The Y chromosome and its use in forensic DNA analysis.
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ABSTRACT:
SUBMITTER: Syndercombe Court D
PROVIDER: S-EPMC8457770 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases. Y-STR haplotyping applied in crime scene investigation can (i) exclude male suspects from involvement in crime, (ii) identify the paternal lineage of male perpetrators, (iii) highlight multiple male contributors to a trace, and (iv) provide investigative leads for finding unknown male perpetrators. Y-STR haplotype analysis is employed in paternity disputes of male offspring and other types of paternal kinship testing, including historical cases, as well as in special cases of missing person and disaster victim identification involving men. Y-chromosome polymorphisms are applied for inferring the paternal bio-geographic ancestry of unknown trace donors or missing persons, in cases where autosomal DNA profiling is uninformative. In this overview, all different forensic applications of Y-chromosome DNA are described. To illustrate the necessity of forensic Y-chromosome analysis, the investigation of a prominent murder case is described, which initiated two changes in national forensic DNA legislation both covering Y-chromosome use, and was finally solved via an innovative Y-STR dragnet involving thousands of volunteers after 14 years. Finally, expectations for the future of forensic Y-chromosome DNA analysis are discussed.
| S-EPMC5418305 | biostudies-literature
Project description:The unique structure of the X chromosome shaped by evolution has led to the present gender-specific genetic differences, which are not shared by its counterpart, the Y chromosome, and neither by the autosomes. In males, recombination between the X and Y chromosomes is limited to the pseudoautosomal regions, PAR1 and PAR2; therefore, in males, the X chromosome is (almost) entirely transmitted to female offspring. On the other hand, the X chromosome is present in females with two copies that recombine along the whole chromosome during female meiosis and that is transmitted to both female and male descendants. These transmission characteristics, besides the obvious clinical impact (sex chromosome aneuploidies are extremely frequent), make the X chromosome an irreplaceable genetic tool for population genetic-based studies as well as for kinship and forensic investigations. In the early 2000s, the number of publications using X-chromosomal polymorphisms in forensic and population genetic applications increased steadily. However, nearly 20 years later, we observe a conspicuous decrease in the rate of these publications. In light of this observation, the main aim of this article is to provide a comprehensive review of the advances and applications of X-chromosomal markers in population and forensic genetics over the last two decades. The foremost relevant topics are addressed as: (i) developments concerning the number and types of markers available, with special emphasis on short tandem repeat (STR) polymorphisms (STR nomenclatures and practical concerns); (ii) overview of worldwide population (frequency) data; (iii) the use of X-chromosomal markers in (complex) kinship testing and the forensic statistical evaluation of evidence; (iv) segregation and mutation studies; and (v) current weaknesses and future prospects.
| S-EPMC7527635 | biostudies-literature
Project description:When evaluating the weight of evidence (WoE) for an individual to be a contributor to a DNA sample, an allele frequency database is required. The allele frequencies are needed to inform about genotype probabilities for unknown contributors of DNA to the sample. Typically databases are available from several populations, and a common practice is to evaluate the WoE using each available database for each unknown contributor. Often the most conservative WoE (most favourable to the defence) is the one reported to the court. However the number of human populations that could be considered is essentially unlimited and the number of contributors to a sample can be large, making it impractical to perform every possible WoE calculation, particularly for complex crime scene profiles. We propose instead the use of only the database that best matches the ancestry of the queried contributor, together with a substantial FST adjustment. To investigate the degree of conservativeness of this approach, we performed extensive simulations of one- and two-contributor crime scene profiles, in the latter case with, and without, the profile of the second contributor available for the analysis. The genotypes were simulated using five population databases, which were also available for the analysis, and evaluations of WoE using our heuristic rule were compared with several alternative calculations using different databases. Using FST=0.03, we found that our heuristic gave WoE more favourable to the defence than alternative calculations in well over 99% of the comparisons we considered; on average the difference in WoE was just under 0.2 bans (orders of magnitude) per locus. The degree of conservativeness of the heuristic rule can be adjusted through the FST value. We propose the use of this heuristic for DNA profile WoE calculations, due to its ease of implementation, and efficient use of the evidence while allowing a flexible degree of conservativeness.
| S-EPMC4275602 | biostudies-literature
Project description:Touch samples typically contain a limited quantity of DNA, which can be further reduced during collection and analysis. It is not clear, however, at which point(s) the majority of the DNA is lost because there is not a reliable positive control to track the quantity of DNA through the analysis procedures. To take the first step in bridging this gap, we established a set of laboratory-created eccrine, or mock, fingerprints containing known quantities of DNA. Next, we defined a set of process controls to quantify loss at key fail points in the collection/extraction procedures, analyzing a total of 1200 mock fingerprints deposited on four different surfaces. We quantified DNA loss to the surface, the swab and at extraction, completing the evaluation with ANOVA. With better understanding of DNA yields and the mechanisms of loss, targeted process improvements will bring touch DNA samples into even more routine use with standardized, optimized procedures.
| S-EPMC7219128 | biostudies-literature
Project description:Age-related CpG (AR-CpG) sites are currently the most promising molecular markers for age estimation. However, AR-CpG sites for the Han Chinese population have not yet been systematically identified. Besides, there may be high-performance AR-CpG sites beyond the coverage of the commonly used Illumina HumanMethylation450 BeadChip that covers over 450,000 CpG sites (450K), which accounts only 1.6% of CpG sites in the human genome. Therefore, we initiated a project to perform genome-wide methylation analysis on whole blood samples from 42 healthy Han Chinese individuals (21 males and 21 females, 18–62 years) using the newly developed Illumina Infinium MethylationEPIC array that assesses over 850,000 CpG sites (850K) to identify AR-CpG sites for forensic use systematically. The 850K methylation array contains > 90% of 450K CpG sites but adds 413,745 CpG sites. As expected, we not only replicated several high-performance AR-CpG sites previously discovered using the Illumina 450K BeadChip, such as cg16867656 (ELOVL2), cg22454769 (FHL2), and cg10501210 (C1orf132), but also identified 41 (60.3%), 34 (22.5%), and 382 (48.7%) novel AR-CpG sites from the methylation profiles of 21 males, 21 females, and all individuals, respectively.
2020-12-31 | GSE141682 | GEO
Project description:With deceased and decayed bodies, personal identification is performed using hard tissue DNA, commonly extracted from bone. The quantity and quality of DNA used in the polymerase chain reaction (PCR) amplification step is critical for a successful outcome. Since enamel is the strongest tissue in the human body, it was hypothesized that teeth may preserve DNA better than bones. In the present study, porcine teeth and bone samples were exposed to a variety of environments that imitated personal identification conditions, and DNA extracted from the teeth and bone samples was compared, using a PCR amplification method. The porcine teeth and bones were exposed to 11 different conditions for 5 different time periods to imitate a series of common crime scenes. DNA was extracted by a standard phenol-chloroform method. To test DNA quality, PCR was performed with primers designed to amplify porcine ?-actin (ACTB) and mitochondrial DNA (mtDNA) sequences. The results demonstrated that the quality of DNA extracted from teeth was greater than that extracted from bone in the following environments: Buried in sand, soaked in caustic soda and burnt with rubber. By contrast, the quality of DNA extracted from bone was greater than that extracted from teeth when samples were buried in soil or submerged in water. There was no discernable difference in the quality of DNA extracted from bones and teeth in several environments, including being submerged in seawater, soaked in sulfuric acid, left in open air, and stored at 4, -20 and -80°C. Additionally, the results suggested that PCR using mtDNA primers performed better than that using ACTB primers. Finally, it was indicated that components of seawater may inhibit PCR amplification. The preliminary data reported here may provide basic guidelines for selecting the optimum source of DNA in each case.
| S-EPMC6200996 | biostudies-literature
Project description:BackgroundLittle is known regarding the oral conditions in nonelderly methamphetamine users, such as the presence of dental caries and periodontitis. We aimed the oral conditions between methamphetamine users and non-users stratified by age groups.MethodsIn this cross-sectional study, computed tomography images were obtained from 3,338 decedents at two forensic medicine departments in Japan. Decedents aged > 20 or ≤ 64 years were included in the study and categorised into methamphetamine-detected (MA) and undetected (control) groups based on toxicological examinations. Decedents in the MA and control groups were matched for age and sex in a 1:4 ratio. The matched pairs were further categorised into young adults (20-44 years) and middle-aged adults (45-64 years). Oral characteristics, including the decayed, missing, and filled teeth (DMFT) index; periodontitis; distributional patterns of each tooth condition; and occlusal status, were compared between the MA and control groups for each age category. Among 3,338 decedents, 37 young and 55 middle-aged adults in the MA group were matched with 148 and 220 adults in the control group, respectively.ResultsIn the young adult group, methamphetamine use was significantly associated with higher DMFT index (mean [standard deviation], 14.2 [7.6] vs 11.0 [6.1]; p = 0.007), smaller number of filled teeth (2.8 [2.9] vs 5.3 [4.0]; p = 0.001), higher proportion of periodontitis (39.0% vs 6.8%; p < 0.001), and lower proportion of occlusal support (54.1% vs 81.1%; p = 0.001). Young adult methamphetamine users tended to have untreated decayed canines and molars and missing molars. These findings were similar to those in middle-aged adults except the tendency to have missing maxillary incisors.ConclusionsNonelderly methamphetamine users had distinctive oral characteristics that may help screen for methamphetamine abuse through dental examinations.
| S-EPMC9044830 | biostudies-literature
Project description:Pet hair has a demonstrated value in resolving legal issues. Cat hair is chronically shed and it is difficult to leave a home with cats without some level of secondary transfer. The power of cat hair as an evidentiary resource may be underused because representative genetic databases are not available for exclusionary purposes. Mitochondrial control region databases are highly valuable for hair analyses and have been developed for the cat. In a representative worldwide data set, 83% of domestic cat mitotypes belong to one of twelve major types. Of the remaining 17%, 7.5% are unique within the published 1394 sample database. The current research evaluates the sample size necessary to establish a representative population for forensic comparison of the mitochondrial control region for the domestic cat. For most worldwide populations, randomly sampling 50 unrelated local individuals will achieve saturation at 95%. The 99% saturation is achieved by randomly sampling 60-170 cats, depending on the numbers of mitotypes available in the population at large. Likely due to the recent domestication of the cat and minimal localized population substructure, fewer cats are needed to meet mitochondria DNA control region database practical saturation than for humans or dogs. Coupled with the available worldwide feline control region database of nearly 1400 cats, minimal local sampling will be required to establish an appropriate comparative representative database and achieve significant exclusionary power.
| S-EPMC4400830 | biostudies-literature
Project description:A new 19 X- short tandem repeat (STR) multiplex PCR system has recently been developed, though its applicability in forensic studies has not been thoroughly assessed. In this study, 932 unrelated individuals from four Chinese ethnic groups (Han, Tibet, Uighur and Hui) were successfully genotyped using this new multiplex PCR system. Our results showed significant linkage disequilibrium between markers DXS10103 and DXS10101 in all four ethnic groups; markers DXS10159 and DXS10162, DXS6809 and DXS6789, and HPRTB and DXS10101 in Tibetan populations; and markers DXS10074 and DXS10075 in Uighur populations. The combined powers of discrimination in males and females were calculated according to haplotype frequencies from allele distributions rather than haplotype counts in the relevant population and were high in four ethnic groups. The cumulative powers of discrimination of the tested X-STR loci were 1.000000000000000 and 0.999999999997940 in females and males, respectively. All 19 X-STR loci are highly polymorphic. The highest Reynolds genetic distances were observed for the Tibet-Uighur pairwise comparisons. This study represents an extensive report on X-STR marker variation in minor Chinese populations and a comprehensive analysis of the diversity of these 19 X STR markers in four Chinese ethnic groups.
| S-EPMC5314363 | biostudies-literature
Project description:Despite the benefits of quantitative data generated by massively parallel sequencing, resolving mitotypes from mixtures occurring in certain ratios remains challenging. In this study, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated. The method was first tested on 270 in silico two-person mixtures varying in mixture proportions. An assortment of external reference panels containing information on haplotypic variation (from similar and different haplogroups) was leveraged to assess the effect of panel composition on phasing accuracy. Building on these simulations, mitochondrial genomes from the Human Mitochondrial DataBase were sourced to populate the panels and key parameter values were identified by deconvolving an additional 7290 in silico two-person mixtures. Finally, employing an optimized reference panel and phasing parameters, the approach was validated with in vitro two-person mixtures with differing proportions. Deconvolution was most accurate when the haplotypes in the mixture were similar to haplotypes present in the reference panel and when the mixture ratios were neither highly imbalanced nor subequal (e.g., 4:1). Overall, errors in haplotype estimation were largely bounded by the accuracy of the mixture's genotype results. The proposed framework is the first available approach that automates the reconstruction of complete individual mitotypes from mixtures, even in ratios that have traditionally been considered problematic.
| S-EPMC7909279 | biostudies-literature