Autosomal InDel Research Articles

Dissecting the genetic admixture and forensic signatures of ethnolinguistically diverse Chinese populations via a 114-plex NGS InDel panel

Comprehensive characterizations of genetic diversity and demographic models of ethnolinguistically diverse Chinese populations are essential for elucidating their forensic characteristics and evolutionary past. We developed a 114-plex NGS InDel panel to genotype 114 genome-wide markers and investigated the genetic structures of Zhuang, Hui, Miao, Li, Tibetan, Yi, and Mongolian populations, encompassing five language families. This panel demonstrated robust performance, with exceptional potential for forensic individual identification and paternity testing, evidenced by the combined power of discrimination for 77 autosomal InDels (ranged from 1-3.6400 × 10–30 to 1-3.5713 × 10–32) and the combined power of exclusion (ranged from 1-2.1863 × 10–6 to 1-2.1261 × 10–7). The cumulative mean exclusion chance for 32 X-chromosomal InDels varied between 0.99996 and 0.99999 for trios and 0.99760 to 0.99898 for duos. We also analyzed genetic similarities and differences between these populations and 27 global populations, revealing distinct clusters among African, South Asian, East Asian, and European groups, with a close genetic affinity to East Asians. Notably, we identified geography-related genetic substructures: Inner Mongolia Mongolians and Gansu Huis formed a northern branch, Tibetans and Yis from Sichuan constituted a highland branch, and Guangxi Zhuangs exhibited close ties with Hainan Lis and Guangxi Miaos in the southern branch. Additionally, many InDels proved to be ancestry-informative markers for biogeographic ancestry inference. Collectively, these findings underscore the utility of the 114-plex NGS InDel panel as a complementary tool for forensic investigations and as a source of insights into the genetic architecture of ethnolinguistically distinct Chinese populations.

Insertion/deletion polymorphism for genetic background and forensic performance exploration of the Sui group from Guizhou

Insertion/deletion polymorphisms (InDels) as ideal genetic markers for forensic genetics are appreciated by scholars both nationally and internationally because they integrated the favorable features of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Nevertheless, with the limited identification efficiency of InDels, the multiplex amplification systems of InDels might just be applied as the supplementary methods in paternity testing with respect to commonly used STRs.In the current research, we successfully genotyped 105 unrelated individuals from the Guizhou Sui population based on a six-color fluorescence multiplex panel that could simultaneously detect 64 genetic markers (59 autosomal InDels, two autosomal miniSTRs and three Y chromosomal genetic markers). In addition, frequency distributions and forensic statistical parameters of these loci in the Sui group were assessed using the STRAF software. Phylogenetic relationships among the Sui group and other reference populations were dissected by two methods (principal component analysis and phylogenetic trees) based on 59 InDels. The combined discrimination power and probability of exclusion values of 61 autosomal genetic markers in the Sui group were nearly equal to 1–1.90063 × 10−27 and 0.999998272, respectively. Furthermore, we observed that the Sui group from Guizhou had closer genetic affinities with East Asian populations with respect to other continental populations.In summary, we stated that the multiplex amplification system might be utilized as a prospective independent tool for human individual identification and parentage testing in the Sui group residing in Guizhou.

Development and validation of a custom panel including 114 InDels using massively parallel sequencing for forensic application.

Insertion/deletion polymorphisms (InDels) have particular characteristics, such as a relatively low mutation rate, small amplicon size, and no stutter artifacts when genotyped via the capillary electrophoresisplatform. It would be an important complementary tool for individual identification and certain kinship analyses. At present, massively parallel sequencing (MPS) has shown excellent application value in forensic studies. Therefore, in this study, we developed a custom MPS InDel panel that contains 114 InDels [77 autosomal InDels (A-InDels), 32 X-chromosomal InDels (X-InDels), and 5 Y-chromosomal InDels) based on previous studies. To assess this panel's performance, several validation experiments were performed, including sensitivity, inhibitor, degraded DNA testing, species specificity, concordance, repeatability, case-type samples, and population studies. The results showed that the lowest DNA input was 0.25ng. All genotypes were obtained in the presence of 80ng/µL humic acid, 2000µmol/L calcium, 3000µmol/L EDTA and indigo. In degraded DNA testing, 90% of loci could be detected for 16-day-old formalin-fixed hearts. In addition, this panel has good species specificity. The values of combined power of discrimination and the combined power of exclusion for 77 A-InDels were 1-3.9951×10-32 and 1-4.2956×10-7 , respectively. The combined mean exclusion chance for 32 X-InDels was 0.99999 in trios and 0.99904 in duos. The validation results indicate that this newly developed MPS multiplex system is a robust tool for forensic applications.

Genetic polymorphisms and population genetic analyses of 57 autosomal InDel loci in Hubei Tujia group.

Introduction: The Tujia is the eighth most populous population in China, but its genetic structure has not been fully studied. Methods: In this study, we utilized 57 autosomal Insertion/deletion (InDel) loci to evaluate the genetic polymorphisms and efficiency of forensic applications in the Chinese Hubei Tujia group, and analyzed the genetic structure variances among the studied group and other 26 different reference populations from five continents in 1000 Genomes Project (1KG). Results: The results showed that 57 InDels have no significant deviations from Hardy-Weinberg equilibrium and linkage equilibrium. The combined power of discrimination (CPD) and the combined probability of exclusion (CPE) values for 57 InDels were 0.99999999999999999999999699822 and 0.999975177214539 in the Hubei Tujia group, respectively. In addition, the results of genetic structure analyses indicated that the Hubei Tujia group has close genetic relationships with the Chinese Han population and other East Asian populations. Discussion: These 57 autosomal InDels can be used as reliable tools for forensic individual identification and paternity testing, and are more suitable for East Asian populations. Furthermore, three InDels (rs72085595, rs145941537, and rs34529639) are promising for inferring ancestral information.

Comprehensive Understanding the Forensic Systematic Effectiveness in Chinese Yunnan Hani Group and Intercontinental Population Architecture Differentiation Analyses via a Novel Set of Autosomal InDel Markers.

Chinese Yunnan Hani group is an East Asian ethnic group mainly distributed in China, Thailand, Laos, Vietnam, and Burma. The genetic makeup of Chinese Yunnan Hani ethnic group remains to be further investigated. The insertion/deletion (InDel) polymorphism genetic markers are highlighted by their merits such as shorter amplified fragments, lower mutation rates, and are considered effective tools for population genetic investigations. The 221 individuals of Chinese Yunnan Hani group were enrolled to obtain the genetic data and polymorphic profiles of 57 autosomal InDels through multiplex amplification and genotyping. Population genetic analyses were performed between Chinese Yunnan Hani group and 30 global reference populations. The forensic parameters, especially cumulative power of discrimination and combined probability of exclusion values, which were 0.9999999999999999999999968 and 0.999958, separately, illustrated that this novel InDel multiplex amplification system could be utilized as a powerful tool for personal identification and paternity testing in Chinese Yunnan Hani group. The results of population genetic analyses indicated that Chinese Yunnan Hani group showed relatively smaller genetic distances and similar genetic structures with the reference East Asian populations. The genetic polymorphisms and results of intercontinental population architecture differentiation analyses demonstrated the high efficiency of this novel InDel multiplex amplification system. The genomic data and findings of this research will contribute to the ongoing genetic exploration of Chinese Yunnan Hani group and increase our insights into the genetic architecture of worldwide populations.

Analysis of Genetic Polymorphism and Population Genetic Structure of 57 Autosomal InDel Loci in Beichuan Qiang Population.

To investigate the genetic information of 57 autosomal InDel loci (A-InDels) included in AGCU InDel 60 fluorescence detection kit in the Beichuan Qiang population of Sichuan Province and evaluate its application value in forensic medicine. A total of 200 unrelated healthy individuals from Beichuan Qiang population of Sichuan Province were typing detected by AGCU InDel 60 fluorescence detection kit. Allele frequencies and population genetic parameters of the 57 A-InDels were statistically analyzed and compared with the available data of 26 populations. After Bonferroni correction, there was no linkage disequilibrium between the 57 A-InDels, and all loci were in Hardy-Weinberg equilibrium. Except for rs66595817 and rs72085595, the minor allele frequencies of 55 A-InDels were above 0.3. PIC ranged from 0.298 3 to 0.375 0, CDP was 1-2.974 8×10-24, CPEduo was 0.999 062 660, and CPEtrio was 0.999 999 999. The calculation of the genetic distance showed that Beichuan Qiang population had the closest genetic distances with Beijing Han and South China Han populations, but far away from African populations. The 57 A-InDels in AGCU InDel 60 fluorescence detection kit have a good genetic polymorphism in Beichuan Qiang population of Sichuan Province, which can be used as effective supplemental for individual identification and paternity identification in forensic medicine.

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 and validation of a forensic multiplex InDel assay: The AGCU InDel 60 kit.

Marker sets based on insertion/deletion polymorphisms (InDels) combine the characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms and have served as effective complementary or stand-alone systems for human identification in forensics. We developed a novel multiplex amplification detection system, designated the AGCU InDel 60 kit, containing 57 autosomal InDels, 2 Y-chromosomal InDels, and the amelogenin locus and validated the kit in a series of studies, which included tests of the PCR conditions; tests for sensitivity, species specificity, reproducibility, stability, and mock case samples; degradation studies; and a population study. The results indicated that the AGCU InDel 60 kit was accurate, specific, reproducible, stable, and robust. Complete DNA profiles were obtained even with 125pg of human DNA. In tests of artificially degraded samples, we found that the number of alleles detected by the validated kit was considerably greater than that detected by the STR-based AGCU 21+1 kit, even as the degree of degradation increased. Additionally, 564 unrelated individuals from three Han groups were investigated using this novel system, and the values of combined power of discrimination and combined power of exclusion were not less than 1-4.9026 × 10-24 and 1-3.1123 × 10-5 , respectively. Thus, the results indicated that the novel kit was more powerful than the previous version of the InDel kit (the AGCU InDel 50 kit). Our results suggest that the AGCU InDel 60 kit can serve as an efficient tool for human forensics and a supplementary kit for population genetics research.

Forensic efficacy evaluation and genetic structure exploration of the Yunnan Miao group by a multiplex InDel panel

The aim of the study was to better understand the genetic characteristics of the Miao group in China. Herein, genetic characteristics and forensic application values of 57 autosomal insertion-deletion (InDel) loci were investigated in 210 unrelated healthy individuals from the Chinese Yunnan Miao (YM) group. Meanwhile, the genetic differences in these InDels were compared among the YM group and 26 reference populations. The results of forensic statistical analyses showed that all 57 autosomal InDels were in accordance with the Hardy-Weinberg and linkage equilibria of pairwise loci in the Chinese YM group. Moreover, the combined probability of discrimination and probability of exclusion in the YM group were 0.9999999999999999999999801 and 0.999928, respectively, which indicated that the multiplex amplification including 57 autosomal InDels was suitable for forensic individual identification and paternity testing in the Chinese YM group. In addition, the results of allelic frequency distribution differential analyses, principal component analyses, phylogenetic tree reconstruction, and genetic structure analyses between the Chinese YM group and 26 reference populations revealed that the genetic similarities between the YM group and East Asian populations were more than that between the YM group and other geographical populations. This 57 autosomal InDels system can also effectively distinguish East Asian, European, and African populations.

Forensic features and genetic structure revealed by 47 individual identification InDels in the Shaanxi Han population

Insertion/deletion (InDel) polymorphism genetic marker is a powerful and prospective tool for human identification and population genetic studies. Considering that the genetic polymorphisms and ethnic background of the Shaanxi Han population have not been fully explored to this day, herein, the novel developed AGCU InDel 50 kit which included 47 autosomal InDels was applied in the 556 unrelated healthy Han individuals from Shaanxi province for the first time. There were no significant deviations from Hardy–Weinberg equilibrium and linkage equilibrium at the 47 InDels after Bonferroni correction. In the Shaanxi Han population, the values of combined discrimination power and cumulative exclusion probability for the 47 InDels were 0.999999999999999999891 and 0.99966, respectively. Furthermore, the interpopulation comparisons and population genetic structure analyses based on the 47 InDels were performed among the Shaanxi Han population and 43 reference populations, and the results showed that the Shaanxi Han population exhibited similar genetic structure and closer genetic affinities with the East Asian populations.

Assessing Autosomal InDel Loci With Multiple Insertions or Deletions of Random DNA Sequences in Human Genome.

Multiple mutational events of insertion/deletion occurring at or around InDel sites could form multi-allelic InDels and multi-InDels (abbreviated as MM-InDels), while InDels with random DNA sequences could imply a unique mutation event at these loci. In this study, preliminary investigation of MM-InDels with random sequences was conducted using high-throughput phased data from the 1000 Genomes Project. A total of 3,599 multi-allelic InDels and 6,375 multi-InDels were filtered with multiple alleles. A vast majority of the obtained MM-InDels (85.59%) presented 3 alleles, which implies that only one secondary insertion or deletion mutation event occurred at these loci. The more frequent presence of two adjacent InDel loci was observed within 20 bp. MM-InDels with random sequences presented an uneven distribution across the genome and showed a correlation with InDels, SNPs, recombination rate, and GC content. The average allelic frequencies and prevalence of multi-allelic InDels and multi-InDels presented similar distribution patterns in different populations. Altogether, MM-InDels with random sequences can provide useful information for population resolution.

Systematic Evaluation of a Novel 6-dye Direct and Multiplex PCR-CE-Based InDel Typing System for Forensic Purposes.

Insertion/deletion (InDel) polymorphisms, combined desirable characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), are considerable potential in the fields of forensic practices and population genetics. However, most commercial InDel kits designed based on non-Asians limited extensive forensic applications in East Asian (EAS) populations. Recently, a novel 6-dye direct and multiplex PCR-CE-based typing system was designed on the basis of genome-wide EAS population data, which could amplify 60 molecular genetic markers, consisting of 57 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels), and Amelogenin in a single PCR reaction and detect by capillary electrophoresis, simultaneously. In the present study, the DNA profiles of 279 unrelated individuals from the Hainan Li group were generated by the novel typing system. In addition, we collected two A-InDel sets to evaluate the forensic performances of the novel system in the 1,000 Genomes Project (1KG) populations and Hainan Li group. For the Universal A-InDel set (UAIS, containing 44 A-InDels) the cumulative power of discrimination (CPD) ranged from 1–1.03 × 10–14 to 1–1.27 × 10–18, and the cumulative power of exclusion (CPE) varied from 0.993634 to 0.999908 in the 1KG populations. For the East Asia-based A-InDel set (EAIS, containing 57 A-InDels) the CPD spanned from 1–1.32 × 10–23 to 1–9.42 × 10–24, and the CPE ranged from 0.999965 to 0.999997. In the Hainan Li group, the average heterozygote (He) was 0.4666 (0.2366–0.5448), and the polymorphism information content (PIC) spanned from 0.2116 to 0.3750 (mean PIC: 0.3563 ± 0.0291). In total, the CPD and CPE of 57 A-InDels were 1–1.32 × 10–23 and 0.999965, respectively. Consequently, the novel 6-dye direct and multiplex PCR-CE-based typing system could be considered as the reliable and robust tool for human identification and intercontinental population differentiation, and supplied additional information for kinship analysis in the 1KG populations and Hainan Li group.

Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs

Sherpa people, one of the high-altitude hypoxic adaptive populations, mainly reside in Nepal and the southern Tibet Autonomous Region. The genetic origin and detailed evolutionary profiles of Sherpas remain to be further explored and comprehensively characterized. Here we analyzed the newly-generated InDel genotype data from 628 Dingjie Sherpas by merging with 4222 worldwide InDel profiles and collected genome-wide SNP data (approximately 600K SNPs) from 1612 individuals in 191 modern and ancient populations to explore and reconstruct the fine-scale genetic structure of Sherpas and their relationships with nearby modern and ancient East Asians based on the shared alleles and haplotypes. The forensic parameters of 57 autosomal InDels (A-InDels) included in our used new-generation InDel amplification system showed that this focused InDel panel is informative and polymorphic in Dingjie Sherpas, suggesting that it can be used as the supplementary tool for forensic personal identification and parentage testing in Dingjie Sherpas. Descriptive findings from the PCA, ADMIXTURE, and TreeMix-based phylogenies suggested that studied Nepal Sherpas showed excess allele sharing with neighboring Tibeto-Burman Tibetans. Furthermore, patterns of allele sharing in f-statistics demonstrated that Nepal Sherpas had a different evolutionary history compared with their neighbors from Nepal (Newar and Gurung) but showed genetic similarity with 2700-year-old Chokhopani and modern Tibet Tibetans. QpAdm/qpGraph-based admixture sources and models further showed that Sherpas, core Tibetans, and Chokhopani formed one clade, which could be fitted as having the main ancestry from late Neolithic Qijia millet farmers and other deep ancestries from early Asians. Chromosome painting profiles and shared IBD fragments inferred from fineSTRUCTURE and ChromoPainter not only confirmed the abovementioned genomic affinity patterns but also revealed the fine-scale genetic microstructures among Sino-Tibetan speakers. Finally, natural-selection signals revealed via iHS, nSL and iHH12 showed natural selection signatures associated with disease susceptibility in Sherpas. Generally, we provided the comprehensive landscape of admixture and evolutionary history of Sherpa people based on the shared alleles and haplotypes from the InDel-based genotype data and high-density genome-wide SNP data. The more detailed genetic landscape of Sherpa people should be further confirmed and characterized via ancient genomes or single-molecule real-time sequencing technology.

Developmental validation of the novel six-dye GoldeneyeTM DNA ID System 35InDel kit for forensic application

Insertion/deletion polymorphisms (InDels) have been treated as a prospective and helpful genetic marker in the fields of forensic human identification, anthropology and population genetics for the past few years. In this study, we developed a six-dye multiplex typing system consisting of 34 autosomal InDels and Amelogenin for forensic application. The contained InDels were specifically selected for Chinese population with the MAF ≥ 0.25 in East Asia, which do not overlap with the markers of Investigator® DIPplex kit. The typing system was named as GoldeneyeTM DNA ID System 35InDel Kit, and a series of developmental validation studies including repeatability/reproducibility, concordance, accuracy, sensitivity, stability, species specificity and population genetics were conducted on this kit. We confirmed that the 35InDel kit is precise, sensitive, species specific and robust for forensic practice. Moreover, the 35InDel kit is capable of typing DNA extracted from forensic routine case-type samples as well as degraded samples and mixture samples. All markers are proved to be highly polymorphic with an average observed heterozygosity (He) of 0.4582. The combined power of discrimination (CPD) is 0.999 999 999 999 978 and the combined power of exclusion in duos (CPED) and trios (CPET) are 0.978 837 and 0.999573, respectively, which are higher than those of the Investigator® DIPplex kit. Thus, the GoldeneyeTM DNA ID System 35InDel kit is suitable for forensic human identification and could serve as a supplementary typing system for paternity testing. Supplemental data for this article is available online at https://doi.org/10.1080/20961790.2021.1945723 .

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.

Revisiting the genetic background and phylogenetic structure of five Sino-Tibetan-speaking populations: insights from autosomal InDels.

The Tibetan-Yi Corridor, located on the eastern edge of the Tibetan Plateau, is the main route of the people of the plateau. Human settlement and diffusion along the corridor have played a pivotal role in shaping the genetic architecture of Sino-Tibetan-speaking (STs) populations in China. In this study, five STs groups (Chengdu Tibetan, Chengdu Han, Muli Tibetan, Lugu Lake Mosuo and Xichang Yi) settling in the Tibetan-Yi Corridor were genotyped via AGCU InDel 50 kit on the capillary electrophoresis platform to decrypt the genetic landscape and phylogenetic relationship of STs populations and investigate the forensic characteristics. Allele frequency distributions of all autosomal insertion/deletion polymorphisms (InDels) in studied groups comply with Hardy-Weinberg equilibrium. The combined power of discrimination values are 0.9999999999999999998, 0.9999999999999999995, 0.9999999999999999999, 0.999999999999999993 and 0.99999999999999999994, respectively, and all the combined probability of exclusion values exceed 0.9990. Forensically relevant statistics implied that these InDels could be used for individual identification and as a promising alternative to STR profiling in paternity testing. Typical population comparisons showed strikingly high homogeneity among studied STs people, indicating complicated genetic admixture among populations in the Tibetan-Yi Corridor. The STs groups in the Tibetan-Yi Corridor keep close genetic affinity with geographically or linguistically close populations, and the genetic components of investigated populations arose from a mixture of multiple ancestral gene pools (resulting from the admixture from the ancestral Highland Tibetans and ancestral Lowland indigenous populations).

Forensic features and genetic background exploration of a new 47-autosomal InDel panel in five representative Han populations residing in Northern China.

BackgroundInsertion/deletion (InDel) analysis plays an indispensable role in human identification, population genetics, and biogeographic research. Profiles of individuals in forensic applications worldwide based on a set of autosomal InDel loci (A‐InDels) in human genomes have been widely used over the past few years.MethodsThe new AGCU InDel 50 Kit contains 47 well‐chosen A‐InDels, ensuring high discriminatory power, and the 2 Y chromosome InDel loci (Y‐InDels) are used for sex determination in case of allele dropout at Amelogenin. In this study, five Northern Han populations residing in different geographic areas of China were recruited and genotyped using the assay.ResultsAfter Bonferroni correction, all 47 A‐InDels were in accordance with the lack of significant departures of Hardy–Weinberg equilibrium in all loci and investigated groups. The combined probability of discrimination and the probability of exclusion in the Han population range from 1–3.2240 × 10–19 to 1–1.3030 × 10–19 and 0.9997, respectively. A comprehensive population genetic relationship investigation between Han Chinese and 26 worldwide populations based on allele frequency correlation was carried out. Our results revealed no significant genetic differentiation in Chinese Han groups. Hierarchical clustering, phylogenetic relationship reconstructions, multidimensional scaling, principal component analysis, and structure analysis were performed, and the results indicated that, genetically, Han populations are closely related to East Asians.ConclusionOverall, this novel 47 A‐InDel assay is a valuable tool that could potentially be used for forensic identification and parentage tests.

Forensic features, genetic diversity and structure analysis of three Chinese populations using 47 autosomal InDels

Insertion/deletion polymorphisms (InDels), which combine the desirable features of both short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs), have become widely used genetic markers for forensic investigations, anthropology and population genetics. The AGCU InDel 50 kit is a newly developed panel that contains 47 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels) and Amelogenin and is designed to provide a higher discriminatory power in Chinese populations compared with the Qiagen DIPplex kit. In this study, 542 unrelated individuals were first genotyped to evaluate the forensic efficiency of this novel panel in three Chinese ethnicities (Hainan Han, Hainan Li and Zunyi Gelao groups). Additionally, genetic relationships among the three investigated populations (geographically close but linguistically different populations: Han and Li; geographically diverse but from the same language family: Li and Gelao) and 31 worldwide populations were analyzed using pairwise genetic distances, multidimensional scaling (MDS), phylogenetic tree, principal component analysis (PCA) and STRUCTURE. The combined powers of discrimination (CPD) for the Han, Li and Gelao groups were 0.999999999999999999635, 0.999999999999999997668 and 0.999999999999999999840, respectively, and the combined powers of exclusion (CPE) were 0.999715, 0.999283 and 0.999575, respectively. The genetic relationship between the Hainan Han and Zunyi Gelao groups was relatively closer than that between the Hainan Li and Zunyi Gelao groups, demonstrating that there was little gene communication between Li and Han living on Hainan Island as well as between Li and Gelao in the Tai-Kadai language family. The aforementioned results suggest that the AGCU InDel 50 kit is an effective tool that is appropriate for personal identification and population genetics.

Genetic diversity and phylogenetic analysis of Chinese Han and Li ethnic populations from Hainan Island by 30 autosomal insertion/deletion polymorphisms

With the characteristics of low mutation rate, length variation and short amplicon size, insertion/deletion polymorphisms (InDels) have the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Herein, people of two ethnicities from Hainan Island were genotyped for the first time using the Investigator DIPplex kit. We investigated the forensic parameters of the 30 InDels and the phylogenetic relationships among different populations. The accumulated powers of discrimination and powers of exclusion were 0.999 999 999 9646 and 0.9897 in the Hainan Han population and 0.999 999 999 9292 and 0.9861 in the Hainan Li population, respectively. Additionally, population comparisons among geographically, ethnically and linguistically diverse populations via cluster heatmap, multidimensional scaling, principal component analysis, phylogenetic tree and STRUCTURE analyses demonstrated that the Hainan Han population had genetic similarities to the other Han, She and Tujia populations, while the Hainan Li population had close genetic relationships to the Zhuang and Miao groups; both populations had a high degree of genetic differentiation from most Turkic-speaking populations. Aforementioned results suggested that the 30 autosomal InDels are highly polymorphic and informative, which are suitable for human identification and population genetics.KEYPOINTSFour hundred and forty-five Chinese individuals from two ethnicities (Hainan Han and Hainan Li) were firstly analyzed by 30 autosomal InDels included in the Investigator DIPplex panel.Forensic parameters of the 30 InDels in the two populations showed high polymorphism and universality for human identification purposes.The Investigator DIPplex panel had a certain capacity of differentiating intercontinental populations and different language populations.

Forensic characteristics of Tibeto-Burman-speaking Tibetans revealed by 50 InDels

Insertion/deletion polymorphism (InDel) profiling has become a promising tool in forensic investigations and biogeographical ancestry inferences. Recently, the AGCU has designed an advanced InDel assay that allows co-amplification and fluorescent detection of the 47 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels) and Amelogenin. In this study, 103 Tibeto-Burman-speaking Tibetan individuals were genotyped to investigate the effectiveness of this novel InDel kit. No significant deviation from Hardy-Weinberg equilibrium was observed at the 47 A-InDels after applying the Bonferroni correction. The allelic frequencies of insertion alleles at the 47 A-InDels ranged from 0.2087 to 0.7767, and the mean observed heterozygosity varied from 0.3010 to 0.5922. The combined power of discrimination reached 1–4.0688E-19, and the combined probability of exclusion was 0.9997. Overall, the observed results demonstrate that this novel InDel assay can be used as an efficient tool for individual identification and forensic paternity testing.