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To explore the efficacy of commonly used forensic identification panels in complex paternity testing of trios that involved close relatives, we wrote a code by R to generate 10,000 pedigrees at 20 CODIS STR, 21 non-CODIS STR and 30 InDel loci in Chinese five ethnic groups based on their allele frequencies. Parentage identification index——cumulative paternity index (CPI) value was set as output and was further analyzed to evaluate the performance of the aforementioned panels in complex paternity testing when the alleged parent is a random individual, biological parent, grandparent, sibling of biological parent, half-sibling of biological parent, etc. The results showed that the false inclusion of parent sibling posed as parent demonstrated no statistically significant difference from that of grandparent posed as parent. The scenarios where both biological parent and alleged parent were consanguineous to the other parent were also simulated. The results revealed that the complexity of paternity testing would raise when biological parents were consanguineous and the alleged parent was a close relative of theirs. Despite the values of non-conformity number could vary in different genetic relationships, populations and panels, 20 CODIS STRs and 21 non-CODIS STRs performed satisfactorily in most simulated scenarios. However, the joint use of 20 CODIS STRs and 21 non-CODIS STRs is more recommendable when resolving the paternity testing of the incest mating case. Overall, the current study could be regarded as a worthwhile reference in complex paternity testing of trios that involved close relatives. •Thoroughly compared the efficiency of 3 commonly used commercial kits in complex paternity testing among 5 populations.•11 Scenarios were simulated to analyze the influence of close relatives on paternity testing.•The marker set combined CODIS and non-CODIS STRs provides a powerful tool for complex paternity testing.

There is an increasing demand for prenatal paternity testing in the forensic applications, which identify biological fathers before the birth of children. Currently, one of the most effective and safe Non-Invasive Prenatal Paternity Testing (NIPPT) methods is high-throughput Next-Generation Sequencing (NGS)-based SNP genotyping of cell-free DNA in maternal peripheral blood. To the best of our knowledge, nearly all methods being used in such applications are based on traditional postnatal paternity tests and/or statistical models of conventional polymorphism sites. These methods have shown unsatisfactory performance due to the uncertainty of fetal genotype. In this study, we propose a cutting-edge methodology called the Prenatal paternity Test Analysis System (PTAS) for cell-free fetal DNA-based NIPPT using NGS-based SNP genotyping. With the implementation of our proposed PTAS methodology, 63 out of 64 early-pregnancy (i.e., less than seven weeks) samples can be precisely identified to determine paternity, except for one sample that does not meet quality control requirements. Although the fetal fraction of the non-identified sample is extremely low (0.51%), its paternity can still be detected by our proposed PTAS methodology through unique molecular identifier tagging. Paternity of the total 313 samples for mid-to-late pregnancy (i.e., more than seven weeks) can be accurately identified. Extensive experiments indicate that our methodology makes a significant breakthrough in the NIPPT theory and will bring substantial benefits to forensic applications. •We propose a cutting-edge methodology called the Prenatal paternity Test Analysis System (PTAS).•The PTAS consists of several novel statistical models for NIPPT.•High performance is achieved to detect both early and late pregnancy.•This work can establish the standards for NIPPT in the forensic field.

Dyer reports that a man has won the right of paternity testing against a dead putative father. 1 We considered a case series of posthumous paternity testing on retained tissue samples. 2 Our cases all occurred in a single hospital and were covered by the Human Tissue Act 2004; the consent issues could be resolved without recourse to the courts.The act is complex, particularly in the way it deals with genetic testing.

The role of genetic counselors in prenatal paternity testing has not been widely studied in the genetic counseling literature. In South Australia, the genetic counselors of the State’s public sector clinical genetics service are the primary contact point for women seeking information and testing, also coordinating the testing process. This has provided the opportunity to review all prenatal paternity testing performed in the State over a 13 year period and to consider the role played by the genetic counselor. We explored the reasons why women requested prenatal paternity testing and whether the genetic counselor was an appropriate health professional to facilitate this testing for women. The study had two parts, an audit of the clinical genetics files of 160 women who requested prenatal paternity testing between March 2001 and March 2014, and qualitative interviews of genetic counselors, clinical geneticists, obstetricians and social workers with involvement in this area. The audit determined that in 69.9 % of cases the long-term partner was the father of the pregnancy, for 23.7 % the short-term or other partner was the father and for 6.4 % the paternity results were not known by the genetic counselor. For 45.5 % of women whose long-term partner was excluded as the father, the women chose to have a termination of pregnancy. The results of the qualitative interviews yielded five major themes: accessibility of testing, role of the genetic counselor, social and relationship issues, decision making in pregnancy and emotional issues. We conclude that the genetic counselor is an appropriate health professional to facilitate prenatal paternity testing. Genetic counselors did not view their role as significantly different from a request for prenatal testing for another indication.

Microhaplotypes are playing an increasingly important role in forensic evidence analysis. However, the impact of meiotic recombination events on the efficacy of microhaplotypes in paternity testing remains poorly understood. Based on the data from the 1000 Genomes Project and a high-resolution recombination map, we identified microhaplotypes from low recombination-rate regions (recombination rate < 0.1 cM/Mb) and validated their efficacy for paternity testing by assessing their performance in 580 trio families and in simulated datasets. The results showed that: (1) The low-recombination microhaplotypes outperformed their high-recombination counterparts in paternity testing; (2) A panel of 30 microhaplotypes, selected from low-recombination, non-coding regions of the autosomes, achieved a cumulative power of discrimination (CPD) of 1-6.77 × 10 − 37 and cumulative probability of exclusion (CPE) of 1-1.72 × 10 − 13 ; (3) Validation using real-world trios demonstrated that low-recombination microhaplotypes had significantly higher cumulative paternity index (CPI) values ( p  < 2e-16), outperforming conventional STR markers by seven orders of magnitude; (4) Simulation analyses revealed that low-recombination markers could distinguish true parentage with 100% accuracy and had higher paternity testing accuracy compared to high-recombination counterparts; (5) An online microhaplotype database ( http://bioinformatics.gqliulab.com/microhaplotype/ ) was established, enabling users to query information and calculate forensic parameters. An open-access microhaplotype screening tool, MHpatools, was developed and is freely available at http://bioinformatics.gqliulab.com/MHpatools/ . Collectively, the established microhaplotype system, database, and analytical tools would be useful in forensic genetics.

Introduction: In legal paternity cases, genetic testing holds crucial evidential value. The standard practice involves the participation of the mother, child, and alleged father in these tests. There is an approach that considers the child’s mother’s profile unnecessary for such tests. While testing fewer participants may be cost-effective, it is essential to obtain clear and conclusive results. Therefore, it is worth examining whether the absence of the mother’s profile in the tests negatively impacts the results of kinship analysis.Materials and methods: The results of disputed paternity genetic tests that included the mother, child, and alleged father were evaluated. These tests were conducted between 2018–2023 at the Department of Forensic Medicine of the Medical University of Warsaw. Genetic profiles were obtained using the PowerPlex® Fusion 6C System reagent kit (Promega, USA).Results: Analysis of 557 paternity tests revealed that 148 cases resulted in the exclusion of paternity, 406 confirmed paternity, and 3 cases remained unsolved. Further analysis of cases with paternity exclusions showed inconsistencies in an average of 14 loci. The most frequently excluding marker was SE33, while TPOX had the weakest excluding strength. No false positive results were obtained in tests that included the mother’s profile, and the percentage of unresolved cases was 0.54%. When simulating the results without the mother’s profile, 5.21% of cases remained unresolved, and it was determined that a false positive result could occur.Conclusions: The necessity of the mother’s participation in genetic paternity testing has been confirmed. Omitting the mother’s profile may lead to an inconclusive result or even an erroneous genetic opinion.

The International Society for Forensic Genetics (ISFG) has established a Paternity Testing Commission (PTC) with the purpose of formulating international recommendations concerning genetic investigations in paternity testing. The PTC recommends that paternity testing be performed in accordance with the ISO 17025 standards. The ISO 17025 standards are general standards for testing laboratories and the PTC offers explanations and recommendations concerning selected areas of special importance to paternity testing.

Massively parallel sequencing (MPS) has emerged as a promising technology for targeting multiple genetic loci simultaneously in forensic genetics. Here, a novel 193-plex panel was designed to target 28 A-STRs, 41 Y-STRs, 21 X-STRs, 3 sex-identified loci, and 100 A-SNPs by employing a single-end 400 bp sequencing strategy on the MGISEQ-2000™ platform. In the present study, a series of validations and sequencing of 1642 population samples were performed to evaluate the overall performance of the MPS-based panel and its practicality in forensic application according to the SWGDAM guidelines. In general, the 193-plex markers in our panel showed good performance in terms of species specificity, stability, and repeatability. Compared to commercial kits, this panel achieved 100% concordance for standard gDNA and 99.87% concordance for 14,560 population genotypes. Moreover, this panel detected 100% of the loci from 0.5 ng of DNA template and all unique alleles at a 1:4 DNA mixture ratio (0.2 ng minor contributor), and the applicability of the proposed approach for tracing and degrading DNA was further supported by case samples. In addition, several forensic parameters of STRs and SNPs were calculated in a population study. High CPE and CPD values greater than 0.9999999 were clearly demonstrated and these results could be useful references for the application of this panel in individual identification and paternity testing. Overall, this 193-plex MPS panel has been shown to be a reliable, repeatable, robust, inexpensive, and powerful tool sufficient for forensic practice.

Background A large number of variants have been employed in various medical applications, such as providing medication instructions, disease susceptibility testing, paternity testing, and tumour diagnosis. A high multiplicity PCR will outperform other technologies because of its lower cost, reaction time and sample consumption. To conduct a multiplex PCR with higher than 100 plex multiplicity, primers need to be carefully designed to avoid the formation of secondary structures and nonspecific amplification between primers, templates and products. Thus, a user-friendly, highly automated and highly user-defined web-based multiplex PCR primer design software is needed to minimize the work of primer design and experimental verification. Results Ultiplex was developed as a free online multiplex primer design tool with a user-friendly web-based interface ( http://ultiplex.igenebook.cn ). To evaluate the performance of Ultiplex, 294 out of 295 (99.7%) target primers were successfully designed. A total of 275 targets produced qualified primers after primer filtration, and 271 of those targets were successfully clustered into one compatible PCR group and could be covered by 108 primers. The designed primer group stably detected the rs28934573(C > T) mutation at lower than a 0.25% mutation rate in a series of samples with different ratios of HCT-15 and HaCaT cell line DNA. Conclusion Ultiplex is a web-based multiplex PCR primer tool that has several functions, including batch design and compatibility checking for the exclusion of mutual secondary structures and mutual false alignments across the whole genome. It offers flexible arguments for users to define their own references, primer Tm values, product lengths, plex numbers and tag oligos. With its user-friendly reports and web-based interface, Ultiplex will provide assistance for biological applications and research involving genomic variants.

Short tandem repeat (STR) loci are frequently utilized in kinship testing, and mutations of a single base occurring in the primer-binding region of the STR locus can result in the failure of allelic amplification and the emergence of silent genes. Silent genes are not observable and, therefore, are excluded from the genotypes assessed. Pedigree likelihood ratios (LRs) are often employed in kinship testing to determine the likelihood of different kinship scenarios. LR values are derived from various types of genotypes. LRexact values are based on the exact or actual genotypes, which may include silent genes. Conversely, LRobserve values are based on observed genotypes that exclude silent genes, while LRadjust values incorporate all potential genotypes, including both observed and those with silent genes. Initially, the formulae for LRs in 1st degree, 2nd degree, and 3rd degree kinship testing are presented according to different genotype forms of pairwise individuals. The correctness of these formulae is then verified using the Familias software, and the results are compared with those from the GeneVisa software (www.genevisa.net). Lastly, the simulation modules of GeneVisa are used to assess the impact of silent genes on pairwise kinship testing. The findings indicate that the overall impact of silent genes is minimal, although in some cases, the effects can be relatively significant. The influence of silent genes generally decreases as the kinship relationship becomes more distant. In specific kinship tests, the effect of silent genes is reduced when the individuals are unrelated compared to when there is a kinship relationship. Utilizing the LRadjust value for 1st degree and 2nd degree kinship testing can substantially mitigate the effects of silent genes. •Silent genes affect pedigree likelihood ratio used for kinship testing.•The effects of silent genes are evaluated by computer program.•The formulae for pedigree likelihood ratio involving silent gene are presented.•The overall impact of silent genes on pairwise kinship testing is minimal.•In some cases, the effects of silent genes can be relatively significant.