ABSTRACT
Introdução: A análise do DNA salivar é uma dos métodos de identificação humana relacionados à Odontologia Legal. A coleta do material genético salivar consiste num processo simples e pouco invasivo, por possuir grande potencial discriminatório tem sido amplamente aplicado em investigações criminais. Objetivo: Por meio de uma revisão de escopo, objetivou-se mapear o tempo de viabilidade da saliva humana em meio externo para fins de extração e purificação de DNA. Material e Métodos: A revisão foi conduzida seguindo o protocolo JBI e registrada (doi: 10.17605/OSF.IO/PN9ET). A estratégia de busca foi adaptada para as bases: Pubmed, Web of Science, Scopus, LILACS, Cochrane e Google Scholar, sem restrições sobre período de publicação ou idioma. Foram excluídos estudos que exploraram apenas as metodologias e materiais relacionados a extração de DNA , também aqueles que estudaram DNA de outros componentes que não a saliva. Resultados: Identificou-se 283 estudos. Após triagem inicial, 15 referências foram lidas na íntegra, sendo 6 incluídas na revisão, em função da confirmação da elegibilidade. Bitucas de cigarro, próteses dentárias, pastilhas de compressão dentária, cavidade oral e cartões de FTA foram os substratos descritos como fonte de saliva coletada. A viabilidade do DNA foi verificada em tempos que variaram de 1 dia à 11 anos. Conclusão: O protocolo de coleta e armazenamento das amostras é um fator que pode influenciar a quantidade e qualidade do material examinado, todavia, observou-se DNA viável em análise realizada uma década após a coleta da saliva e esse foi o tempo máximo de acompanhamento relatado nos estudos
Introduction: Salivary DNA analysis is one of the human identification methods related to forensic dentistry. Collection of salivary genetic material consists of a simple and poorly invasive process because it has great discriminatory potential has been widely applied in criminal investigations. Objective: Through a scope review, the feasibility time of human saliva was mapped in the external environment for DNA extraction and purification purposes. Material and Methods: The review was conducted following the JBI protocol and registered (doi: 10.17605/OSF.IO/PN9ET). The search strategy was adapted for the databases: Pubmed, Web of Science, Scopus, LILACS, Cochrane and Google Scholar, with no restrictions on period of publication or language. Studies that explored only methodologies and materials related to DNA extraction were excluded, as well as those that studied DNA from components other than saliva. Results: 283 studies were identified. After initial screening, 15 references were read in full, 6 of which were included in the review. Cigarette butts, dentures, dental compression tablets, oral cavity and FTA cards were the substrates described as a source of collected saliva. DNA viability was verified in times ranging from 1 day to 11 years. Conclusion: The sample collection and storage protocol is a factor that can influence the quantity and quality of the material examined, however, viable DNA was observed in an analysis performed a decade after saliva collection and this was the maximum reported follow-up time in the studies
ABSTRACT
OBJECTIVES@#To provide a guideline for genealogy inference and family lineage investigation through a study of the mismatch tolerance distribution of Y-STR loci in Chinese Han male lineage.@*METHODS@#Three Han lineages with clear genetic relationships were selected. YFiler Platinum PCR amplification Kit was used to obtain the typing data of 35 Y-STR loci in male samples. The variation of Y-STR haplotypes in generation inheritance and the mismatch tolerance at 1-7 kinship levels were statistically analyzed.@*RESULTS@#Mutations in Y-STR were family-specific with different mutation loci and numbers of mutation in different lineages. Among all the mutations, 66.03% were observed on rapidly and fast mutating loci. At 1-7 kinship levels, the number of mismatch tolerance ranged from 0 to 5 on all 35 Y-STR loci, with a maximum step size of 6. On medium and slow mutant loci, the number of mismatch tolerance ranged from 0 to 2, with a maximum step size of 3; on rapidly and fast mutant loci, the number of mismatch tolerance ranged from 0 to 3, with a maximum step size of 6.@*CONCLUSIONS@#Combined use of SNP genealogy inference and Y-STR lineage investigation, both 0 and multiple mismatch tolerance need to be considered. Family lineage with 0-3 mismatch tolerance on all 35 Y-STR loci and 0-1 mismatch tolerance on medium and slow loci can be prioritized for screening. When the number of mismatch tolerance is eligible, family lineages with long steps should be carefully excluded. Meanwhile, adding fast mutant loci should also be handled with caution.
Subject(s)
Male , Humans , Haplotypes , Chromosomes, Human, Y/genetics , Microsatellite Repeats , Mutation , Asian People/genetics , China , Genetics, PopulationABSTRACT
OBJECTIVES@#To investigate the efficacy of different numbers of microhaplotype (MH) loci and the introduction of different reference samples on the identification of full sibling, half sibling and differentiation between full sibling and half sibling kinships, and to explore the effect of changing mutation rate on sibling testing.@*METHODS@#First, a family map involving three generations was established, and four full sibling identification models, five half sibling identification models and five models distinguishing full and half siblings were constructed for different reference samples introduced. Based on the results of the previous study, two sets of nonbinary SNP-MH containing 34 and 54 loci were selected. Based on the above MH loci, 100 000 pairs of full sibling vs. unrelated individuals, 100 000 pairs of half sibling vs. unrelated individuals and 100 000 pairs of full sibling vs. half sibling were simulated based on the corresponding sibling kinship testing models, and the efficacy of each sibling kinship testing model was analyzed by the likelihood ratio algorithm under different thresholds. The mutant rate of 54 MH loci was changed to analyze the effect of mutation rate on sibling identification.@*RESULTS@#In the same relationship testing model, the systematic efficacy of sibling testing was positively correlated with the number of MH loci detected. With the same number of MH loci, the efficacy of full sibling testing was better than that of uncle or grandfather when the reference sample introduced was a full sibling of A, but there was no significant difference in the identification efficacy of the four reference samples introduced for full sibling and half sibling differentiation testing. In addition, the mutation rate had a slight effect on the efficacy of sibling kinship testing.@*CONCLUSIONS@#Increasing the number of MH loci and introducing reference samples of known relatives can increase the efficacy of full sibling testing, half sibling testing, and differentiation between full and half sibling kinships. The level of mutation rate in sibling testing by likelihood ratio method has a slight but insignificant effect on the efficacy.
Subject(s)
Humans , Siblings , Polymorphism, Single Nucleotide , DNA Fingerprinting/methodsABSTRACT
OBJECTIVES@#To calculate the likelihood ratios of incest cases using identity by descent (IBD) patterns.@*METHODS@#The unique IBD pattern was formed by denoting the alleles from the members in a pedigree with a same digital. The probability of each IBD pattern was obtained by multiplying the prior probability by the frequency of non-IBD alleles. The pedigree likelihoods of incest cases under different hypotheses were obtained by summing all IBD pattern probabilities, and the likelihood ratio(LR) was calculated by comparing the likelihoods of different pedigrees.@*RESULTS@#The IBD patterns and the formulae of calculating LR for father-daughter incest and brother-sister incest were obtained.@*CONCLUSIONS@#The calculations of LR for incest cases were illustrated based on IBD patterns.
Subject(s)
Male , Humans , Incest , Siblings , ProbabilityABSTRACT
OBJECTIVES@#To derive general formulas for calculating commonly used kinship index (KI).@*METHODS@#By introducing the Kronecker symbol, the formulas used to calculate the same KI under different genotype combinations were summarized into a unified expression.@*RESULTS@#The general formulas were successfully derived for KI in various case situations, including the paternity index, full sibling index, half sibling index, avuncular index, grandpaternity index, first-cousin index, and second-cousin index between two individuals without or with the mother being involved; grandpaternity index between grandparents and a grandchild without or with the mother being involved; half sibling index between two children with two mothers being involved; full sibling index among three children; and half sibling index among three children with no, one, or two mothers being involved.@*CONCLUSIONS@#The general formulas given in this study simplify the calculation of KIs and facilitate fast and accurate calculation through programming.
Subject(s)
Female , Child , Humans , Paternity , Siblings , Genotype , Mothers , Models, GeneticABSTRACT
OBJECTIVES@#To derive the paternity index (PI) calculation formula of the alleged father (AF) when the AF is a relative (parent/child, siblings, grandparent/grandchild, uncle/nephew, first cousins) of the child's biological mother.@*METHODS@#For the case when the AF is related to the child's biological mother, the existence of the relationship in the numerator and denominator hypothesis of PI was considered. The genotype frequency of the AF was calculated by using the frequency formula in which the mother's genotype was considered, while the random male in the denominator was substituted as another relative of the mother's same rank. The PI calculation formula was derived to eliminate the effect of the relationship between AF and the child's biological mother.@*RESULTS@#When the AF and the biological mother have first, second and tertiary kinship, a more conservative PI was obtained from the PI calculation formula derived in this study compared with the PI calculation method which did not consider kinship.@*CONCLUSIONS@#The calculation method provided in this study can eliminate the effect of the relation of the AF and mother on the PI in incest cases, to obtain more accurate and conservative identification conclusions.
Subject(s)
Female , Humans , Male , Child , Paternity , Mothers , Genotype , FathersABSTRACT
OBJECTIVES@#To compare the application value of the likelihood ratio (LR) method and identity by state (IBS) method in the identification involving half sibling relationships, and to provide a reference for the setting of relevant standards for identification of half sibling relationship.@*METHODS@#(1) Based on the same genetic marker combinations, the reliability of computer simulation method was verified by comparing the distributions of cumulated identity by state score (CIBS) and combined full sibling index in actual cases with the distributions in simulated cases. (2) In different numbers of three genetic marker combinations, the simulation of full sibling, half sibling and unrelated individual pairs, each 1 million pairs, was obtained; the CIBS, as well as the corresponding types of cumulative LR parameters, were calculated. (3) The application value of LR method was compared with that of IBS method, by comparing the best system efficiency provided by LR method and IBS method when genetic markers in different amounts and of different types and accuracy were applied to distinguish the above three relational individual pairs. (4) According to the existing simulation data, the minimum number of genetic markers required to distinguish half siblings from the other two relationships using different types of genetic markers was estimated by curve fitting.@*RESULTS@#(1) After the rank sum test, under the premise that the real relationship and the genetic marker combination tested were the same, there was no significant difference between the simulation method and the results obtained in the actual case. (2) In most cases, under the same conditions, the system effectiveness obtained by LR method was greater than that by IBS method. (3) According to the existing data, the number of genetic markers required for full-half siblings and half sibling identification could be obtained by curve fitting when the system effectiveness reached 0.95 or 0.99.@*CONCLUSIONS@#When distinguishing half sibling from full sibling pairs or unrelated pairs, it is recommended to give preference to the LR method, and estimate the required number of markers according to the identification types and the population data, to ensure the identification effect.
Subject(s)
Humans , Siblings , Genetic Markers , Computer Simulation , Irritable Bowel Syndrome/genetics , Reproducibility of Results , GenotypeABSTRACT
OBJECTIVES@#To establish an analytical method for half sibling testing involving common three relatives' participation.@*METHODS@#Based on the half sibling testing scenarios with the known biological mother, grandfather or uncle, and two unidentified controversial half siblings participating, two opposing hypotheses were set. Lineage reconstruction according to Mendel's law of heredity was carried out, and the calculation formula of the half sibling kinship index was derived. Verification of actual cases was carried out and the results were compared with duo half sibling testing.@*RESULTS@#In the scenarios of the known biological mother, grandfather and uncle participating in half sibling testing, the kinship calculation formulae of 54, 91 and 99 genotype combinations for kinship index calculation were deduced respectively. The actual cases showed higher kinship indexes in trio half sibling testing compared with duo half sibling testing.@*CONCLUSIONS@#It is beneficial to obtain more genetic information for family reconstruction and improvement of the strength of genetic evidence for half sibling testing by adding known relatives.
Subject(s)
Female , Humans , Siblings , Genotype , Mothers , Microsatellite RepeatsABSTRACT
OBJECTIVES@#To study the detection efficiency of trio full sibling with another known full sibling reference added under different number of autosomal STR typing systems.@*METHODS@#Based on 43 detection systems consisting of 13 to 55 representative autosomal STR loci, 10 000 true families (full sibling group) and 10 000 false families (unrelated individual group) were randomly simulated. The full sibling index (FSI) was calculated based on the method of family reconstruction. The cumulative sibling relationship index (CFSI) of 0.000 1 and 10 000 were used as the evaluation thresholds, and the detection efficiency parameters were calculated and compared with the identification of the duo full sibling testing.@*RESULTS@#With the increasing number of STR loci, the error rate and inability of judgement rate gradually decreased; the sensitivity, specificity, correct rate of judgment and other parameters gradually increased, and the system efficiency gradually improved. Under the same detection system, trio full sibling testing showed higher sensitivity, specificity, system efficiency and lower inability of judgement rate compared with duo full sibling testing. When the system efficiency was higher than 0.85 and inability of judgement rate was less than 0.01%, at least 20 STRs should be detected for trio full sibling testing, which was less than 29 STRs required by duo full sibling testing.@*CONCLUSIONS@#The detection efficiency of trio full sibling testing is superior to that of duo full sibling testing with the same detection system, which is an effective identification scheme for laboratories with inadequate detection systems or for materials with limited conditions.
Subject(s)
Humans , Siblings , Microsatellite Repeats/genetics , DNA Fingerprinting , Gene FrequencyABSTRACT
Tri-allelic pattern in autosomal STR is a common abnormal typing phenomenon in forensic DNA analysis, which brings difficulties and uncertainties to the evaluation of the evidence weight in actual cases. This paper reviews the types, formation mechanism, occurrence frequency, genetic pattern and quantitative evaluation of evidence of the tri-allelic pattern in autosomal STR in forensic DNA analysis. This paper mainly explains the formation mechanism and genetic patterns based on different types of tri-allelic pattern. This paper also discusses the determination of tri-allelic pattern and the quantitative method of evidence evaluation in paternity testing and individual identification. This paper aims to provide references for scientific and standardized analysis of this abnormal typing phenomenon in forensic DNA analysis.
Subject(s)
Humans , Alleles , DNA/genetics , Forensic Medicine , Gene Frequency , Microsatellite RepeatsABSTRACT
Kinship testing is widely needed in forensic science practice. This paper reviews the definitions of common concepts, and summarizes the basic principles, advantages and disadvantages, and application scope of kinship analysis methods, including identity by state (IBS) method, likelihood ratio (LR) method, method of moment (MoM), and identity by descent (IBD) segment method. This paper also discusses the research hotspots of challenging kinship testing, complex kinship testing, forensic genetic genealogy analysis, and non-human biological samples.
Subject(s)
Humans , DNA Fingerprinting , Forensic Genetics/methods , Forensic Sciences , PedigreeABSTRACT
With the advance of molecular biology, DNA analysis technology has been widely applied in forensic science. Non-human DNA analysis can be used in some special cases and has unique forensic value to provide investigation clues and trial basis. Animal DNA typing plays a more prominent role in the detection of all kinds of non-human DNA related cases and is the main content of forensic non-human DNA analysis. This paper reviews the development history, present situation, advantages and disadvantages of animal DNA typing according to its technology, characteristic, challenges facing forensic science application scenarios, and also its future development.
Subject(s)
Animals , DNA Fingerprinting , Forensic Medicine , DNA/analysis , Forensic Sciences , Molecular Biology , Forensic GeneticsABSTRACT
With the improvement of DNA methylation detection techniques, studies on age-related methylation sites have found more age-specific ones across tissues, which improves the sensitivity and accuracy of age estimation. In addition, the establishment of various statistical models also provides a new direction for the age estimation of tissues from different sources. This review summarizes the related studies of age estimation based on DNA methylation from the aspects of detection technology, age-related cytosine phosphate guanine site and model selection in recent years.
Subject(s)
DNA Methylation , Forensic Genetics/methods , CpG Islands , Forensic MedicineABSTRACT
OBJECTIVES@#To compare the effects of cell lysis method and magnetic beads method in forensic DNA identification and to explore these two methods in forensic DNA identification.@*METHODS@#The genome DNA of THP-1 cells in different quantities was extracted by the cell lysis method and magnetic beads method, and the DNA content was quantified by real-time quantitative PCR. The cell lysis method and magnetic beads method were used to type the STR of human blood with different dilution ratios.@*RESULTS@#When the numbers of THP-1 cell were 100, 400 and 800, the DNA content extracted by cell lysis method were (1.219±0.334), (5.081±0.335), (9.332±0.318) ng, respectively; and the DNA content extracted by magnetic beads method were (1.020±0.281), (3.634±0.482), (7.896±0.759) ng, respectively. When the numbers of THP-1 cells were 400 and 800, the DNA content extracted by the cell lysis method was higher than that by the magnetic beads method. The sensitivity of cell lysis method and magnetic beads method was similar in STR typing of human blood at different dilution ratios. Complete STR typing could be obtained at 100, 300 and 500-fold dilutions of blood samples, but could not be detected at 700-fold dilution. STR typing of undiluted human blood could not be detected by cell lysis method.@*CONCLUSIONS@#The cell lysis method is easy to operate and can retain template DNA to the maximum extend. It is expected to be suitable for trace blood evidence tests.
Subject(s)
Humans , Forensic Medicine , DNA/genetics , Real-Time Polymerase Chain Reaction , Magnetic Phenomena , DNA Fingerprinting/methods , Microsatellite RepeatsABSTRACT
Age estimation based on tissues or body fluids is an important task in forensic science. The changes of DNA methylation status with age have certain rules, which can be used to estimate the age of the individuals. Therefore, it is of great significance to discover specific DNA methylation sites and develop new age estimation models. At present, statistical models for age estimation have been developed based on the rule that DNA methylation status changes with age. The commonly used models include multiple linear regression model, multiple quantile regression model, support vector machine model, artificial neural network model, random forest model, etc. In addition, there are many factors that affect the level of DNA methylation, such as the tissue specificity of methylation. This paper reviews these modeling methods and influencing factors for age estimation based on DNA methylation, with a view to provide reference for the establishment of age estimation models.
Subject(s)
Humans , DNA Methylation , CpG Islands , Forensic Genetics , Neural Networks, Computer , Linear Models , Aging/geneticsABSTRACT
OBJECTIVES@#To investigate the technical performance of IDentifier DNA typing kit (YanHuang34) and evaluate its forensic application value.@*METHODS@#Following the Criterion of Forensic Science Human Fluorescence STR Multiplex Amplification Reagent (GB/T 37226-2018), IDentifier DNA typing kit (YanHuang34) was verified in 11 aspects of species specificity, veracity, sensibility, adaptability, inhibitor tolerance, consistency, balance, reaction condition verification, mixed samples, stability and inter batch consistency. The system efficiency of IDentifier DNA typing kit (YanHuang34) was compared with the PowerPlex® Fusion 6C System, VersaPlex® 27PY System and VeriFilerTM Plus PCR Amplification Kit. The IDentifier DNA typing kit (YanHuang34) was used to detect the swabs of biological samples in daily cases and the STR performances were observed.@*RESULTS@#IDentifier DNA typing kit (YanHuang34) had good species specificity, veracity, adaptability, inhibitor tolerance and balance. The sensibility was up to 0.062 5 ng. It was able to detect different types of samples, degraded samples and inhibitor mixed samples. Complete DNA typing could be obtained for samples with the mixture ratio less than 4∶1. The system efficiency of IDentifier DNA typing kit (YanHuang34) was very high, with TDP up to 1-1.08×10-37, CPEtrio and CPEduo up to 1-5.47×10-14 and 1-6.43×10-9, respectively. For the touched biological samples in actual cases, the effective detection rate was 21.05%. The system efficiency of kinship, single parent and full sibling identifications was effectively improved.@*CONCLUSIONS@#The IDentifier DNA typing kit (YanHuang34) is adaptive to the GB/T 37226-2018 requirements. It can be used for individual identification and paternity identification, and is suitable for application in the field of forensic science.
Subject(s)
Humans , DNA Fingerprinting , Polymerase Chain Reaction , Microsatellite Repeats , Paternity , Species SpecificityABSTRACT
OBJECTIVES@#To explore the possibility of using human skin and oral microorganisms to estimate the geographic origin of an individual through the sequencing analysis of bacterial 16S rRNA gene.@*METHODS@#Microbial DNA was extracted from the palm and oral microorganisms of the Han population in Shanghai and Chifeng, Inner Mongolia, and the composition and diversity of the microbiota were analyzed by full-length 16S rRNA gene sequencing. Then, differential species were screened and a geographic location prediction model was constructed.@*RESULTS@#The compositions of palm and oral microorganisms between Shanghai and Chifeng samples were both different. The abundance and uniformity of palm side skin microorganisms were higher in Chifeng samples than in Shanghai samples, while there was no significant difference in oral microorganisms. Permutational multivariate analysis of variance (PERMANOVA) confirmed that th e β -diversity between the samples from the two places were statistically significant, and the coefficients of determination (R2) for skin and oral samples were 0.129 and 0.102, respectively. Through principal co-ordinates analysis (PCoA), the samples from the two places could be preliminarily distinguished. The predictive model had the accuracies of 0.90 and 0.83 for the geographic origin using the skin and oral samples, respectively.@*CONCLUSIONS@#There are differences in the compositions of palm and oral microbiota between Han populations in Shanghai and Chifeng. The prediction model constructed by the random forest algorithm can trace the unknown individuals from the above two places.
Subject(s)
Humans , China , DNA, Bacterial/genetics , Microbiota/genetics , RNA, Ribosomal, 16S/genetics , Skin/microbiology , Forensic Genetics , High-Throughput Nucleotide Sequencing , Mouth/microbiologyABSTRACT
As an important anthropometric characteristic, human height not only contributes to the recognition of other anthropological characteristics and genetic risk factors, but also is an important part of forensic DNA phenotyping studies. Accurate estimation of height can provide more complete information about the phenotype of suspects and provide help to solve cases. In recent years, having benefited from the rapid development of molecular biological techniques and bioinformatics, height-related genetics research has made some progress. This paper describes the research progress of human height estimation from the genetic variation and the epigenetic inheritance perspectives and looks into the future research direction.
Subject(s)
Humans , Phenotype , DNA/genetics , Molecular Biology , Forensic Genetics/methodsABSTRACT
Skeleton and teeth are important biological samples. Due to their special structure and strong ability to resist degradation, they are ideal biological materials to retain DNA under natural condition. In many cases, such as historical figure identification, aged skeleton and teeth are usually the only biological samples. However, their DNA is in a state of trace, damage and degradation to different degrees, which requires special experimental treatment to achieve identification. This paper reviews the sample selection, DNA extraction, DNA enrichment and analysis approaches based on relevant research reports in recent years, aiming to promote the further development and improvement of the aged skeleton and teeth identification system.
Subject(s)
Humans , Aged , Body Remains , DNA/analysis , Tooth , DNA Fingerprinting , Sequence Analysis, DNAABSTRACT
OBJECTIVES@#To explore the feasibility of genetic marker detection of semen-specific coding region single nucleotide polymorphism (cSNP) based on SNaPshot technology in semen stains and mixed body fluid identification.@*METHODS@#Genomic DNA (gDNA) and total RNA were extracted from 16 semen stains and 11 mixtures composed of semen and venous blood, and the total RNA was reverse transcribed into complementary DNA (cDNA). The cSNP genetic markers were screened on the validated semen-specific mRNA coding genes. The cSNP multiplex detection system based on SNaPshot technology was established, and samples were genotyped by capillary electrophoresis (CE).@*RESULTS@#A multiplex detection system containing 5 semen-specific cSNPs was successfully established. In 16 semen samples, except the cSNP located in the TGM4 gene showed allele loss in cDNA detection results, the gDNA and cDNA typing results of other cSNPs were highly consistent. When detecting semen-venous blood mixtures, the results of cSNP typing detected were consistent with the genotype of semen donor and were not interfered by the genotype of venous blood donor.@*CONCLUSIONS@#The method of semen-specific cSNPs detection by SNaPshot technology method can be applied to the genotyping of semen (stains) and provide information for determining the origin of semen in mixed body fluids (stains).