A Novel Panel of 43 Insertion/Deletion Loci for Human Identifications of Forensic Degraded DNA Samples: Development and Validation

Comprehensive investigation of the Applied Biosystems™ SeqStudio™ Genetic Analyzer platform for forensic DNA typing

Capillary electrophoresis (CE) is the conventional method for separating and detecting amplified DNA fragments for forensic human identification (HID). The Applied Biosystems™ SeqStudio™ Genetic Analyzer, referred to herein as the SeqStudio™, is the most recent CE platform introduced for forensic purposes. The SeqStudio™ includes an all-in-one reagent cartridge containing four capillaries. Validating a CE platform requires consideration of injection time, sensitivity and reproducibility, and mixture performance. The evaluation of the SeqStudio™ was performed using a standard polymerase chain reaction (PCR)-CE workflow. Injection time, sensitivity, and mixture studies were performed to determine the optimal parameters for reproducible and reliable data. The injection time study yielded a general decline in the relative florescence units (RFU) as injection time decreased from ten to one second. The sensitivity study showed no locus or allelic dropout from one nanogram (ng) to 250 picogram (pg) DNA input at the one second injection time, however, when not considering the TH01 locus, the sensitivity was further reduced to 62.5pg. The two-person and three-person mixture studies demonstrated that the SeqStudio™ is capable of detecting a large range of DNA mixture ratios. The evaluation serves as a model for best practices and supports the use of the SeqStudio™ for HID.

Development and evaluation of a panel of newly screened Y chromosome InDels for inferring paternal ancestry information in Southwest China

Y-InDels (insertions/deletions) are genetic markers which are extremely understudied. It is unknown whether this type of markers can be utilized for genetic ancestry inference. We have developed an innovative Y chromosome ancestry inference system tailored for forensic applications. This panel amplifies 21 Y chromosome loci, encompassing Y-InDels and Y-SNPs (Single Nucleotide Polymorphism), utilizing the capillary electrophoresis (CE) platform. The system performed well at DNA concentrations greater than 0.125 ng/ul and produced accurate results at a 1:100 mixing ratio of male and female DNA. The Cumulative probability of matching (CPM) was between 0.95 and 0.97 in the experimental population. The system's efficacy in inferring ancestral origins was demonstrated through intercontinental population discrimination, revealing high discrimination power between African and East Asian populations. Population genetic analyses conducted on Han, Qiang and Hui populations in Southwest China, where the smallest FST value was 0.0002 between Han Chinese in Beijing (from 1000 Genomes Project) and Qiang Chinese from Sichuan (CQSC). Phylogenetic tree construction further illuminated distinct haplotypes among populations, with ethnically unique haplotypes observed in 34.6% of Hui and 7.1% of Qiang populations. K-fold cross-validation show the system's inference abilities at the intercontinental level. In addition, our investigations identified potential associations between the Y-InDel locus Y: 15,385,547 (GRCh37) and haplogroup R1a1a1b2a2- Z2124, as well as locus Y: 13,990,180 (GRCh37) and haplogroup F-M89. In conclusion, we have established a Y-chromosome inference system tailored for grassroots-level application, underscoring the value of incorporating Y-InDel markers in forensic analyses.

Ancestry analysis using a self-developed 56 AIM-InDel loci and machine learning methods

Insertion/deletion (InDel) polymorphisms can be used as one of the ancestry-informative markers in ancestry analysis. In this study, a self-developed panel consisting of 56 ancestry-informative InDels was used to investigate the genetic structures and genetic relationships between Chinese Inner Mongolia Manchu group and 26 reference populations. The Inner Mongolia Manchu group was closely related in genetic background to East Asian populations, especially the Han Chinese in Beijing. Moreover, populations from northern and southern East Asia displayed obvious variations in ancestral components, suggesting the potential value of this panel in distinguishing the populations from northern and southern East Asia. Subsequently, four machine learning models were performed based on the 56 AIM-InDel loci to evaluate the performance of this panel in ancestry prediction. The random forest model presented better performance in ancestry prediction, with 91.87% and 99.73% accuracy for the five and three continental populations, respectively. The individuals of the Inner Mongolia Manchu group were assigned to the East Asian populations by the random forest model, and they exhibited closer genetic affinities with northern East Asian populations. Furthermore, the random forest model distinguished 87.18% of the Inner Mongolia Manchus from the East Asian populations, suggesting that the random forest model based on the 56 ancestry-informative InDels could be a potential tool for ancestry analysis.

Development of a multiplex panel with 36 insertion/deletion markers (InDel) for individual identification

In recent years, the insertion/deletion (InDel) polymorphism has become a preferred genetic marker in forensic genetics due to its low mutation rates and small amplicon sizes. In this study, a 36-InDelplex identification panel, consisting of autosomal 34 InDel loci, 1 Y InDel locus, and amelogenin, was developed, and gene frequencies in the Turkish population were determined. The loci of the InDel panel with global minimum allele frequencies (MAF) ≥ 0.4 were selected from the 1000 Genomes Project Phase 3 data. The amplicon sizes of the loci were designed in the range of 69-252 bp. In the validation study of the developed panel, analysis threshold, dynamic range, sensitivity, stochastic threshold, inhibitor tolerance, and reproducibility parameters were studied by following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The sensitivity studies indicated that complete and reliable InDel profiles could be obtained with 0.25 ng of DNA. A population study was evaluated using 250 samples from Turkey. The mean observed heterozygosity ratio (Ho) of all loci was 0.48. The combined discrimination power (CPD) is 0.999999999990867 and the combined exclusion probability (CPE) was 0.9930. The population comparison was also made using Turkish and the five major populations from the 1000 Genomes Phase 3 populations' data (Africa, Europe, East Asia, South Asia, and America). In conclusion, the results showed that the 36-InDelplex panel is a reliable, sensitive, and accurate system that is suitable for human identification and population genetics purposes.

Systematical explorations of forensic feature and population genetic diversity of the Chinese Mongolian group from northwest China via a self-constructed Multi-InDel panel

This study aimed to investigate the genetic polymorphisms and population characteristics of Chinese Mongolian group from northwest China (NCM) through a self-developed panel including 43 autosomal insertion/deletion (A-InDel) polymorphism genetic markers. Herein, 288 unrelated healthy individuals from the NCM group were employed to obtain the genetic data of 43 A-InDels through multiplex PCR amplification and InDel genotyping using capillary electrophoresis platform. In addition, multiplex population genetic analyses were performed between the NCM group and 27 reference populations. There were no deviations at 43 loci from Hardy-Weinberg equilibrium in the NCM group. The observed heterozygosity (Ho) values ranged from 0.312 8 to 0.559 2, and the combined power of discrimination (CPD) and cumulative probability of exclusion (CPE) values in the NCM group were 0.999 999 999 999 999 998 77 and 0.999 814, respectively. The forensic parameter values indicated that this panel was polymorphic and informative in the NCM group and could be used as an effective tool for forensic personal identification. Furthermore, the results of pairwise genetic distances, principal component analysis, multidimensional scaling analysis, phylogenetic tree construction, and admixture analysis among the NCM group and 27 reference populations revealed that there were closer genetic relationships between the NCM group and East Asian populations, especially Chinese Hui group (CHH) from the northwest China, which is consistent with the geographical location. These present findings contributed to the ongoing genetic explorations and insights into the genetic architecture of the NCM group.

Developmental validation of a custom-designed Multi-InDel panel: A five-dye multiplex amplification system for challenging DNA samples

The continual investigation of novel genetic markers has yielded promising solutions for addressing the challenges encountered in forensic DNA analysis. In this study, we have introduced a custom-designed panel capable of simultaneously amplifying 41 novel Multi-insertion/deletion (Multi-InDel) markers and an amelogenin locus using the capillary electrophoresis platform. Through a developmental validation study conducted in accordance with guidelines recommended by the Scientific Working Group on DNA Analysis Methods, we demonstrated that the new Multi-InDel system exhibited the sensitivity to produce reliable genotyping profiles with as little as 62.5 pg of template DNA. Accurate and complete genotyping profiles could be obtained even in the presence of specific concentrations of PCR inhibitors. Furthermore, the maximum amplicon size for this system was limited to under 220 bp in the genotyping profile, resulting in its superior efficiency compared to commercially available short tandem repeat kits for both naturally and artificially degraded samples. In the context of mixed DNA analysis, the Multi-InDel system was proved informative in the identification of two-person DNA mixture, even when the template DNA of the minor contributor was as low as 50 pg. In conclusion, a series of performance evaluation studies have provided compelling evidence that the new Multi-InDel system holds promise as a valuable tool for forensic DNA analysis.

Development of a 39 MM-InDel multiplex assay for the forensic application

Insertion/deletion polymorphisms (InDels) are a category of highly prevalent markers in the human genome, characterized by their distinctive attributes, including short amplicon sizes and low mutation rates, which have shown great potential in forensic applications. Multi-allelic InDel and multi-InDel markers, collectively abbreviated as MM-InDels, were developed to enhance polymorphism by the introduction of novel alleles. Nevertheless, the relatively low mutation rates of InDels, coupled with the founder effect, result in distinct allele frequency distributions among populations. The divergent characteristics of InDels in different populations also pose challenges to the establishment of universally efficient InDel multiplex assays. To enhance the system efficiency of the InDel assay and its applicability across diverse populations, 39 MM-InDels with high polymorphism in five different ancestry superpopulations were selected from the 1000 Genomes Project dataset and combined with an amelogenin gender marker to construct a multiplex assay (named MMIDplex). The combined power of discrimination and the cumulative probability of exclusion of 39 MM-InDels were 1 - 1.3 × 10-23 and 1 - 9.83 × 10-6 in the Chinese Han population, and larger than 1-10-19 and 1-10-4 in the reference populations, relatively. These results demonstrate that the MMIDplex assay has the potential to obtain sufficient power for individual identification and paternity test in global populations.

Unveiling the genetic landscape of high-altitude adaptive ethnic groups with polymorphic markers: Implications of comprehensive forensic appraisals and population genetic investigations

Background

Deletion/insertion polymorphisms (DIPs), a novel class of biomarker, have been widely utilized in forensic areas for individual identification, paternity tests, and ancestral origin inference due to its applicability to degraded samples and low mutation rates. Despite the availability of a well-established commercial kit, the Investigator® DIPplex kit (Qiagen), certain loci exhibit limited levels of polymorphisms in East Asian populations, particularly in Chinese populations.

Objective

This dissertation seeks to undertake a comprehensive evaluation about the forensic efficiency of a self-developed multiplex amplification system in high-altitude adaptive ethnic groups of China. Healthy unrelated Tibetan individuals residing in Tibet Autonomous Region and Qinghai Province were genotyped using previously reported 43 deletion/insertion polymorphism loci. Forensic statistical analyses including allele frequencies and forensic parameters were conducted in the two Tibetan groups, and the genetic relatedness of the studied groups with reference populations from the 1000 Genomes Project Phase 3 were investigated.

Results

Forensic statistical results showed that the polymorphism information content values of the 43 deletion/insertion polymorphism loci in the two Tibetan groups exceeded 0.35. Moreover, the combined power of discrimination using the 43 deletion/insertion polymorphism loci was calculated to be 0.9999999999999999984 in the Qinghai Tibetan group and 0.9999999999999999921 in the Tibet Tibetan group. The cumulative power of exclusion using the 43 deletion/insertion polymorphism loci was calculated to be 0.999782512 in the Qinghai Tibetan group and 0.999886205 in the Tibet Tibetan group. Analysis of population genetics demonstrated that the two studied Tibetan groups shared close genetic relationships with East Asia populations.

Conclusion

The set of 43 deletion/insertion polymorphism loci exhibited remarkable forensic efficacy, rendering it a promising tool for forensic practice. Population genetic analyses indicated that the two Tibetan groups had closer genetic affinities to East Asian populations.

Comprehensive evaluations of individual discrimination, kinship analysis, genetic relationship exploration and biogeographic origin prediction in Chinese Dongxiang group by a 60-plex DIP panel

BACKGROUND

Dongxiang group, as an important minority, resides in Gansu province which is located at the northwest China, forensic detection system with more loci needed to be studied to improve the application efficiency of forensic case investigation in this group.

METHODS

A 60-plex system including 57 autosomal deletion/insertion polymorphisms (A-DIPs), 2 Y chromosome DIPs (Y-DIPs) and the sex determination locus (Amelogenin) was explored to evaluate the forensic application efficiencies of individual discrimination, kinship analysis and biogeographic origin prediction in Gansu Dongxiang group based on the 60-plex genotype results of 233 unrelated Dongxiang individuals. The 60-plex genotype results of 4582 unrelated individuals from 33 reference populations in five different continents were also collected to analyze the genetic background of Dongxiang group and its genetic relationships with other continental populations.

RESULTS

The system showed high individual discrimination power, as the cumulative power of discrimination (CPD), cumulative power of exclusion (CPE) for trio and cumulative match probability (CMP) values were 0.99999999999999999999997297, 0.999980 and 2.7029E^- 24, respectively. The system could distinguish 98.12%, 93.78%, 82.18%, 62.35% and 39.32% of full sibling pairs from unrelated individual pairs, when the likelihood ratio (LR) limits were set as 1, 10, 100, 1000 and 10,000 based on the simulated family samples, respectively. Additionally, Dongxiang group had the close genetic distances with populations in East Asia, especially showed the intimate genetic relationships with Chinese Han populations, which were concluded from the genetic affinities and genetic background analyses of Dongxiang group and 33 reference populations. In terms of the effectiveness of biogeographic origin inference, different artificial intelligent algorithms possessed different efficacies. Among them, the random forest (RF) and extreme gradient boosting (XGBoost) algorithm models could accurately predict the biogeographic origins of 99.7% and 90.59% of three and five continental individuals, respectively.

CONCLUSION

This 60-plex system had good performance for individual discrimination, kinship analysis and biogeographic origin prediction in Dongxiang group, which could be used as a powerful tool for case investigation.

Systematically exploring the performance of a self-developed Multi-InDel system in forensic identification, ancestry inference and genetic structure analysis of Chinese Manchu and Mongolian groups

The insertion/deletion (InDel) polymorphism has promising applications in forensic DNA analysis. However, the insufficient forensic efficiencies of the present InDel-based systems restrict their applications in parentage testing, due to the lower genetic polymorphism of the biallelic InDel locus and the limited number of InDel loci in a multiplex amplification system. Here, we introduced an in-house developed system which contained 41 polymorphic Multi-InDel markers (equivalent to 82 InDels in total), to serve as an efficient and reliable tool for different forensic applications in the Manchu and Mongolian groups. We demonstrated that the new system exhibited potential efficiencies for personal identification, parentage testing, two-person DNA mixture interpretation and ancestry inference of intercontinental populations. Meanwhile, we explored the genetic backgrounds of the Manchu and Mongolian groups by conducting a series of population genetic analyses. We showed that the Manchu and Mongolian groups shared closer genetic relationships with East Asian populations, especially Han Chinese populations in northern China. Moreover, more similar genetic compositions were detected between the Manchu group and the northern Han populations in this study, suggesting that the Manchu group had higher genetic affinities with northern Han populations than the Mongolian group. Overall. this study provided the necessary evidence that these Multi-InDel genetic markers could play an important role in forensic applications.

The effectiveness of various strategies to improve DNA analysis of formaldehyde-damaged tissues from embalmed cadavers for human identification purposes

Formalin-fixed tissues provide the medical and forensic communities with alternative and often last resort sources of DNA for identification or diagnostic purposes. The DNA in these samples can be highly degraded and chemically damaged, making downstream genotyping using short tandem repeats (STRs) challenging. Therefore, the use of alternative genetic markers, methods that pre-amplify the low amount of good quality DNA present, or methods that repair the damaged DNA template may provide more probative genetic information. This study investigated whether whole genome amplification (WGA) and DNA repair could improve STR typing of formaldehyde-damaged (FD) tissues from embalmed cadavers. Additionally, comparative genotyping success using bi-allelic markers, including INDELs and SNPs, was explored. Calculated random match probabilities (RMPs) using traditional STRs, INDEL markers, and two next generation sequencing (NGS) panels were compared across all samples. Overall, results showed that neither WGA nor DNA repair substantially improved STR success rates from formalin-fixed tissue samples. However, when DNA from FD samples was genotyped using INDEL and SNP-based panels, the RMP of each sample was markedly lower than the RMPs calculated from partial STR profiles. Therefore, the results of this study suggest that rather than attempting to improve the quantity and quality of severely damaged and degraded DNA prior to STR typing, a more productive approach may be to target smaller amplicons to provide more discriminatory DNA identifications. Furthermore, an NGS panel with less loci may yield better results when examining FD samples, due to more optimized chemistries that result in greater allelic balance and amplicon coverage.

Efficiency evaluation of common forensic genetic markers for parentage identification involving close relatives

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.

Forensic efficiency evaluation of a novel multiplex panel of InDels and STRs in the Guizhou Han population and its phylogenetic relationships with other reference populations

BACKGROUND

Insertion/deletion polymorphism (InDel), as the third genetic marker, has been given a lot of attention by forensic geneticists since it has the advantages of extensive distributions in the human genome, small amplicon, and low mutation rate. However, the extant InDel panels were only viewed as supplemental tools for kinship analyses. In addition, these panels were not conductive to mixture deconvolution because InDels in these panels mainly displayed two alleles.

AIMS

The purpose of this study is to investigate genetic distributions of a novel panel of InDels and STRs in the Guizhou Han population; assess the forensic application value of the panel; and conduct population genetic analyses of the Guizhou Han and other reference populations based on the overlapping loci.

SUBJECTS AND METHODS

The bloodstain samples of 209 Guizhou Han were gathered and genotyped by the novel panel. Allelic frequencies and forensic parameters of two miniSTRs and 59 InDels in the panel were estimated. In addition, we assessed phylogenetic relationships among the Guizhou Han and other reference populations by principal component analysis, D_A genetic distance, and neighbor-joining tree.

RESULTS

A total of 139 alleles of 61 loci could be observed in the Guizhou Han population. Polymorphic information content values of 59 InDels were greater than 0.3 in the Guizhou Han population. The cumulative power of discrimination and probability of exclusion of two miniSTRs and 59 InDels in the Guizhou Han population were 0.999999999999999999999999997984 and 0.9999986, respectively. Principal component analysis of 14 populations showed that the Guizhou Han population located closer to Hunan Han and Southern Han Chinese (CHS) populations. Similar results were also discerned from D_A genetic distances and the neighbor-joining tree.

CONCLUSION

To sum up, the novel panel could be employed for forensic personal identification and paternity testing in the Guizhou Han population as a promising independent tool. Besides, the principal component analysis and phylogenetic tree of the Guizhou Han and other compared populations revealed that the Guizhou Han population possesses close genetic affinities with Hunan Han, CHS, and Han Chinese in Beijing (CHB) populations.

Insight into forensic efficiency and genetic structure of the Guizhou Dong group via a 64-plex panel

Insertion/deletion polymorphisms (InDels) show great application values in forensic research because they own superiorities of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Whereas, InDels commonly display low genetic diversities in comparison to STRs. Therefore, they may provide limited genetic information in forensic kinship testing. Here, we evaluated forensic application efficiency of a novel multiplex amplification system including two STRs, 59 InDels, and three sex-determination loci in the Guizhou Dong group. In addition, we explored the genetic background of the Guizhou Dong group in comparison to other reported populations based on 59 InDels. We found that 59 InDels displayed relatively high genetic diversities in the Guizhou Dong group. Moreover, the cumulative forensic efficiency of two STRs and 59 InDels could meet the requirement of individual identification and paternity testing in the Guizhou Dong group. For these 59 InDels, we observed that some loci exhibited relatively high genetic differentiations among different continental populations, especially for African and Non-African populations, which could be viewed as candidate ancestry informative markers in the future. Genetic structure results indicated that the Dong group had close genetic relationships with East Asian and some Southern Chinese Han populations. To sum up, we stated that the 64-plex panel could be performed for forensic application of the Guizhou Dong group.

Forensic efficiencies of individual identification, kinship testing and ancestral inference in three Yunnan groups based on a self-developed multiple DIP panel

Deletion/insertion polymorphism (DIP), as a short insertion/deletion sequence polymorphic genetic marker, has attracted the attention of forensic genetic scientist due to its lack of stutter, short amplicon and abundant ancestral information. In this study, based on a self-developed 43 autosomal deletion/insertion polymorphism (A-DIP) loci panel which could meet the forensic application purposes of individual identification, kinship testing and ancestral inference to some extent, we evaluated the forensic efficiencies of the above three forensic objectives in Chinese Yi, Hani and Miao groups of Yunnan province. The cumulative match probability (CPM) and combined probability of exclusion (CPE) of these three groups were 1.11433E-18, 8.24299E-19, 4.21721E-18; 0.999610217, 0.999629285 and 0.999582084, respectively. Average 96.65% full sibling pairs could be identified from unrelated individual pairs (as likelihood ratios > 1) using this DIP panel, whereas the average false positive rate was 3.69% in three target Yunnan groups. With the biogeographical ancestor prediction models constructed by extreme gradient boosting (XGBoost) and support vector machine (SVM) algorithms, 0.8239 (95% CI 0.7984, 0.8474) of the unrelated individuals could be correctly divided according to the continental origins based on the 43 A-DIPs which were large frequency distribution differentiations among different continental populations. The present results of principal component analysis (PCA), multidimensional scaling (MDS), neighbor joining (NJ) and maximum likelihood (ML) phylogenetic trees and STRUCTURE analyses indicated that these three Yunnan groups had relatively close genetic distances with East Asian populations.

Performance evaluation of an in-house panel containing 59 autosomal InDels for forensic identification in Chinese Hui and Mongolian groups

In recent years, a novel multiplex system containing two mini-short tandem repeats, 59 autosomal InDels, two Y-chromosomal InDels, and the Amelogenin gene with all amplicons less than 200 bp has been constructed and validated by ourselves for forensic degration sample, and its forensic application efficiency has been studied in Chinese some populations. Herein, the population genetic polymorphisms of these loci were investigated in Chinese Hui (n = 249) and Mongolian (n = 222) ethnic groups using direct multiplex amplification and capillary electrophoresis platform. The forensic identification efficiencies of this self-developed system were further evaluated in these two groups. And the results showed that the values of the combined power of discrimination were 0.9999999999999999999999999999006 (Hui) and 0.999999999999999999999999999738 (Mongolian), respectively. Moreover, the combined power of exclusion values were 0.99999817 (Hui) and 0.99999779 (Mongolian). The 59 autosomal InDels used in this study exhibited high forensic identification efficiencies in 10 East Asian populations, which was also expected to be a new powerful tool for identifying degraded biological materials in East Asian populations.

Development of a multiplex panel with 31 multi-allelic InDels for forensic DNA typing

Insertion/Deletion (InDel) polymorphic genetic markers are abundant in human genomes. Diallelic InDel markers have been widely studied for forensic purposes, yet the low polymorphic information content limits their application and current InDel panels remain to be improved. In this study, multi-allelic InDels located out of low complexity sequence regions were selected in the datasets from East Asian populations, and a multiplex amplification system containing 31 multi-allelic InDel markers and the Amelogenin marker (FA-HID32plex) was constructed and optimized. The preliminary study on sensitivity, species specificity, inhibitor tolerance, mixture resolution, and the detection of degraded samples demonstrates that the FA-HID32plex is highly sensitive, specific, and robust for traces and degraded samples. The combined power of discrimination (CPD) of 31 multi-allelic InDel markers was 0.999 999 999 999 999 999 85, and the cumulative probability of exclusion (CPE) was 0.999 920 in a Chinese Han population, which indicates a high discrimination power. Altogether, the FA-HID32plex panel could provide reliable supplements or stand-alone information in individual identification and paternity testing, especially for challenging samples.

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019-2022

This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.

Development and forensic efficiency evaluations of a novel multiplex amplification panel of 17 Multi-InDel loci on the X chromosome

Multi-InDel, as the novel genetic markers, showed great potential in forensic research. Whereas, most scholars mainly focused on autosomal Multi-InDels, which might provide limited genetic information in some complex kinship cases. In this study, we selected 17 Multi-InDels on the X chromosome and developed a multiplex amplification panel based on the next-generation sequencing (NGS) technology. Genetic distributions of these 17 loci in Beijing Han, Chinese Southern Han, and the studied Guizhou Han populations revealed that most loci showed relatively high forensic application values in these Han populations. In addition, more allelic variations of some loci were observed in the Guizhou Han than those in Beijing Han and Southern Han populations. Pairwise FST values, multi-dimensional analysis, and phylogenetic tree of different continental populations showed that selected 17 loci generally could differentiate African, European, East Asian, and South Asian populations. To sum up, the developed panel in this study is not only viewed as the high-efficient supplementary tool for forensic individual identification and paternity analysis, but it is also beneficial for inferring biogeographical origins of different continental populations.

Applications of massively parallel sequencing in forensic genetics

Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.

Conventional Gel Electrophoresis-Resolvable Insertion/Deletion Markers for Individual Identification and Analysis of Population Genetics in Red-Crowned Cranes in Eastern Hokkaido, Japan

Red-crowned crane Grus japonensis is an endangered species in two separate populations: the mainland population in the Eurasian continent and the island population in eastern Hokkaido, Japan. We found 11 insertion/deletion (InDel) markers in the genome of the red-crowned crane and designed primer sets across these InDels that can be analyzed with conventional agarose gel electrophoresis. Sixty-six samples of whole blood and skeletal muscle obtained from red-crowned cranes, including 12 families in eastern Hokkaido from 1994 to 2021, showed different patterns in gel images of 11 InDel PCR reactions except for two pairs. The combined non-exclusion probability of the 11 markers indicates that individuals can be determined with a probability of 99.9%. In 39 non-relative chicks, the expected heterozygosity (He) was 0.316, suggesting low genetic diversity. This might not be caused by high levels of inbreeding since the average FIS was not significantly different from zero (0.095, p = 0.075). The results suggest that the 11 InDel primer sets can be used for fairly accurate individual identification as well as genetic population analyses in red-crowned cranes in the island population.

Insights into AIM-InDel diversities in Yunnan Miao and Hani ethnic groups of China for forensic and population genetic purposes

BACKGROUND

Ancestry informative markers are regarded as useful tools for inferring the ancestral information of an individual, which have been widely used in the criminal investigations and population genetic studies. Previously, a multiplex amplification panel containing 39 AIM-InDel loci was constructed. This study aims to investigate the genetic polymorphisms of these 39 AIM-InDel loci in Yunnan Hani and Miao ethnic groups, and to uncover their genetic affinities with reference populations based on the AIM-InDel markers.

MATERIALS AND METHODS

In this research, 39 AIM-InDel profiles of 203 unrelated Miao individuals and 203 unrelated Hani individuals in Yunnan province of China were acquired. Additionally, we evaluated the genetic polymorphisms of 39 InDel loci in Yunnan Miao and Hani groups. Moreover, the genetic relationships among Yunnan Miao, Hani and reference populations were also clarified based on Nei's genetic distances, pairwise fixation indexes, principal component analyses, phylogenetic analyses, and STRUCTURE analyses.

RESULTS

Genetic diversity analyses demonstrated that these InDel loci showed varying degrees of genetic polymorphisms, and could be utilized in forensic identifications in Yunnan Miao and Hani groups. The results of principal component analyses, phylogenetic analyses and Structure analyses revealed that Yunnan Miao and Hani groups had closer genetic relationships with East Asian populations, especially with the populations from Southern China. This research enriched the genetic data of Chinese ethnic minority, and provided ancestral information of Yunnan Miao and Hani groups from the perspective of population genetics.

Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set

The MPS technology has expanded the potential applications of DNA markers and increased the discrimination power of the targeted loci by taking variations in their flanking regions into consideration. Here, a collection of nuclear and extranuclear DNA markers (totally six kinds of nuclear genetic markers and mtDNA hypervariable region variations) were comprehensively and systematically assessed for polymorphism detections, further employed to dissect the population backgrounds in the Yugu ethnic group from Gansu province (Yugu) and Han population from the Inner Mongolia Autonomous Region (NMH) of China. The elevated efficiencies of the marker set in separating full sibling and challenging half sibling determination cases in parentage tests (iiSNPs), as well as predicting ancestry origins of unknown individuals from at least four continental populations (aiSNPs) and providing informative characteristic-related clues for Chinese populations (piSNPs) are highlighted in the present study. To sum up, different sets of DNA markers revealed sufficient effciencies to serve as promising tools in forensic applications. Genetic insights from the perspectives of autosomal DNA, Y chromosomal DNA, and mtDNA variations yielded that the Yugu ethnic group was genetically close related to the Han populations of the northern region. But we admit that more reference populations (like Mongolian, Tibetan, Hui, and Tu) should be incorporated to gain a refined genetic background landscape of the Yugu group in future studies.

Genetic diversity analysis of forty-three insertion/deletion loci for forensic individual identification in Han Chinese from Beijing based on a novel panel

Due to the virtues of no stutter peaks, low rates of mutation, and short amplicon sizes, insertion/deletion (InDel) polymorphism is an indispensable tool for analyzing degraded DNA samples from crime scenes for human identifications (Wang et al., 2021). Herein, a self-developed panel of 43 InDel loci constructed previously by our group was utilized to evaluate the genetic diversities and explore the genetic background of the Han Chinese from Beijing (HCB) including 301 random healthy individuals. The lengths of amplicons at 43 InDel loci in this panel ranged from 87 to 199 bp, which indicated that the panel could be used as an effective tool to utilize highly degraded DNA samples for human identity testing. The loci in this panel were validated and performed well for forensic degraded DNA samples (Jin et al., 2021). The combined discrimination power (PD) and combined probability of exclusion (PE) values in this panel indicated that the 43 InDel loci could be used as the candidate markers in personal identification and parentage testing of HCB. In addition, population genetic relationships between the HCB and 26 reference populations from five continents based on 19 overlapped InDel loci were displayed by constructing a phylogenetic tree, principal component analysis (PCA), and population genetic structure analysis. The results illustrated that the HCB had closer genetic relationships with the Han populations from Chinese different regions.