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Electrophoresis Mar 2024Insertion/deletion polymorphisms (InDels) are a category of highly prevalent markers in the human genome, characterized by their distinctive attributes, including short...
Insertion/deletion polymorphisms (InDels) are a category of highly prevalent markers in the human genome, characterized by their distinctive attributes, including short amplicon sizes and low mutation rates, which have shown great potential in forensic applications. Multi-allelic InDel and multi-InDel markers, collectively abbreviated as MM-InDels, were developed to enhance polymorphism by the introduction of novel alleles. Nevertheless, the relatively low mutation rates of InDels, coupled with the founder effect, result in distinct allele frequency distributions among populations. The divergent characteristics of InDels in different populations also pose challenges to the establishment of universally efficient InDel multiplex assays. To enhance the system efficiency of the InDel assay and its applicability across diverse populations, 39 MM-InDels with high polymorphism in five different ancestry superpopulations were selected from the 1000 Genomes Project dataset and combined with an amelogenin gender marker to construct a multiplex assay (named MMIDplex). The combined power of discrimination and the cumulative probability of exclusion of 39 MM-InDels were 1 - 1.3 × 10 and 1 - 9.83 × 10 in the Chinese Han population, and larger than 1-10 and 1-10 in the reference populations, relatively. These results demonstrate that the MMIDplex assay has the potential to obtain sufficient power for individual identification and paternity test in global populations.
Topics: Humans; Asian People; China; Forensic Genetics; Gene Frequency; Genetics, Population; INDEL Mutation; Polymorphism, Genetic
PubMed: 38037287
DOI: 10.1002/elps.202300181 -
Journal of Molecular Evolution Dec 2023Deletion/insertion polymorphism (DIP) is one of the more promising genetic markers in the field of forensic genetics for personal identification and biogeographic...
Deletion/insertion polymorphism (DIP) is one of the more promising genetic markers in the field of forensic genetics for personal identification and biogeographic ancestry inference. In this research, we used an in-house developed ancestry-informative marker-DIP system, including 56 autosomal diallelic DIPs, three Y-chromosomal DIPs, and an Amelogenin gene, to analyze the genetic polymorphism and ancestral composition of the Chinese Korean group, as well as to explore its genetic relationships with the 26 reference populations. The results showed that this novel panel exhibited high genetic polymorphism in the studied Korean group and could be effectively applied for forensic individual identification in the Korean group. In addition, the results of multiple population genetic analyses indicated that the ancestral component of the Korean group was dominated by northern East Asia. Moreover, the Korean group was more closely related to the East Asian populations, especially to the Japanese population in Tokyo. This study enriched the genetic data of the Korean ethnic group in China and provided information on the ancestry of the Korean group from the perspective of population genetics.
Topics: Humans; Ethnicity; Polymorphism, Genetic; Genetics, Population; China; Republic of Korea; Gene Frequency; Polymorphism, Single Nucleotide
PubMed: 38006428
DOI: 10.1007/s00239-023-10143-y -
Genes Oct 2023The study of gender markers is essential in forensic genetic analysis. Mutations in the X or Y homologs of the amelogenin gene can be misleading, resulting in serious...
The study of gender markers is essential in forensic genetic analysis. Mutations in the X or Y homologs of the amelogenin gene can be misleading, resulting in serious mistakes in forensic genetic analysis. We recently discovered two male cases of the X homolog of the amelogenin (AMELX) allelic dropout while analyzing short tandem repeat genotypes obtained from crime scene evidence. Subsequently, we evaluated the molecular characteristics of AMELX allelic dropout in this study. We used two previously reported amelogenin primers to verify a half level of amelogenin gene amplification intensity in the two male cases, which we confirmed was caused by AMELX allelic dropout. We then characterized the point mutation using Sanger sequencing and designed mutation-specific primers that could overcome AMELX allelic dropout. Short tandem repeat genotyping analysis confirmed that the AMELX allelic dropout was recovered by the mutation-specific primer designed specifically for this case. The sequencing of the AMELX allele revealed a single-point variant from A→G at base position 7 downstream from the 3' end in the amelogenin forward primer-binding region. This point mutation was identically found in two different male cases, resulting in AMELX allelic dropout. To our knowledge, these mutations and the X homolog amplification failure of amelogenin have not been reported in the Korean population. Our study provides a reliable approach to AMELX allelic dropout due to rare case mutations and could enable the better interpretation of gender markers for forensic samples.
Topics: Humans; Male; Alleles; Amelogenin; Asian People; Point Mutation
PubMed: 38002929
DOI: 10.3390/genes14111986 -
Scientific Reports Nov 2023When subadult skeletons need to be identified, biological sex diagnosis is one of the first steps in the identification process. Sex assessment of subadults using...
When subadult skeletons need to be identified, biological sex diagnosis is one of the first steps in the identification process. Sex assessment of subadults using morphological features is unreliable, and molecular genetic methods were applied in this study. Eighty-three ancient skeletons were used as models for poorly preserved DNA. Three sex-informative markers on the Y and X chromosome were used for sex identification: a qPCR test using the PowerQuant Y target included in PowerQuant System (Promega), the amelogenin test included in ESI 17 Fast STR kit (Promega), and a Y-STR amplification test using the PowerPlex Y-23 kit (Promega). Sex was successfully determined in all but five skeletons. Successful PowerQuant Y-target, Y-amelogenin, and Y-chromosomal STR amplifications proved the presence of male DNA in 35 skeletons, and in 43 subadults female sex was established. No match was found between the genetic profiles of subadult skeletons, and the elimination database and negative control samples produced no profiles, indicating no contamination issue. Our study shows that genetic sex identification is a very successful approach for biological sexing of subadult skeletons whose sex cannot be assessed by anthropological methods. The results of this study are applicable for badly preserved subadult skeletons from routine forensic casework.
Topics: Male; Humans; Female; Body Remains; Amelogenin; Microsatellite Repeats; Forensic Medicine; DNA; DNA Fingerprinting; Chromosomes, Human, Y
PubMed: 37993531
DOI: 10.1038/s41598-023-47836-9 -
Journal of Dental Research Jan 2024Histone methylation assumes a crucial role in the intricate process of enamel development. Our study has illuminated the substantial prevalence of H3K4me3 distribution,...
Histone methylation assumes a crucial role in the intricate process of enamel development. Our study has illuminated the substantial prevalence of H3K4me3 distribution, spanning from the cap stage to the late bell stage of dental germs. In order to delve into the role of H3K4me3 modification in amelogenesis and unravel the underlying mechanisms, we performed a conditional knockout of , a core subunit essential for the establishment of H3K4me3 within the dental epithelium of mice. The absence of resulted in reduced H3K4me3 modification, subsequently leading to abnormal morphology of dental germ at the late bell stage. Notably, knockout of resulted in a loss of polarity in ameloblasts and odontoblasts. The proliferation and apoptosis of the inner enamel epithelium cells underwent dysregulation. Moreover, there was a notable reduction in the expression of matrix-related genes, and , accompanied with impaired enamel and dentin formation. Cut&Tag-seq (cleavage under targets and tagmentation sequencing) analysis substantiated a reduction of H3K4me3 modification on , and others in the dental epithelium of knockout mice. Validation through real-time polymerase chain reaction, immunohistochemistry, and immunofluorescence consistently affirmed the observed downregulation of Shh and Sp6 in the dental epithelium following knockout. Intriguingly, the expression of isomers, and , was perturbed in defect dental epithelium. Furthermore, the downstream target of TAp63, P21, exhibited aberrant expression within the cervical loop of mandibular first molars and incisors. Collectively, our findings suggest that ASH2L orchestrates the regulation of crucial amelogenesis-associated genes, such as , and others, by modulating H3K4me3 modification. Loss of ASH2L and H3K4me3 can lead to aberrant differentiation, proliferation, and apoptosis of the dental epithelium by affecting the expression of , and others genes, thereby contributing to the defects of amelogenesis.
Topics: Animals; Mice; Ameloblasts; Amelogenesis; Dental Enamel; Dental Enamel Proteins; Methylation; Mice, Knockout
PubMed: 37990471
DOI: 10.1177/00220345231207309 -
BMC Oral Health Nov 2023Amelogenesis imperfecta (AI) is a developmental enamel defect affecting the structure of enamel, esthetic appearance, and the tooth masticatory function. Gene mutations...
BACKGROUND
Amelogenesis imperfecta (AI) is a developmental enamel defect affecting the structure of enamel, esthetic appearance, and the tooth masticatory function. Gene mutations are reported to be relevant to AI. However, the mechanism underlying AI caused by different mutations is still unclear. This study aimed to reveal the molecular pathogenesis in AI families with 2 novel pre-mRNA splicing mutations.
METHODS
Two Chinese families with AI were recruited. Whole-exome sequencing and Sanger sequencing were performed to identify mutations in candidate genes. Minigene splicing assays were performed to analyze the mutation effects on mRNA splicing alteration. Furthermore, three-dimensional structures of mutant proteins were predicted by AlphaFold2 to evaluate the detrimental effect.
RESULTS
The affected enamel in family 1 was thin, rough, and stained, which was diagnosed as hypoplastic-hypomature AI. Genomic analysis revealed a novel splicing mutation (NM_001142.2: c.570 + 1G > A) in the intron 6 of amelogenin (AMELX) gene in family 1, resulting in a partial intron 6 retention effect. The proband in family 2 exhibited a typical hypoplastic AI, and the splicing mutation (NM_031889.2: c.123 + 4 A > G) in the intron 4 of enamelin (ENAM) gene was observed in the proband and her father. This mutation led to exon 4 skipping. The predicted structures showed that there were obvious differences in the mutation proteins compared with wild type, leading to impaired function of mutant proteins.
CONCLUSIONS
In this study, we identified two new splicing mutations in AMELX and ENAM genes, which cause hypoplastic-hypomature and hypoplastic AI, respectively. These results expand the spectrum of genes causing AI and broaden our understanding of molecular genetic pathology of enamel formation.
Topics: Humans; Female; Amelogenin; Amelogenesis Imperfecta; Dental Enamel Proteins; Mutation; Mutant Proteins; Extracellular Matrix Proteins
PubMed: 37985977
DOI: 10.1186/s12903-023-03508-8 -
Journal of Dental Research Apr 2024
Topics: Ameloblasts; Dental Enamel; Amelogenin; Cell Differentiation; Autophagy
PubMed: 37968790
DOI: 10.1177/00220345231210462 -
Scientific Reports Nov 2023The sex profile estimation of pre-historic communities is often complicated by the commingled and scattered nature of skeletal assemblages. Demographic profiles are...
The sex profile estimation of pre-historic communities is often complicated by the commingled and scattered nature of skeletal assemblages. Demographic profiles are usually lacking and provide very truncated representations of these populations but proteomic analysis of sex-specific amelogenin peptides in tooth enamel brings new promise to these studies. The main objective was to obtain the sex profile of the human assemblage recovered from the Neolithic cave-necropolis of Escoural (Montemor-o-Novo, southern Portugal) through liquid chromatography-mass spectrometry. The secondary objective was to analyse sex-specific linear enamel hypoplasias (LEH), and to test the reliability of canine odontometric sex estimation. Sex estimation through peptide analysis was carried out in 36 left permanent canines which were macroscopically examined for the presence of LEH. The canine buccolingual diameter was used for odontometric sex estimation. The obtained sex ratio (0.5:1, M:F) is biased to female individuals, probably due to cultural factors since the natural sex ratio of the human population falls between 0.95:1 and 1.02:1 (M:F). A high frequency of LEH was observed, but with no significant sexual differences (p = 0.554). The mean LEH age of onset occurred at 3 years of age, with no significant differences between the sexes (p = 0.116), and was possibly related to the weaning process. Odontometric sex estimation revealed a correct classification of 80%, with a high number of males mistakenly attributed to females. This study is one of the largest samples subjected to peptide analysis, and thus demonstrates its usefulness on the research of commingled and scattered skeletal assemblages.
Topics: Male; Humans; Female; Child, Preschool; Portugal; Sex Ratio; Proteomics; Reproducibility of Results; Peptides
PubMed: 37964077
DOI: 10.1038/s41598-023-47037-4 -
International Journal of Molecular... Nov 2023The matter constituting the enamels of four types of organisms was studied. The variability of the ions was presented in molar units. It was proven that the changes in...
The matter constituting the enamels of four types of organisms was studied. The variability of the ions was presented in molar units. It was proven that the changes in water contents of the enamel are significantly positively related to changes in Mg; inversely, there is also a strong connection with changes in Ca and P, the main components of bioapatite. The variability in the organic matter has the same strong and positive characteristics and is also coupled with changes in Mg contents. Amelogenins in organic matter, which synthesize enamel rods, likely have a role in adjusting the amount of Mg, thus establishing the amount of organic matter and water in the whole enamel; this adjustment occurs through an unknown mechanism. Ca, P, Mg, and Cl ions, as well as organic matter and water, participate in the main circulation cycle of bioapatites. The selection of variations in the composition of bioapatite occurs only along particular trajectories, where the energy of transformation linearly depends on the following factors: changes in the crystallographic d parameter; the increase in the volume, V, of the crystallographic cell; the momentum transfer, which is indirectly expressed by ΔsinΘ value. To our knowledge, these findings are novel in the literature. The obtained results indicate the different chemical and crystallographic affinities of the enamels of selected animals to the human ones. This is essential when animal bioapatites are transformed into dentistic or medical substitutes for the hard tissues. Moreover, the role of Mg is shown to control the amount of water in the apatite and in detecting organic matter in the enamels.
Topics: Humans; Animals; Apatites; Molar; Dental Enamel; Crystallography; Ions
PubMed: 37958956
DOI: 10.3390/ijms242115974 -
IScience Nov 2023Assignment of biological sex to skeletal remains is critical in the accurate reconstruction of the past. Analysis of sex-chromosome encoded AMELX and AMELY peptides from...
Assignment of biological sex to skeletal remains is critical in the accurate reconstruction of the past. Analysis of sex-chromosome encoded AMELX and AMELY peptides from the enamel protein amelogenin underpins a minimally destructive mass spectrometry (MS) method for sex determination of human remains. However, access to such specialist approaches limits applicability. As a convenient alternative, we generated antibodies that distinguish human AMELX and AMELY. Purified antibodies demonstrated high selectivity and quantitative detection against synthetic peptides by ELISA. Using acid etches of enamel from post-medieval skeletons, antibody determinations corrected osteological uncertainties and matched parallel MS, and for Bronze Age samples where only enamel was preserved, also matched MS analyses. Toward improved throughput, automated stations were applied to analyze 19th-century teeth where sex of individuals was documented, confirming MS can be bypassed. Our immunological tools should underpin development of routine, economical, high-throughput methods for sex determination, potentially even in a field setting.
PubMed: 37953951
DOI: 10.1016/j.isci.2023.108191