Homologous loci DXYS156X and DXYS156Y contain a polymorphic pentanucleotide repeat (TAAAA)n and map to human X and Y chromosomes

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.

Deletion of amelogenin Y-locus in forensics: literature revision and description of a novel method for sex confirmation

Today, the molecular technique routinely for sex determination in forensics is based the detection of length variations in the X-Y homologous amelogenin gene (AMELX and AMELY). In humans, the amelogenin gene is a single-copy gene located on Xp22.1-Xp22.3 and Yp11.2; the simultaneous detection of the X and Y alleles using polymerase chain reaction (PCR) can lead to gender determination. Several studies have shown that normal males may be typed as females with this test: AMELY deletions may result in no product of amplification and normal males being typed as female as a result of the test (negative male). Considering the consequences of the result obtained using only the amelogenin marker, and the related potential difficulties in interpreting the results, the gender misinterpretation may be troublesome in clinical practice and in forensic casework. In this article, beginning with a review of the incidence of gender-testing failures among different populations, and with the different strategies proposed in the literature in case of doubt regarding the presence of deleted AMEL in the DNA profile, we propose a method for the identification of samples with deleted AMEL that can be applied, as an additional assay, in case of doubt regarding PCR results of sex determination.

A comparative analysis of two different sets of Y-chromosome short tandem repeats (Y-STRs) on a common population panel

A comparative analysis of two Y-STR loci sets was conducted on a population sample of 224 individuals, 114 Caucasians and 110 African Americans. One set of loci, designated the OSU 10-locus set, comprises variable, single copy, male-specific loci that are dispersed across the Y-chromosome. Parallel evaluations were performed using the 10 Y-chromosome loci most frequently used for forensic analysis, the loci chosen as the SWGDAM Y-STR loci. The OSU 10-locus set had a greater average number of alleles per locus and higher average gene diversity than the SWGDAM loci. The OSU 10-locus set found 220 unique haplotypes in 224 individuals. In approximately 6000 pairwise haplotype comparisons for each population with each set of loci, the OSU 10-locus set also yielded a greater average number of allelic differences per pair than the SWGDAM loci. Finally, the overall linkage disequilibrium levels were lower for the OSU 10-locus set in the Caucasian population. In general, the OSU 10-locus set revealed a higher power of discrimination than the SWGDAM set.

DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis

The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. A previous recommendation published in 2001 has already addressed Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). Since then, the use of Y-STRs has become very popular, and a numerous new loci have been introduced. The current recommendations address important aspects to clarify problems regarding the nomenclature, the definition of loci and alleles, population genetics and reporting methods.

Forensic potential of the STR DXYS156 in Mexican populations: inference of X-linked allele null

The pentanucleotide STR (TAAAA)n DXYS156 offers advantages for genetic identity testing. In addition to establish the gender, DXYS156 expands the DNA profile and is able to indicate the possible geographic origin of the individual. We analyzed DXYS156 in 757 individuals of both sexes from Mexican populations. We studied the cosmopolitan Mestizo population and six Mexican ethnic groups: Tarahumaras, Purépechas, Nahuas, Mayas, Huicholes and Mezcala Indians. The six shorter (4-10) and the three larger alleles (11-13) were specific for the X and Y-chromosomes, respectively. A random distribution of alleles into genotypes was observed in males and females from each population. We estimated the power of exclusion for paternity testing according to the son's gender, and the power of discrimination in forensic casework. In addition, we detected a relatively high frequency of an X-linked allele null, principally in Mexican-Mestizos (3.6%), which must be considered when DXYS156 be applied for identification purposes.

DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis

The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. A previous recommendation published in 2001 has already addressed Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). Since then, the use of Y-STRs has become very popular, and numerous new loci have been introduced. The current recommendations address important aspects to clarify problems regarding the nomenclature, the definition of loci and alleles, population genetics and reporting methods

Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia

We have analyzed 11 Y-STR loci (DYS19, the two DYS385 loci, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DXYS156Y) in 700 males from ten ethnic groups in east Asia in order to evaluate their usefulness for forensic and population genetic studies. A total of 644 different haplotypes were identified, among which 603 (86.14%) were individual-specific. The haplotype diversity averaged over all populations was 0.9997; using only the nine Y-STRs comprising the "minimal haplotype" (excluding DYS388 and DXYS156Y) it was 0.9996, a value similar to that found in 1924 samples from other Asian populations (0.9996; Lessig et al. Legal Medicine 5(2003) 160-163), and slightly higher than in European populations (0.9976; n=11,610; Roewer et al. For Sci International (2001) 118:103-111). All of the individual east Asian populations examined here had high haplotype diversity (> or =0.997), except for the Mongolians (0.992) and Manchurians (0.960). The most frequent haplotype identified by the nine markers was present at only 1% (7/700). Population comparisons based on Phi(ST) or rho genetic distance measures revealed clustering according to the traditional northeast-southeast distinction, but with exceptions. For example, the Yunnan population from southern China lay among the northern populations, possibly reflecting recent migration, while the Korean population, traditionally considered northern, lay at the boundary between northern and southern populations. An admixture estimate suggested 55(51-59)% northern, 45(41-49)% southern contribution to the Koreans, illustrating the complexity of the genetic history of this region.

A comprehensive survey of human Y-chromosomal microsatellites

We have screened the nearly complete DNA sequence of the human Y chromosome for microsatellites (short tandem repeats) that meet the criteria of having a repeat-unit size of > or = 3 and a repeat count of > or = 8 and thus are likely to be easy to genotype accurately and to be polymorphic. Candidate loci were tested in silico for novelty and for probable Y specificity, and then they were tested experimentally to identify Y-specific loci and to assess their polymorphism. This yielded 166 useful new Y-chromosomal microsatellites, 139 of which were polymorphic, in a sample of eight diverse Y chromosomes representing eight Y-SNP haplogroups. This large sample of microsatellites, together with 28 previously known markers analyzed here--all sharing a common evolutionary history--allowed us to investigate the factors influencing their variation. For simple microsatellites, the average repeat count accounted for the highest proportion of repeat variance (approximately 34%). For complex microsatellites, the largest proportion of the variance (again, approximately 34%) was explained by the average repeat count of the longest homogeneous array, which normally is variable. In these complex microsatellites, the additional repeats outside the longest homogeneous array significantly increased the variance, but this was lower than the variance of a simple microsatellite with the same total repeat count. As a result of this work, a large number of new, highly polymorphic Y-chromosomal microsatellites are now available for population-genetic, evolutionary, genealogical, and forensic investigations.

Forensic value of 14 novel STRs on the human Y chromosome

We identified and characterized 14 novel short-tandem-repeats (STRs) on the Y chromosome and typed them in two samples, a globally diverse panel of 73 cell lines, and 148 individuals from a European-American population. These Y-STRs include eight tetranucleotide repeats (DYS449, DYS453, DYS454, DYS455, DYS456, DYS458, DYS459, and DYS464), five pentanucleotide repeats (DYS446, DYS447, DYS450, DYS452, and DYS463), and one hexanucleotide repeat (DYS448). Sequence data were obtained to designate a repeat number nomenclature. The gene diversities of an additional 22 Y-STRs, including the most commonly used in forensic databases, were directly compared in the cell line DNAs. Six of the 10 most polymorphic markers include the newly identified Y-STRs. Furthermore, these novel Y-STRs greatly improved the resolution of paternal lineages, above the level obtained with commonly used Y-STRs, in the European-American population.

Allele sharing for schizophrenia and schizo-affective disorder within a region of Homo sapiens specific XY homology

A case (based upon an association with cerebral asymmetry) has been presented for a gene for psychosis within the Xq21.3/Yp region of homology that is specific to Homo sapiens. We tested this hypothesis using the pentanucleotide marker DXYS 156 that is located within this region. In 84 families affected by schizophrenia or schizo-affective disorder no tendency toward increased allele sharing amongst siblings was observed (chi(2) = 0.002). We conclude either that this region does not include a gene predisposing to psychosis or that if it does, the relevant variation is epigenetic rather than sequence-based. With respect to the latter possibility we draw attention to the recent evolutionary history of the Xq21.3/Yp region. Genes within the region are in transition to protection from X inactivation and therefore may be epigenetically labile.

DNA diversity and population admixture in Anatolia

The Turkic language was introduced in Anatolia at the start of this millennium, by nomadic Turkmen groups from Central Asia. Whether that cultural transition also had significant population-genetics consequences is not fully understood. Three nuclear microsatellite loci, the hypervariable region I of the mitochondrial genome, six microsatellite loci of the Y chromosome, and one Alu insertion (YAP) were amplified and typed in 118 individuals from four populations of Anatolia. For each locus, the number of chromosomes considered varied between 51-200. Genetic variation was large within samples, and much less so between them. The contribution of Central Asian genes to the current Anatolian gene pool was quantified using three different methods, considering for comparison populations of Mediterranean Europe, and Turkic-speaking populations of Central Asia. The most reliable estimates suggest roughly 30% Central Asian admixture for both mitochondrial and Y-chromosome loci. That (admittedly approximate) figure is compatible both with a substantial immigration accompanying the arrival of the Turkmen armies (which is not historically documented), and with continuous gene flow from Asia into Anatolia, at a rate of 1% for 40 generations. Because a military invasion is expected to more deeply affect the male gene pool, similar estimates of admixture for female- and male-transmitted traits are easier to reconcile with continuous migratory contacts between Anatolia and its Asian neighbors, perhaps facilitated by the disappearance of a linguistic barrier between them.

An extensive analysis of Y-chromosomal microsatellite haplotypes in globally dispersed human populations

The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were.86-.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, phi(ST) statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure.

Commentary on Annett, Yeo et al., Klar, Saugstad and Orr: cerebral asymmetry, language and psychosis--the case for a Homo sapiens-specific sex-linked gene for brain growth

Annett, Yeo et al. and Klar have each proposed theories that relate the genetics of cerebral lateralization to predisposition to psychosis. These theories are considered in relation to the central paradox that psychosis is associated with a substantial biological disadvantage. Annett's heterozygote advantage hypothesis critically identified lateralization as a major determinant of ability, but it appears that what is inherited is degrees (as suggested by Yeo et al.) rather than (or as well as) direction of lateralization. Relative hand skill has been shown (Crow, T.J., Crow, L.R., Done, D.J., Leask, S.J., 1998. Relative hand skill predicts academic ability: global deficits at the point of hemispheric indecision. Neuropsychologia 36, 1275-1282.) to be a powerful predictor (interacting with sex) of academic ability but the greatest region of vulnerability (that includes reading disability and predisposition to psychosis) is close to the point of equal hand skill ('hemispheric indecision'). In contrast with Annett's single locus, Yeo's polygenic and Klar's strand-segregation hypotheses, each of which postulates an autosomal locus or loci, the hypothesis of a single gene for asymmetry located in a sex-specific region of homology on both X and Y chromosomes can account for sex differences, as observed in age of onset, and premorbid precursors of psychosis, as well as differences in the general population in relation to degrees of hand skill, verbal ability and cerebral asymmetry. The evolutionarily recent transposition to, and subsequent paracentric inversion in, the Y chromosome short arm of a 4-Mb block from Xq21.3 (the proximal long arm of the X) are candidates for speciation events in the lineage that led to Homo sapiens. A gene associated with a range of variation (that may be due to a high mutation site, or perhaps to epigenetic modification) on the Y that overlaps with, but differs quantitatively from, that on the X may explain the sex differences associated with psychosis, and may be relevant to its persistence. Such a gene could be the principal determinant in Man of the rate of brain growth, as suggested by Saugstad and by the findings of a recent study of adolescent onset psychosis (James, A., Crow, T.J., Renowden, S., Wardell, M., Smith, D.M., Anslow, P., in press. Is the course of brain development in schizophrenia delayed? Evidence from onsets in adolescence. Schizophr. Res.).

Complete androgen insensitivity in a 47,XXY patient with uniparental disomy for the X chromosome

We describe a unique patient with complete androgen insensitivity syndrome and a 47,XXY karyotype. Androgen receptor assay using cultured pubic skin fibroblasts showed no androgen-binding capacity. Sequence analysis of the androgen receptor gene demonstrated two nonsense mutations, one in exon D and one in exon E. Microsatellite marker analysis showed that the patient is homozygous for all five Xq loci examined. The results suggest that the long-arms of the two X chromosomes are identical, i.e., uniparental isodisomy at least for Xq, and carry the same mutations in the androgen receptor gene. This explains how complete androgen insensitivity syndrome occurred in this 47,XXY individual.

Development of an oligonucleotide probe specific for Trichophyton rubrum

A species-specific DNA probe was developed to detect the dermatophyte species Trichophyton rubrum. The selected oligonucleotide sequence is derived from the highly variable internal transcribed spacer 2 region of the ribosomal DNA operon. The specificity of the non-radioactive labelled oligonucleotide probe was tested against related dermatophytes, other eukaryotic microorganisms and against human DNA. No cross-hybridization was found, and hybridization signals were invariably detected in all T. rubrum strains investigated. In addition, no homologous sequences were found searching the EMBL database. Experiments to establish a method for isolating DNA directly from clinical specimens gave successful amplification and hybridization products in about 30% of the samples.

Relative hand skill predicts academic ability: global deficits at the point of hemispheric indecision

Population variation in handedness (a correlate of cerebral dominance for language) is in part genetic and, it has been suggested, its persistence represents a balanced polymorphism with respect to cognitive ability. This hypothesis was tested in a sample of 12,770 individuals in a UK national cohort (the National Child Development Study) by assessing relative hand skill (in a square checking task) as a predictor of verbal, non-verbal, and mathematical ability and reading comprehension at the age of 11 years. Whereas some modest decrements were present in extreme right handers the most substantial deficits in ability were seen close to the point of equal hand skill ('hemispheric indecision'). For verbal ability females performed better than males, but the relationship to relative hand skill was closely similar for the two sexes; for reading comprehension males close to the point of equal hand skill showed greater impairments than females. Analysed by writing hand the relationship of ability to hand skill appeared symmetrical about the point of 'hemispheric indecision'. The variation associated with degrees of dominance may reflect the operation of continuing selection on the gene (postulated to be X-Y linked) by which language evolved and speciation occurred.

Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population

An analysis of Y-chromosomal haplotypes in several European populations reveals an almost monomorphic pattern in the Finns, whereas Y-chromosomal diversity is significantly higher in other populations. Furthermore, analyses of nucleotide positions in the mitochondrial control region that evolve slowly show a decrease in genetic diversity in Finns. Thus, relatively few men and women have contributed the genetic lineages that today survive in the Finnish population. This is likely to have caused the so-called "Finnish disease heritage"-i.e., the occurrence of several genetic diseases in the Finnish population that are rare elsewhere. A preliminary analysis of the mitochondrial mutations that have accumulated subsequent to the bottleneck suggests that it occurred about 4000 years ago, presumably when populations using agriculture and animal husbandry arrived in Finland.

Fathers and sons: the Y chromosome and human evolution

It should be possible to use Y chromosome DNA polymorphisms to trace paternal lineages for evolutionary and other studies, but progress in these areas has been slow because it has been difficult to find suitable markers. However, it is now possible to use selected, slowly evolving polymorphisms to draw a rudimentary Y chromosome tree, while more rapidly evolving polymorphisms allow most independent Y chromosomes to be distinguished. Different populations often have characteristically different Y chromosomes, and Y chromosome studies are soon likely to make a major contribution to our understanding of the origins of modern humans.