessed using proteomic analysis targeting sex chromosome-specific amylogenic peptides. Results showed that the Walker method produced incorrect classification for 36.7 % of individuals. Overwhelmingly, those incorrectly assigned were chromosomally male. Misidentification was due to males within the group having lower trait scores (i.e., more gracile traits) than the standard would predict. There was also a high level of overlap in trait scores between male and females indicating reduced expression of sexual dimorphism. The use of established multivariate statistical techniques improved accuracy of sex estimation in some cases, but larger osteological data sets from South Asian individuals are required to develop population-specific standards. We suggest that peptide analysis may provide a useful tool for the forensic anthropologist when assessing sex in populations without population specific osteological standards.

What we see is what we touch? Sex estimation on the pelvis in virtual anthropology

BACKGROUND

Computed tomography (CT) scans are a convenient means to study 3D reconstructions of bones. However, errors associated with the different nature of the observation, e.g. visual and tactile (on dry bone) versus visual only (on a screen) have not been thoroughly investigated.

MATERIALS AND METHODS

We quantified the errors between modalities for sex estimation protocols of nonmetric (categorical and ordinal) and metric data, using 200 dry pelves of archaeological origin and the CT reconstructions of the same bones. In addition, we 3D surface scanned a subsample of 39 pelves to compare observations with dry bone and CT data. We did not focus on the sex estimation accuracy but solely on the consistency of the scoring, hence, the interchangeability of the modalities.

RESULTS

Metric data yielded the most consistent results. Among the nonmetric protocols, ordinal data performed better than categorical data. We applied a slightly modified description for the trait with the highest errors and grouped the traits according to consistency and availability in good, intermediate, and poor.

DISCUSSION

The investigated modalities were interchangeable as long as the trait definition was not arbitrary. Dry bone (gold standard) performed well, and CT and 3D surface scans performed better. We recommend researchers test their affinity for using virtual modalities. Future studies could use our consistency analysis and combine the best traits, validating their accuracy on various modalities.

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.

Progress in forensic bone DNA analysis: Lessons learned from ancient DNA

Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal material and the potential use of the developed protocols in forensic work. We discuss the various steps, from choosing samples for DNA extraction to deciding between classical PCR amplification and massively parallel sequencing approaches. Based on the progress made in ancient DNA analyses combined with the requirements of forensic work, we suggest that there is substantial potential for incorporating ancient DNA approaches into forensic protocols, a process that has already begun to a considerable extent. However, taking full advantage of the experiences gained from ancient DNA work will require comparative studies by the forensic DNA community to tailor the methods developed for ancient samples to the specific needs of forensic studies and case work. If successful, in our view, the benefits for both communities would be considerable.

A novel method of male sex identification of human ancient skeletal remains

Sex identification of ancient individuals is important to understand aspects of the culture, demographic structure, religious practices, disease association, and the history of the ancient civilizations. Sex identification is performed using anthropometric measurements and molecular genetics techniques, including quantification of the X and Y chromosomes. These approaches are not always reliable in subadult, or fragmented, incomplete skeletons or when the DNA is highly degraded. Most of the methods include the identification of the male and female sexes, but the absence of a specific marker for the males does not mean that the sample obtained was from a female. This study aims (1) to identify new male-specific regions that allow male identification; (2) to contrast the effectiveness of these markers against AMELX/AMELY and anthropometric measurement procedures; and (3) to test the efficacy of these markers in archaeological samples. For the first two aims, we used known sex samples, and for the third aim, we used samples from different archaeological sites. A novel molecular technique to identify male-specific regions by amplification of TTTY7, TSPY3, TTTY2, and TTTY22 genes of the human Y chromosome was developed. The results showed amplification of the specific DNA regions of Y chromosome in male individuals, with no amplification being observed in any of the female samples, confirming their specificity for male individuals. This approach complements the current procedures, such as the AMELX/AMELY test and anthropometric principle.

Accurate Sex Identification of Ancient Elephant and Other Animal Remains Using Low-Coverage DNA Shotgun Sequencing Data

Sex identification of ancient animal biological remains can benefit our understanding of historical population structure, demography and social behavior. Traditional methods for sex identification (e.g., osteological and morphometric comparisons) may be ineffective when animal remains are not well preserved, when sex distinguishing characteristics have not yet developed, or where organisms do not exhibit sex-associated phenotypic dimorphisms. Here we adapt a method developed for human sex determination so that it can be used to identify the sex of ancient and modern animal taxa. The method identifies sex by calculating the ratio of DNA reads aligning to the X chromosome to DNA reads aligning to autosomes (termed the Rx ratio). We tested the accuracy of this method using low coverage genomes from 15 modern elephants (Loxodonta africana) for which sex was known. We then applied this method to ancient elephant ivory samples for which sex was unknown, and describe how this method can be further adapted to the genomes of other taxa. This method may be especially useful when only low-coverage genomic data are obtainable. Furthermore, because this method relies on only the X and not the Y chromosome, it can be used to determine the sex of organisms for which a reference genome was obtained from a female or for which only the X chromosome is reported. Such taxa include the domestic cat, sheep, goat, and horse; and non-domesticated animals such as the Sumatran orangutan, western lowland gorilla and meerkat.

Identification of trace metals and potential anthropogenic influences on the historic New York African Burial Ground population: A pXRF technology approach

The New York African Burial Ground (NYABG) is the country’s oldest and largest burial site of free and enslaved Africans. Re-discovered in 1991, this site provided evidence of the biological and cultural existence of a 17^th and 18^th Century historic population viewing their skeletal remains. However, the skeletal remains were reburied in October 2003 and are unavailable for further investigation. The analysis of grave soil samples with modern technology allows for the assessment of trace metal presence. Portable X-ray fluorescence (pXRF) spectrometry provides a semi-quantitative and non-destructive method to identify trace metals of this population and in the surrounding environment. Sixty-five NYABG soil samples were analyzed on a handheld Bruker Tracer III- SD XRF with 40 kV of voltage and a 30μA current. Presence of As, Cu, and Zn can potentially decipher the influence of the local 18^th Century pottery factories. Elevated levels of Sr validate the assumed heavy vegetative diets of poor and enslaved Africans of the time. Decreased levels of Ca may be due in part to the proximity of the Collect Pond, the existing water table until the early 19^th Century, and Manhattan’s rising sea level causing an elevated water table washing away the leached Ca from human remains. These data help us reconstruct the lives of these early Americans in what became New York City.

Molecular sexing assays in 114 mammalian species: In silico sequence reanalysis and a unified graphical visualization of diagnostic tests

Molecular-based methods for identifying sex in mammals have a wide range of applications, from embryo manipulation to ecological studies. Various sex-specific or homologous genes can be used for this purpose, PCR amplification being a common method. Over the years, the number of reported tests and the range of tested species have increased greatly. The aim of the present analysis was to retrieve PCR-based sexing assays for a range of mammalian species, gathering the gene sequences from either the articles or online databases, and visualize the molecular design in a uniform manner. For nucleotide alignment and diagnostic test visualization, the following genomic databases and tools were used: NCBI, Ensembl Nucleotide BLAST, ClustalW2, and NEBcutter V2.0. In the 45 gathered articles, 59 different diagnostic tests based on eight different PCR-based methods were developed for 114 mammalian species. Most commonly used genes for the analysis were ZFX, ZFY, AMELX, and AMELY. The tests were most commonly based on sex-specific insertions and deletions (SSIndels) and sex-specific sequence polymorphisms (SSSP). This review provides an overview of PCR-based sexing methods developed for mammals. This information will facilitate more efficient development of novel molecular sexing assays and reuse of previously developed tests. Development of many novel and improvement of previously developed tests is also expected with the rapid increase in the quantity and quality of available genetic information.

Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization

Erstwhile, sex was determined by observation, which is not always feasible. Nowadays, genetic methods are prevailing due to their accuracy, simplicity, low costs, and time-efficiency. However, there is no comprehensive review enabling overview and development of the field. The studies are heterogeneous, lacking a standardized reporting strategy. Therefore, our aim was to collect genetic sexing assays for mammals and assemble them in a catalogue with unified terminology. Publications were extracted from online databases using key words such as sexing and molecular. The collected data were supplemented with species and gene IDs and the type of sex-specific sequence variant (SSSV). We developed a catalogue and graphic presentation of diagnostic tests for molecular sex determination of mammals, based on 58 papers published from 2/1991 to 10/2016. The catalogue consists of five categories: species, genes, SSSVs, methods, and references. Based on the analysis of published literature, we propose minimal requirements for reporting, consisting of: species scientific name and ID, genetic sequence with name and ID, SSSV, methodology, genomic coordinates (e.g., restriction sites, SSSVs), amplification system, and description of detected amplicon and controls. The present study summarizes vast knowledge that has up to now been scattered across databases, representing the first step toward standardization regarding molecular sexing, enabling a better overview of existing tests and facilitating planned designs of novel tests. The project is ongoing; collecting additional publications, optimizing field development, and standardizing data presentation are needed.

A Molecular Approach to the Sexing of the Triple Burial at the Upper Paleolithic Site of Dolní Věstonice

In the past decades ancient DNA research has brought numerous insights to archaeological research where traditional approaches were limited. The determination of sex in human skeletal remains is often challenging for physical anthropologists when dealing with incomplete, juvenile or pathological specimens. Molecular approaches allow sexing on the basis of sex-specific markers or by calculating the ratio of DNA derived from different chromosomes. Here we propose a novel approach that relies on the ratio of X chromosome-derived shotgun sequencing data to the autosomal coverage, thus establishing the probability of an XX or XY karyotype. Applying this approach to the individuals of the Upper Paleolithic triple burial of Dolní Věstonice reveals that all three skeletons, including the individual DV 15, whose sex has long been debated due to a pathological condition, were male.

Preliminary Study to Test the Feasibility of Sex Identification of Human (Homo sapiens) Bones Based on Differences in Elemental Profiles Determined by Handheld X-ray Fluorescence

Sex assignment of human remains is a crucial step in forensic anthropological studies. The aim of this study was to examine elemental differences between male and female bones using X-ray fluorescence (XRF) and determine if elemental profiling could be used for sex discrimination. Cranium, humerus, and os coxae of 60 skeletons (30 male, 30 female) from the Chiang Mai University Skeletal Collection were scanned by XRF and differences in elemental profiles between male and female bones determined using discriminant analysis. In the cranium, three elements (S, Ca, Pb) were significantly higher in males and five elements (Si, Mn, Fe, Zn, Ag) plus light elements (atomic number lower than 12) were higher in females. In humerus and os coxae, nine elements were significantly higher in male and one element was higher in female samples. The accuracy rate for sex estimation was 60, 63, and 61 % for cranium, humerus, and os coxae, respectively, and 67 % when data for all three bones were combined. We conclude that there are sex differences in bone elemental profiles; however, the accuracy of XRF analyses for discriminating between male and female samples was low compared to standard morphometric and molecular methods. XRF could be used on small samples that cannot be sexed by traditional morphological methods, but more work is needed to increase the power of this technique for gender assignment.

Forensic Analysis of Mitochondrial and Autosomal Markers Using Pyrosequencing®

Forensic casework analyses often face challenges, such as limited genetic material with or without fragmentation and damage. To compensate for low amounts and degradation, shorter amplicons are often applied in the analysis. Also, a change of markers might be necessary using mitochondrial instead of autosomal markers. In addition, forensic research often involves analysis of large number of samples for marker evaluation and population-database compilation. Therefore, a flexible, robust but also rapid method for the detection of variation is highly useful. Pyrosequencing(®) is a rapid, reliable, easy-to-use method for sequence analysis. The method is well suited for rapid forensic analysis of a few targets or analysis of a single target in many samples. It allows sequencing of very short amplicons, which facilitates analysis of degraded DNA. Here we present the use of Pyrosequencing, a robust method for sensitive forensic analysis of mitochondrial DNA, autosomal STRs, and Y-chromosome STRs and SNPs.

Sex determination from femora in late antique sample from Eastern Adriatic coast (Salona necropolis)

The determination of sex is one of the first steps in anthropological analysis. When skeletal remains are fragmented, the most useful approach is application of osteometric methods. The methods are population specific, and therefore require development of discriminant functions for each population group.

The aim of this study was to test sexual dimorphism of femoral measurements and to calculate discriminant functions applicable for sex determination on fragmented skeletal remains on the late antique sample from the Eastern Adriatic coast (2nd-6th century AD).

214 randomly chosen skeletons from the excavation site Solin-Smiljanovac were analyzed. Sex and age were assessed using standard anthropological methods, and skeletons were examined for pathologic and traumatic changes. In the next step, we selected 27 female and 48 male skeletons free of peri- or post-mortem changes that could affect measurements Eight standard femoral measurements were taken. Sexual dimorphism was initially compared using independent sample t test, after which discriminant functions were computed.

All femoral measurements showed statistically significant sexual dimorphism (p<0.001). Ten discriminant functions for every part of femur were calculated and obtained classification accuracy of 73.1-91.8%. This study reached relatively high classification, which will improve further analysis of the skeletal remains from the Salona necropolis. Due to similar population structure in the Roman period across the Adriatic coast, the discriminant functions could be applicable for all populations from the same period and area. This study also raised a few methodological questions showing that when creating discriminant functions we should consider not only the accuracy, but also the applicability based on the experience from the anthropology laboratory that considers the state of preservation and frequent pathology.

Sex determination from dentin and pulp in a medicolegal context

BACKGROUND

The techniques used to determine the sex of skeletons are limited. The authors conducted a study to analyze the accuracy of sex identification from dentin and pulp via DNA isolation.

METHODS

The authors extracted DNA from the dentin and pulp of 14 teeth by using a silica-based methodology. They used the amelogenin gene to determine the sex via polymerase chain reaction. β-actin, a housekeeping gene, was used as a control gene. The authors checked the results in agarose gel and semiquantified them by using gel analysis software.

RESULTS

The DNA yield depended on the type of tooth and was lowest in the smallest teeth (that is, incisors). In all cases, the authors were able to identify the sex, as well as the control gene, which suggests the potential to identify other genes, such as short tandem repeats.

CONCLUSIONS

It is possible to correctly identify a person's sex from dentin and pulp; in instances in which one dental material is not available, the other material can be used with the same efficiency. Practical Implications. The results of this study are applicable to forensic dentistry, particularly in situations in which there is commingling of remains and fragmentary remains, and there may be only one tooth with which to identify a person's sex.

Determined about sex: sex-testing in 45 primate species using a 2Y/1X sex-typing assay

Sex-testing using molecular genetic technique is routinely used in the fields of forensics, population genetics and conservation biology. However, none of the assay used so far allows a non-ambiguous and successful sex determination for human and non-human primate species. The most widely used method, AMELY/X, and its alternatives suffer from a set of drawbacks in humans and can rarely be used in New World primate species. Here, we designed a new sex-typing assay using a multiplexed PCR amplification of UTX and UTY-homologous loci and combined male-specific SRY locus. This method was successfully tested on 1048 samples, including 82 non-human primates from 45 Anthropoidea and Lemuriformes species and 966 human samples from 24 populations (Africans, Europeans, and South Americans). This sex-typing method is applicable across all primate species tested from Hominoidea to Indriidae, and also on various populations with different background origins; it represents a robust and cheap sex-typing assay to be used both by the anthropologist and primatologist communities.

Sex determination in highly fragmented human DNA by high-resolution melting (HRM) analysis

Sex identification in ancient human remains is a common problem especially if the skeletons are sub-adult, incomplete or damaged. In this paper we propose a new method to identify sex, based on real-time PCR amplification of small fragments (61 and 64 bp) of the third exon within the amelogenin gene covering a 3-bp deletion on the AMELX-allele, followed by a High Resolution Melting analysis (HRM). HRM is based on the melting curves of amplified fragments. The amelogenin gene is located on both chromosomes X and Y, showing dimorphism in length. This molecular tool is rapid, sensitive and reduces the risk of contamination from exogenous genetic material when used for ancient DNA studies. The accuracy of the new method described here has been corroborated by using control samples of known sex and by contrasting our results with those obtained with other methods. Our method has proven to be useful even in heavily degraded samples, where other previously published methods failed. Stochastic problems such as the random allele drop-out phenomenon are expected to occur in a less severe form, due to the smaller fragment size to be amplified. Thus, their negative effect could be easier to overcome by a proper experimental design.

Determination of sex origin of meat and meat products on the DNA basis: a review

Sex determination of domestic animal's meat is of potential value in meat authentication and quality control studies. Methods aiming at determining the sex origin of meat may be based either on the analysis of hormone or on the analysis of nucleic acids. At the present time, sex determination of meat and meat products based on hormone analysis employ gas chromatography-mass spectrometry (GC-MS), high-performance liquid chromatography-mass spectrometry/mass spectrometry (HPLC-MS/MS), and enzyme-linked immunosorbent assay (ELISA). Most of the hormone-based methods proved to be highly specific and sensitive but were not performed on a regular basis for meat sexing due to the technical limitations or the expensive equipments required. On the other hand, the most common methodology to determine the sex of meat is unquestionably traditional polymerase chain reaction (PCR) that involves gel electrophoresis of DNA amplicons. This review is intended to provide an overview of the DNA-based methods for sex determination of meat and meat products.

Sex determination in skeletal remains from the medieval Eastern Adriatic coast - discriminant function analysis of humeri

Aim

To investigate the usefulness of humerus measurement for sex determination in a sample of medieval skeletons from the Eastern Adriatic Coast. Additional aim was to compare the results with contemporary female population.

Methods

Five humerus measurements (maximum length, epicondylar width, maximum vertical diameter of the head, maximum and minimum diameter of the humerus at midshaft) for 80 male and 35 female medieval and 19 female contemporary humeri were recorded. Only sufficiently preserved skeletons and those with no obvious pathological or traumatic changes that could affect the measurements were included. For ten samples, analysis of DNA was performed in order to determine sex using amelogenin.

Results

The initial comparison of men and women indicated significant differences in all five measures (P < 0.001). Discriminant function for sex determination indicated that as much as 85% of cases could be properly categorized, with better results in men (86%) than women (80%). Furthermore, the comparison of the medieval and contemporary women did not show significant difference in any of the measured features. Sex results obtained by anthropological and DNA analysis matched in all 10 cases.

Conclusion

The results indicate that humerus measurement in Croatian medieval population may be sufficient to determine the sex of the skeleton. Furthermore, it seems that secular changes have not substantially affected contemporary population, suggesting that the results of this study are transferable to contemporary population as well.

Semiquantitative detection of male pork tissue in meat and meat products by PCR

Consumer awareness has increased concerning castration of piglets without analgesia or anaesthesia. On the other hand the occurrence of boar taint is not tolerated by consumers. Currently no reliable methods exist for the on-line detection of boar taint in the slaughterhouse or for genetic sexing of pigs. Therefore, as an alternative the detection of male pork meat was sought. Based on detection of a length polymorphism of the sex chromosomal amelogenin gene a reliable, specific and highly sensitive PCR method for qualitative and semi-quantitative determination of male pork tissue in meat and meat products was determined. A set of 25 male and 25 female meat samples could be correctly identified and mixtures with as little as 0.1% male meat content could be detected. Therefore the method can be used for production and control of specific meat products containing low amounts of male pork meat and thus avoiding boar taint.