Forensic DNA Identification Research Articles

Population genetics for 18 short tandem repeat loci (Canine GenotypesTM Panel 2.1 Kit) of 150 unrelated dogs from three pure-bred groups in Japan

Similar to that in Europe and the United States, the need for forensic DNA identification in dogs is increasing in Japan. As few studies have used commercial genotyping kits, the effectiveness of the Canine GenotypesTM Panel 2.1 Kit for individual DNA identification in dogs bred in Japan was examined. We genotyped 150 unrelated dogs (50 Golden Retrievers, 50 Miniature Dachshunds, and 50 Shiba Inu) at 18 canine short tandem repeat loci by the Kit. The allele frequency, expected heterozygosity, observed heterozygosity, p-value, power of the discriminant, and of exclusion, polymorphic information content, and random matching probability were calculated for each marker. The random matching probability was subsequently estimated to be 4.394×10-22 in the 150 dogs of the three pure-bred groups based on 18 STR loci; 3.257 × 10−16 in the Golden Retriever, 3.933 × 10−18 in the Miniature Dachshund, and 2.107 × 10−18 in the Shiba Inu breeds. In addition, principal component analysis based on genotype data revealed the Golden Retrievers, Miniature Dachshunds, and Shiba Inus separated into three clusters. The results of the genotype analysis showed that the Canine GenotypesTM Panel 2.1 Kit could be useful for identity testing and tool of population study of canines in Japan.

Video analysis of human and animal interactions for possible use in forensic human DNA identification

ABSTRACT Pets, such as cats and dogs, are present in the majority of households and may, in certain circumstances, be a relevant element in criminal investigations. Dogs, in particular, may interact with an intruder resulting in an exchange of trace evidence between the two. To better understand these interactions, fifty videos of dog contacts with an intruder were analysed, noting the location and the type of an interaction. It was found that dogs were more likely to instigate the interaction, jumping on the intruder, and were most commonly contacted on the head and back.

A panel of tetranucleotide STR markers as an alternative approach to forensic DNA identification of wolf and dog.

Commercial panels of microsatellite (STR) loci are focused on the use of DNA of the domestic dog (Canis lupus familiaris) and are often inapplicable for genotyping the DNA of the gray wolf (Canis lupus lupus). We propose a CPlex test system, including one hexa- and 12 tetranucleotide autosomal STR loci, as well as two sex loci, that is equally efficient in DNA identification of biological samples of the wolf and the dog. Analysis of molecular variance between samples revealed significant differentiation values (FST = 0.0784, p < 0.001), which allows to use the panel to differentiate wolf and dog samples. Population subdivision coefficients (θ-values) were calculated for each of the 13 STR loci of the developed test system. It was shown that the values of the genotype frequency for dogs and wolves, without and with considering the θ-value, differ by three orders of magnitude (for dogs 8.9 × 10-16 and 2.1 × 10-14 and for wolves 1.9 × 10-15 and 4.5 × 10-14, respectively). The use of population subdivision coefficients will allow to identify the most reliable results of an expert identification study and the power of exclusion provided by the STR loci of the CPlex test system makes it possible to achieve a reliable level of evidence in forensic DNA analysis of both wolves and dogs. The test system has been validated for use in forensic identification of the dog and wolf based on biological traces found at crime scenes, as well as for individual identification and establishing biological relationship of animals of these species.

Genetic Polymorphisms and Forensic Parameters of Thirteen X-Chromosome Markers in the Iraqi Kurdish Population.

X-chromosome short tandem repeat (X-STR) tools are crucial in forensic genetics and human population fields. This study presents the development and validation of a multiplex STR system consisting of thirteen X-STR loci and amelogenin specific to the human X chromosome. The system was optimized and tested for species specificity, sensitivity, stability, and DNA mixture using 9947A female and 9948 male control genomic DNA. The amplified products of nine loci were sequenced to determine the correct amplicon length. Allele frequencies, forensic parameters, mean exclusion chance (MEC), linkage disequilibrium (LD), and allelic patterns were investigated using DNA samples from 225 (159 male, 66 female) unrelated Kurdish individuals who live in Sulaymaniyah province in the Kurdistan region of Iraq. The most informative locus in the Kurdish population was GATA172D05, while the least informative locus was DXS10164. The results demonstrated that the 13 X-STR system is highly polymorphic and sensitive for forensic DNA identification. Genetic distance-based clustering, metric multidimensional scaling (MDS), and correlation matrix were analyzed for 19 ethnic groups and populations. The phylogenetic tree showed that populations clustered according to their ethnogeographic relationships. The findings revealed genetic links between the Iraqi Kurds, Caucasians, Iraqi Arabs, United States (U.S.) ethnic groups, and Chinese populations.

Internal validation of the GA118-24B Genetic Analyzer, a stable capillary electrophoresis system for forensic DNA identification.

The GA118-24B Genetic Analyzer (hereafter, "GA118-24B") is an independently developed capillary electrophoresis instrument. In the present research, we designed a series of validation experiments to test its performance at detecting DNA fragments compared to the Applied Biosystems 3500 Genetic Analyzer (hereafter, "3500"). Three commercially available autosomal short tandem repeat multiplex kits were used in this validation. The results showed that GA118-24B had acceptable spectral calibration for three kits. The results of accuracy and concordance studies were also satisfactory. GA118-24B showed excellent precision, with a standard deviation of less than 0.1 bp. Sensitivity and mixture studies indicated that GA118-24B could detect low-template DNA and complex mixtures as well as the results generated by 3500 in parallel experiments. Based on the experimental results, we set specific analytical and stochastic thresholds. Besides, GA118-24B showed superiority than 3500 within certain size ranges in the resolution study. Instead of conventional commercial multiplex kits, GA118-24B performed stably on a self-developed eight-dye multiplex system, which were not performed on 3500 Genetic Analyzer. We compared our validation results with those of previous research and found our results to be convincing. Overall, we conclude that GA118-24B is a stable and reliable genetic analyzer for forensic DNA identification.

Informative Relevance of 11 Microsatellite Loci for Forensic DNA Identification of Wild and Farm American Mink (Mustela vison) in Belarus

Informative Relevance of 11 Microsatellite Loci for Forensic DNA Identification of Wild and Farm American Mink (Mustela vison) in Belarus

Comparative of Forensic DNA Identification Using Cell Lysis Method and Magnetic Beads Method.

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. 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. 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. 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.

Genetic polymorphisms of 66 InDel loci in the Chinese Han population.

Insertion/deletion polymorphism (InDel) genetic markers refer to insertion or deletion of DNA fragments into genomic DNA, which have advantages in the identification of degraded samples. In this study, we independently screened 66 highly polymorphic InDel markers from the dbSNP database to establish a multiplex PCR system for forensic DNA identification using next-generation sequencing system (66-plex InDels). We assessed the population genetic data among 251 Chinese Han population using this system and evaluated their potential forensic application. The results showed that all 66 InDel loci conformed to the Hardy-Weinberg equilibrium (P>0.000 758), and all the pairwise InDel loci were in linkage equilibrium after Bonferroni correction. The mean observed heterozygosity (Ho) was 0.482, the mean expected heterozygosity (He) was 0.483,the mean discrimination power (DP) was 0.612, the mean polymorphism information content (PIC) was 0.365, the total discrimination power (TDP) reached 0.999 999 999 999 999 999 999 999 999 428 18. The cumulative power of exclusion for 66 InDel loci was 0.999 739 in duo cases (CPEduo) and was 0.999 999 999 417 in trios cases (CPEtrio). The results show that the 66 InDel loci have high genetic polymorphisms in the Chinese Han population and can be used independently for forensic DNA identification and paternity testing.

Research of polymorphism of microsatellite markers of Scots pine for the purposes of forensic DNA analysis

Microsatellites as highly polymorphic markers are a valuable tool in identification and population studies. In order to form approaches to forensic DNA identification in the investigation of illegal logging cases, 17 SSR markers of Scots pine (Pinus sylvestris L.) were tested using DNA from plants growing in the western and eastern parts of the Republic of Belarus. High information content was shown for six microsatellite markers. The potential possibility of using a complex of selected markers for the purpose of DNA identification of Scots pine wood samples in forensic examination has been established.

Evaluation of the reliability of SE33 locus in forensic DNA identification in Turkish Population

Forensic DNA studies is a powerful tool in criminal investigations and paternity test. In recent years, STR (Short Tandem Repeat) DNA loci are being used more and more in forensic identification all over the world. In this context, polymorphism rates and frequency of the SE33 region, which is an autosomal STR locus, is aimed to be determined about its reliability. Evaluations were made on the samples of 500 individuals who did not have close relatives. Genomic DNA isolation was carried out by DNA isolation kits (EZ-1 investigator kit and Power Plex Fusion 6C Direct kit) previously by the authorized staff of İzmir Forensic Medicine Group Presidency. SE33 STR locus amplification was achieved with the Powerplex Fusion 6C kit from the isolated DNA. In the study, homozygote genotype rate was 5.4%, heterozygote genotype rate was 94.6%, power of discrimination (PD) 0.992 and matching probability (PM) was 0.008. The lowest frequency alleles were determined as 7,10,16.3,17.2,23,24,29, 34.2,35.2,37 alleles with 0.1%. It is seen that SE33 STR locus is a strong marker in forensic identification compared to other studies in terms of power of discrimination and matching probability.

Biocomputational Screening and Pharmacological Studies of Gymnema sylvester in Contrast to Human CCR5 and CXCR4 Chemokine Receptors

In last twenty years DNA, profiling has become an obligatory technology, which has brought scientists towards forensic identification. Thousands of STR markers are present in human genome but only core set of loci are selected for forensic DNA and human identification. STRs have become famous in forensic labs because even low amount and degraded form can be easily typed. STRs are found in prokaryotes and eukaryotes, including humans. They appear scattered almost evenly throughout the human genome, resulting in about 3% of the genome. However, their distribution in chromosomes is not quite uniform. Usually, STRs occur in the noncoding regions, only about 8% are located in the coding regions. In humans, chromosome 19 has the highest density of STRs. On an average, one STR occurs per 2,000 bp in the human genome. On the basis of repeat units, STRs can be differentiated into different types. The repeats of STR markers are highly variable in human population. STR marker evaluation very precisely figures out individual humans at the molecular level even from very small quantities. STR locus in the identification selected is D7S820 from NIST (National Institute of Standards and Technology). Conditions for STR with the changes in temperature, magnesium ion concentration, primer and setting up, PCR of the marker used to carry out. PCR product is inspected of agarose gel. The results showed that the STR locus being investigated is detectable by PCR. PCR showed that the detection of primer and temperature conditions measured by using the fixed amount of magnesium, D7S820 locus bands are weaker than expected. Using a buffer and setting magnesium condition towards changes in primer and temperature, addition of Taq polymerase at a temperature of 94°C, bands become visible desirably.

An 18 Multi-InDels panel for analysis of highly degraded forensic biological samples.

DNA genotyping from trace and highly degraded biological samples is one of the most significant challenges of forensic DNA identification. There is a lack of simple and effective methods for genotyping highly degraded samples. In this study, a multiple loci insertion/deletion polymorphisms (Multi-InDels) panel was designed for detecting 18 autosomal Multi-InDels through capillary electrophoresis (CE) with amplicon sizes no longer than 125bp.Studiesof sensitivity, degradation, and species specificity were performed and a population study was carried out using 192 samples from Han populations in Hunan province in the south of China. The combined random match probability (CMP) of these 18 Multi-InDels was 3.23 × 10-12 and the cumulative probability of exclusion (CPE) was 0.9989, suggesting this panel could be used independently for human identification and could provide efficient supporting information for parentage testing. Complete profiles were obtained from as low as 62.5pg of total input DNA after increasing the number of PCR cycles. Moreover, all alleles were detected from artificially highly degraded DNA after 80 min of boiling water bath treatment. This 18 Multi-InDels panel is simple, fast, and effective for the forensic analysis of highly degraded DNA.

THE RELIABILITY OF TRACE DNA OR LOW COPY NUMBER (LCN) DNA EVIDENCE IN COURT PROCEEDINGS

Although forensic DNA testing is well established, some experts disagree with the interpretation and statistical significance of test results obtained from very small samples. This article discusses the problems regarding the use of the low copy number (LCN) technique as well as the value that can be derived from such an analysis. It focuses on the problematic results that can arise from using very small samples for forensic DNA identification. Since this kind of analysis is based on low amounts of DNA samples (between 100 picograms and 200 picograms in South Africa) that are amplified by using more than the normal 28 cycles to create larger samples for analysis, the reliability of the analysis has been questioned. The amplification process, known as the Polymerase Chain Reaction (PCR), is associated with risks such as stochastic effects and contamination that could make interpretation of the results difficult for the defence. While standard operating laboratory protocols could prevent contamination and although the electropherograms could aid the detection of contamination, it is highly problematic for the defence counsel to ascertain whether these procedures were indeed strictly followed. Drawing on foreign jurisprudence, this article considers the risks and key controversies and explains what lawyers need to know, in order to be able to recognise controversial results that could stem from using the LCN DNA technique for forensic DNA identification. The conclusions thus drawn may be of particular relevance to the South African context, as no reported case law exists in which the issues relating to the use of LCN DNA have yet come to the fore.

Genetic Polymorphism and Forensic Application of 47 Autosomal InDel Loci in 5 Chinese Ethnic Groups.

Objective To investigate the population genetic data of 47 autosomal insertion/deletion （InDel） polymorphism genetic markers involved in AGCU InDel 50 kit in Guangdong Han, Guangxi Zhuang, Guangxi Yao, Guangxi Jing, and Guangxi Mulam, and to evaluate their application in forensic DNA identification. Methods Multiplex amplification of the 768 unrelated individuals from the 5 ethnic groups mentioned above was performed with the AGCU InDel 50 kit. Genotyping was carried out by 3500xL gene analyzer, population genetic parameters were gathered and polymorphism analysis was performed. Results No linkage disequilibrium was found among 47 autosomal InDel loci in the 5 ethnic groups. The distribution of genotype frequency of 47 autosomal InDel loci confirmed to the Hardy-Weinberg equilibrium in Guangdong Han and Guangxi Zhuang. Except for rs139934789, the other 46 loci confirmed to the Hardy-Weinberg equilibrium in Guangxi Yao, Guangxi Jing, and Guangxi Mulam. The results of genetic variation analysis among the populations showed that 1.12% of genetic variation was caused by ethnic group differences. The cumulative discrimination power of 47 autosomal InDel loci for the 5 ethnic groups were all above 0.999 999 999 999 999. The cumulative probability of exclusion for each ethnic group was less than 0.999 9. The two Y-InDels were identified in all male individuals and were absent in all female individuals. Conclusion Except for rs139934789, the other 46 InDel loci have a relatively good genetic polymorphism in the 5 Chinese ethnic groups, and can be used for forensic individual identification and as effective supplements for paternity testing.

Proposed Genetic Profiling System Based on Gel Electrophoresis for Forensic DNA Identification

Proposed Genetic Profiling System Based on Gel Electrophoresis for Forensic DNA Identification

Typical mistakes when conducting forensic DNA identification

Typical mistakes when conducting forensic DNA identification

Considering DNA transfer issues in a retrospective analysis of forensic examinations

The article deals with evaluating forensic DNA identification data in a case of retrospective analysis with a strong uncertainty factor. The DNA data should be assessed by both the investigator and the court taking into account mechanisms of trace deposits. To solve activity-level issues suggested approaches are using molecular techniques for the forensic cell type identification, the Bayesian networks, the findings of large-scale studies conducted to standardize and corroborate the conclusions on various aspects of DNA transfer, persistence, prevalence and recovery. Nevertheless, in practice there are many cases where considering DNA transfer issues is problematic. The novel techniques cannot be used in a case of retrospective analysis if further research is impossible due to the lack of the biological material. The situation may be aggravated by the revealing expert’s examination defects which might make the results ambiguous, contamination risk factors or potential possibility of DNA transfer due to non-crime everyday activity. Finally, the most difficult situation arises, if there is a combination of the factors above. An example from the casework is considered.

Forensic parameters and mutation analysis of 23 short tandem repeat (PowerPlex® Fusion System) loci in Fujian Han Chinese population.

Kinship testing based on genetic markers has valuable practical applications. Short tandem repeat polymorphisms (STRPs) can have large number of alleles, and become the dominant marker for kinship identification. However, the high mutation rates affect the identification accuracy. Thus, accurate investigation of the mutation rate of STR loci in different populations is crucial for the reliability of phylogenetic relationships. In present study, forensic parameters and mutation rates (include 95% CI) of 23 short tandem repeats (STR) loci (D3S1358, D1S1656, D2S441, D10S1248, D13S317, D16S539, D18S51, D2S1338, CSF1PO, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, FGA, D22S1045, PentaE, PentaD and DYS391) were investigated through PowerPlex® Fusion System in Fujian Han population. The high level of CDP (0.999999999999999999999999992) and CPE (0.999999993) indicated the panel was high efficiency in forensic DNA identification and paternity testing. In mutation analysis, 43 mutation cases were found through 54,124 parent-child meiotic transfers. The observed mutation rates ranged from 0 (D3S1358, D1S1656, D13S317, TH01, D19S433 and D22S1045) to 0.0025 (PentaE and FGA). The overall mutation rate across all loci was 0.0008 and the average mutation rate for the 23 loci was estimated to be 0.00078 per meiosis. The vast majority of mutations were single-step (88.4%) mutation and also include double-step (9.3%) and triple-step (2.3%) mutations. Paternal mutation rate was more common than maternal mutation rate with a ratio of 7.2:1. In addition, mutation rates indicated positive correlation (r = 0.633, p = 0.009) with the expected heterozygosity (He).

Problems of Forensic DNA-Identifi cation by Using Small Quantities of the Substance in Biological Traces

Problems of Forensic DNA-Identifi cation by Using Small Quantities of the Substance in Biological Traces

Study on problems in forensic DNA identification standardization in China and countermeasures for the same

Forensic DNA analysis plays an important role in criminal cases, civil cases, missing persons' identification, and other truth-ascertaining activities. Selection of an appropriate laboratory for DNA testing, use of amplification reagents, management of database and other standardized operations, standardization of system for biological evidence in terms of sample collection, and sample analysis will improve the quality and credibility of the identification work. However, current forensic DNA standardization in China encounters some problems with respect to the development of standard and technical specification, standard documents, and DNA evidence review and acceptance. Thus, introduction and refinement of the standardization system require collective knowledge and continuous efforts. Moreover, standardization could not replace court review, and expert reports still should be cross-examined in courts.