Systematical explorations of forensic feature and population genetic diversity of the Chinese Mongolian group from northwest China via a self-constructed Multi-InDel panel
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PROVIDER: S-EPMC10981549 | biostudies-literature | 2023 Dec
REPOSITORIES: biostudies-literature
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Project description:Insertion/deletion (InDel) markers have been treated as a prospective and helpful aid in the fields of forensic human identifications and biogeography origin researches for the past few years. In this study, we analyzed genetic polymorphisms and forensic efficiencies of 35 InDels in a novel multiplex PCR-InDel panel in a Chinese Mongolian group. All these 35 InDel loci were observed to conform to Hardy-Weinberg equilibrium and linkage equilibrium. The mean values of expected heterozygosity and observed heterozygosity were 0.4788 and 0.4852, respectively. Besides, the interpopulation differentiations and genetic distributions based on 35 InDels found that the Chinese Mongolian group might have closer genetic relationships and similar population genetic structures with East Asian populations.
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Project description:Wolf (Canis lupus) is a species included in appendices of CITES and is often encountered in cases of alleged poaching and trafficking of their products. When such crimes are suspected, those involved may attempt to evade legal action by claiming that the animals involved are domestic dogs (C. l. familiaris). To respond effectively to such claims, law enforcement agencies require reliable and robust methods to distinguish wolves from dogs. Reported molecular genetic methods are either unreliable (mitogenome sequence based), or operationally cumbersome and require much DNA (un-multiplexed microsatellites), or financially expensive (genome wide SNP genotyping). We report on the validation of a panel of 12 ancestral informative single nucleotide polymorphism (SNP) markers for discriminating wolves from dogs. A SNaPshot multiplex genotyping system was developed for the panel, and 97 Mongolian wolves (C. l. chanco) and 108 domestic dogs were used for validation. Results showed this panel had high genotyping success (0.991), reproducibility (1.00) and origin assignment accuracy (0.97 ± 0.05 for dogs and 1.00 ± 0.03 for wolves). Species-specificity testing suggested strong tolerance to DNA contamination across species, except for Canidae. The minimum DNA required for reliable genotyping was 6.25 pg/μl. The method and established gene frequency database are available to support identification of wolves and dogs by law enforcement agencies.
| S-EPMC7413520 | biostudies-literature
Project description:In this research, a self-developed panel comprising 22 X chromosomal multi-InDels and one X-STR was used to explore the genetic polymorphisms and forensic characteristics of these loci in Guizhou Miao and Guizhou Bouyei populations. Besides, genetic affiliations among Guizhou Miao, Guizhou Bouyei and Guizhou Han populations were investigated using principal component analysis, STRUCTURE and machine learning methods. The findings indicated that these loci in the male and female samples had comprehensive discrimination powers greater than 0.999999999. Meanwhile, the cumulative mean exclusion chance of these 23 loci for trio and duo cases were also greater than 0.9999 in Guizhou Miao and Guizhou Bouyei populations. Population genetic analyses of three Guizhou populations revealed that there were relatively low genetic divergences among these populations based on the self-constructed panel. In conclusion, this system could be utilized as the valuable tool for forensic personal identification and parentage testing in Guizhou Miao and Guizhou Bouyei populations.
| S-EPMC11626752 | biostudies-literature
Project description:Comprehensive characterizations of genetic diversity and demographic models of ethnolinguistically diverse Chinese populations are essential for elucidating their forensic characteristics and evolutionary past. We developed a 114-plex NGS InDel panel to genotype 114 genome-wide markers and investigated the genetic structures of Zhuang, Hui, Miao, Li, Tibetan, Yi, and Mongolian populations, encompassing five language families. This panel demonstrated robust performance, with exceptional potential for forensic individual identification and paternity testing, evidenced by the combined power of discrimination for 77 autosomal InDels (ranged from 1-3.6400 × 10-30 to 1-3.5713 × 10-32) and the combined power of exclusion (ranged from 1-2.1863 × 10-6 to 1-2.1261 × 10-7). The cumulative mean exclusion chance for 32 X-chromosomal InDels varied between 0.99996 and 0.99999 for trios and 0.99760 to 0.99898 for duos. We also analyzed genetic similarities and differences between these populations and 27 global populations, revealing distinct clusters among African, South Asian, East Asian, and European groups, with a close genetic affinity to East Asians. Notably, we identified geography-related genetic substructures: Inner Mongolia Mongolians and Gansu Huis formed a northern branch, Tibetans and Yis from Sichuan constituted a highland branch, and Guangxi Zhuangs exhibited close ties with Hainan Lis and Guangxi Miaos in the southern branch. Additionally, many InDels proved to be ancestry-informative markers for biogeographic ancestry inference. Collectively, these findings underscore the utility of the 114-plex NGS InDel panel as a complementary tool for forensic investigations and as a source of insights into the genetic architecture of ethnolinguistically distinct Chinese populations.
| S-EPMC11587575 | biostudies-literature
Project description:To further enrich the genetic data of the Chinese Xinjiang Mongolian group, the genetic distribution and forensic parameters of 19 autosomal short tandem repeats (STRs) were investigated. Altogether, 249 alleles were observed in these 19 STRs. The mean values of the polymorphism information content (PIC), match probability (MP), discrimination power (DP), and probability of exclusion (PE) for these 19 STRs were 0.7775, 0.0699, 0.9301, and 0.6085, respectively. Additionally, the cumulative DP and PE values obtained in the Mongolian group were 0.999 999 999 999 999 999 999 995 67 and 0.999 999 992 163, respectively. Furthermore, population genetic analysis of the Mongolian group and 20 published populations was conducted based on the population data of 15 overlapping STRs. Genetic distances indicated that the Mongolian group had closer genetic similarities with the Uyghur, Xibe, and other Chinese populations rather than the other continental populations. Multidimensional scaling analysis further revealed that the Mongolian group possessed similar genetic distributions as most Chinese populations. To sum it all up, these STRs could be used as an extremely efficient tool for forensic applications in the Xinjiang Mongolian group.
| S-EPMC6421123 | biostudies-literature
Project description:BackgroundInsertion/deletion (InDel) analysis plays an indispensable role in human identification, population genetics, and biogeographic research. Profiles of individuals in forensic applications worldwide based on a set of autosomal InDel loci (A-InDels) in human genomes have been widely used over the past few years.MethodsThe new AGCU InDel 50 Kit contains 47 well-chosen A-InDels, ensuring high discriminatory power, and the 2 Y chromosome InDel loci (Y-InDels) are used for sex determination in case of allele dropout at Amelogenin. In this study, five Northern Han populations residing in different geographic areas of China were recruited and genotyped using the assay.ResultsAfter Bonferroni correction, all 47 A-InDels were in accordance with the lack of significant departures of Hardy-Weinberg equilibrium in all loci and investigated groups. The combined probability of discrimination and the probability of exclusion in the Han population range from 1-3.2240 × 10-19 to 1-1.3030 × 10-19 and 0.9997, respectively. A comprehensive population genetic relationship investigation between Han Chinese and 26 worldwide populations based on allele frequency correlation was carried out. Our results revealed no significant genetic differentiation in Chinese Han groups. Hierarchical clustering, phylogenetic relationship reconstructions, multidimensional scaling, principal component analysis, and structure analysis were performed, and the results indicated that, genetically, Han populations are closely related to East Asians.ConclusionOverall, this novel 47 A-InDel assay is a valuable tool that could potentially be used for forensic identification and parentage tests.
| S-EPMC7216812 | biostudies-literature
Project description:There may be cases where malignant tumor samples can be used for forensic DNA profiling studies. STRs are the first systems preferred in forensic science laboratories for identification purposes. However, genetic instability in tumoral tissues causes STR polymorphism to change, leading to erroneous results. On the other hand, insertion/deletion polymorphism (InDels) are used as genetic markers in forensic science, as they have features that make both STR and SNPs preferable. Although previous studies approved that STR instability is observed in many different tumors, there are only a few studies that have displayed the instability of InDels in tumoral tissues before. In this study, it was aimed to determine whether instability is observed in formalin-fixed paraffin-embedded breast and thyroid tumoral tissues at 36plex InDel Panel. A total of 47 cases, 26 of which were diagnosed as breast cancer and 21 as thyroid cancer, were included in the study. In 21 of 26 (80.76%) breast cancers mutational changes were observed, however only 6 of 21 (28.57%) thyroid carcinoma cases displayed instability.Moreover, in these six cases, mutations were detected at only 1 or 2 loci. The most common change in both tissues was loss of heterozygosity. These findings suggest that paraffin embedded tissues of thyroid tumor can be used in cases of forensic genetic identification, however paraffin embedded breast cancer tissues should be examined with care. In conclusion, low InDel mutation rates compared to STR instability, make InDel analysis from paraffin blocks suitable for forensic genetic identification. However, researchers should keep in mind that there may be differences between the profiles of the tumoral tissues taken as reference and the actual case. In addition, by incorporating additional markers such as SNPs and microhaplotypes with low mutation rates into the study alongside Indels, researchers can significantly enhance the discrimination power in identification processes.
| S-EPMC11790770 | biostudies-literature
Project description:The constructed theory of forensic nursing care is a middle-range nursing theory developed from the integrated practice model for forensic nursing science, a conceptual framework. Theory evolution was achieved following a critique of the conceptual framework and through inductive and deductive reasoning. A review of nursing theory growth and significance of middle-range theories is presented as background information in understanding the importance of this emerging forensic nursing middle-range theory. The philosophical and theoretical foundations of forensic nursing are bolstered with the addition of three nursing theories, two healthcare models and one social theory. Links are made between theory components and the current state of forensic nursing. Assumptions and concepts are clearly defined. The middle-range theory provides three testable propositions to frame forensic nursing practice, education, and research. Research conducted on the propositions will expand the forensic nursing scientific base leading to enhanced evidence-based practice. A pictorial model illustrates the propositions as relational statements. The constructed theory of forensic nursing care affirms the focus of forensic nursing care is on the nurse-patient relationship and improved health outcomes. Additional results of forensic nursing care are improved forensic science and criminal justice system outcomes.
| S-EPMC7678647 | biostudies-literature
Project description:In the present study, a novel multiplex system, AGCU X-InDel 38 kit, was designed to amplify 38 X-InDel markers and amelogenin in a single Polymerase Chain Reaction (PCR). To demonstrate the suitability and efficiency for forensic applications, a series of validation experiments were conducted, including sensitivity, species specificity, reproducibility, stability, case samples, balance of peak height, size precision, as well as allele frequency and forensic parameter analysis. The results showed that AGCU X-InDel 38 kit was capable to get full profiles even with 62.5 pg of template DNA, and full profiles can be obtained when hematin concentration ≤25 μmol/L, or hemoglobin concentration ≤50 μmol/L, showing good tolerance to six common inhibitors. Moreover, the analyzed case samples indicated that AGCU X-InDel 38 kit had better performance for degraded and trace DNA samples. The 200 unrelated males from Guangdong Han population showed that the combined PDMale and PDFemale were both more than 0.999999999, and the combined MECKrüger, MECKishida, and MECDesmarais Duo were 0.999369481, 0.999999917, and 0.999941556, respectively. Robust discrimination capability of this novel multiplex system could be demonstrated through the high values of forensic parameters. In conclusion, AGCU X-InDel 38 kit is sensitive, precise, reproducible, and highly informative and could be used as a complementary tool for complex and challenging kinship cases.
| S-EPMC8416044 | biostudies-literature
Project description:The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal short tandem repeats (A-STRs), into 90 unrelated male individuals from the Chinese Northwest Hui group to comprehensively explore its forensic characteristics and genetic background. Total of 451 length-based and 652 sequence-based distinct alleles were identified from 58 short tandem repeats (STRs) in 90 unrelated Northwest Hui individuals, denoting that the sequence-based genetic markers could pronouncedly provide more genetic information than length-based markers. The forensic characteristics and efficiencies of STRs and IISNPs were estimated, both of which externalized high polymorphisms in the Northwest Hui group and could be further utilized in forensic investigations. No significant departure from the Hardy-Weinberg equilibrium (HWE) expectation was observed after the Bonferroni correction. Additionally, four group sets of reference population data were exploited to dissect the genetic background of the Northwest Hui group separately from different perspectives, which contained 26 populations for 93 IISNPs, 58 populations for 17 Y-STRs, 26 populations for 55 AISNPs (raw data), and 109 populations for 55 AISNPs (allele frequencies). As a result, the analyses based on the Y-STRs indicated that the Northwest Hui group primarily exhibited intimate genetic relationships with reference Hui groups from Chinese different regions except for the Sichuan Hui group and secondarily displayed close genetic relationships with populations from Central and West Asia, as well as several Chinese groups. However, the AISNP analyses demonstrated that the Northwest Hui group shared more intimate relationships with current East Asian populations apart from reference Hui group, harboring the large proportion of ancestral component contributed by East Asia.
| S-EPMC8555763 | biostudies-literature