Forensic features and genetic structure of 23 autosomal STRs in Artux Turkic-speaking population residing in southwestern Xinjiang Uyghur Autonomous Region

Autosomal short tandem repeats (STRs) are viewed as the gold standard in forensic individual identification and parentage testing. The Huaxia Platinum System contains 23 autosomal markers along with rs2032678 (Yindel) and amelogenin. Here, we genotyped 23-STRs in the southwestern Xinjiang Uyghur residing in the Artux Region and assessed the allele frequency and forensic statistical parameters. All investigated STRs are in conformity with the Hardy-Weinberg equilibrium with an effective combined power of discrimination (0.99999999999999999999999999992) and cumulative probability of exclusion (0.9999999997) in the Artux Uyghur population. Population comparisons among 54 worldwide populations via PCA and MDS indicate that the Artux Uyghur population has a close genetic relationship with geographically distinct Uyghurs and Kazakh groups than other East Asians or Eurasians. Genetic ancestry component dissection among 2198 individuals from Sinitic, Turkic, and Tibeto-Burman language groups further demonstrates the genetic homogeneity within the Turkic language family and apparent genetic heterogeneity among other language groups.

     

Forensic performance of 30 InDels included in the Investigator DIPplex system in Miao population and comprehensive genetic relationship in China

Binary markers of insertion and deletion (InDel) play an important role in forensic personal identification, parentage testing, and individual ancestry inference. We first genotyped 30 InDels included in the Investigator DIPplex in 403 unrelated healthy Zunyi Miao people and analyzed the genetic polymorphisms, as well as explored the genetic relationship between Miao and 32 Chinese reference populations. No departures from the HWE were observed. The combined power of discrimination and the combined probability of exclusion were 0.99999999998 and 0.9884, respectively. Forensic parameters demonstrated that 30 markers are polymorphic and informative in the Zunyi Miao population and can be used as a tool for forensic personal identification and parentage testing. Allele frequency divergence analysis found that 12 out of 30 displaying high allele frequency difference between Turkic-speaking populations and other Chinese populations can be used as candidates of ancestry informative markers for ancestry inference of sub-population in East Asia. Population genetic parameters in the comprehensive population comparison among 33 Chinese populations indicated that our studied Hmong-Mien-speaking Miao has a close genetic relationship with geographically adjacent Enshi Tujia and genetically differentiate from Turkic-speaking populations.

     

Forensic genetic analyses in isolated populations with examples of central European Valachs and Roma

Isolated populations present a constant threat to the correctness of forensic genetic casework. In this review article we present several examples of how analyzing samples from isolated populations can bias the results of the forensic statistics and analyses. We select our examples from isolated populations from central and southeastern Europe, namely the Valachs and the European Roma. We also provide the reader with general strategies and principles to improve the laboratory practice (best practice) and reporting of samples from supposedly isolated populations. These include reporting the precise population data used for computing the forensic statistics, using the appropriate θ correction factor for calculating allele frequencies, typing ancestry informative markers in samples of unknown or uncertain ethnicity and establishing ethnic-specific forensic databases.     

Ancestry informative markers: Inference of ancestry in aged bone samples using an autosomal AIM-Indel multiplex

Ancestry informative markers (AIMs) can be useful to infer ancestry proportions of the donors of forensic evidence. The probability of success typing degraded samples, such as human skeletal remains, is strongly influenced by the DNA fragment lengths that can be amplified and the presence of PCR inhibitors. Several AIM panels are available amongst the many forensic marker sets developed for genotyping degraded DNA. Using a 46 AIM Insertion Deletion (Indel) multiplex, we analyzed human skeletal remains of post mortem time ranging from 35 to 60 years from four different continents (Sub-Saharan Africa, South and Central America, East Asia and Europe) to ascertain the genetic ancestry components. Samples belonging to non-admixed individuals could be assigned to their corresponding continental group. For the remaining samples with admixed ancestry, it was possible to estimate the proportion of co-ancestry components from the four reference population groups. The 46 AIM Indel set was informative enough to efficiently estimate the proportion of ancestry even in samples yielding partial profiles, a frequent occurrence when analyzing inhibited and/or degraded DNA extracts.     

Phylogenic analysis and forensic genetic characterization of Guizhou Miao tribes from 58 microareas via autosomal STR

Genetic polymorphism of 17 autosomal short tandem repeat (STR) loci, included in the PowerPlex®18D amplification kit, were analyzed in Miao tribes from 58 different sampling microareas (N = 5255) of Guizhou as well as two cities (N = 151) of Hunan, China. Allele frequencies and forensic efficiency parameters were calculated. Moreover, comprehensive population genetic comparisons among 91 nationwide populations and 174 Asian populations were conducted based on raw genotype data and allele frequency data, respectively. Our results of forensic efficiency parameters showed that the panel was a robust tool in forensic individual identification and paternity cases for this population. Genetic affinities were observed among most of the Miao tribes revealed by multidimensional scaling plot, principal component analysis, and neighboring-joining tree. The genetic distance between Miao tribes and Han nationalities were varies by different geographical positions. Some of the Miao tribes were genetically closer to the Hmong-Mien populations living in southeastern contiguous regions and even the Indochina. The result coincided with the migration or reverse migration routes for Miao nationality in modern history. This study of the Miao tribes from plenty of microareas in Guizhou would be useful in reconstructing the population history and establishing a more comprehensive forensic reference database.     

Population genetics of 30 insertion/deletion polymorphisms in Han Chinese population from Zhejiang Province

Insertion/deletion (InDels) markers can serve as a useful supporting tool to short tandem repeat (STR) typing systems for human identification. The Qiagen DIPplex Investigator kit, which contains 30 biallelic autosomal InDels and amelogenin, has been developed for forensic use. To estimate the genetic diversity of the 30 markers in Han Chinese individuals living in Zhejiang and to further evaluate their applicability in forensic science, 246 unrelated Han Chinese from Zhejiang were genotyped at these loci. No significant departures from Hardy-Weinberg equilibrium were observed at these loci in these participants. The combined power of discrimination was over 0.99999999 and the combined probability of exclusion was over 0.9901. Results demonstrated that the 30 InDel markers could be used as a supporting tool for the human identification of specific Han Chinese individuals from Zhejiang. The genetic differences and phylogenetic relationships among Han Chinese from Zhejiang, Han Chinese from five other areas, nine minority ethnic groups, as well as two other East Asian populations were also investigated. Two InDel markers, HLD39 and HLD40, showed significant allele-frequency differences between Han Chinese from Zhejiang and ethnic minorities. Further analysis can be used to evaluate their role in forensic science.     

Massively parallel sequencing of 74 microhaplotypes and forensic characteristics in three Chinese Sino-Tibetan populations

Microhaplotype (MH), as an emerging type of forensic genetic marker in recent years, has the potential to support multiple forensic applications, especially for mixture deconvolution and biogeographic ancestry inference. Herein, we investigated the genotype data of 74 MHs included in a novel MH panel, the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel, in three Chinese Sino-Tibetan populations (Han, Tibetan, and Yi) using the Ion Torrent semiconductor sequencing. The sequencing performance, allele frequencies, effective number of alleles (A_e), informativeness (I_n), and forensic parameters were subsequently estimated and calculated. In addition, principal component analysis (PCA) and structure analysis were performed to explore the population relationships among the three populations and the ancestry component distribution. Overall, this novel MH panel is robust and reliable, and has an excellent sequencing performance. The A_e values ranged from 1.0126 to 7.0855 across all samples, and 75.68 % of MHs had A_e values >2.0000. Allele frequencies at some loci varied considerably among the three studied populations, and the mean I_n value was 0.0195. Moreover, the genetic affinity between Tibetans and Yis was closer than that between Tibetans and Hans. The aforementioned results suggest that the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel is highly polymorphic in three investigated populations and could be used as an effective tool for human forensics. Although these 74 MHs have demonstrated the competency in continental population stratification, a higher resolution for distinguishing intracontinental subpopulations and a more comprehensive database with sufficient reference population data still remain to be accomplished.     

Population genetics,diversity, forensic characteristics of four Chinese populations inferred from X-chromosomal short tandem repeats

We genotyped 19 X-STRs included in the AGCU X19 kit in 712 unrelated Chinese individuals from four populations (Li, Hui, Tibetan, and Han) and then merged with 4156 previously genotyped subjects from 19 populations to investigate genetic relationships and population structure, as well as the association between the genetic affinity and language classification. The combined mean paternity exclusion chances and the combined probabilities of discrimination based on single allele frequencies of 19-X-STRs and haplotype frequencies of seven linkage groups were high, indicating that this set of markers was very polymorphic in the four populations studied. Therefore, this panel can complement autosomal or uniparental markers in kinship analysis and complex deficient paternity testing. Subsequently, population differentiation analyses among 23 populations based on 19 STRs and 15 populations based on over 62 million single nucleotide polymorphisms consistently demonstrated that genetic stratifications exist between the different language-speaking populations, especially Tibeto-Burman-speaking, Tungusic and Turkic-speaking populations. Our newly studied populations are genetically close to ethnolinguistically adjacent populations. Our datasets can and should be used as an allele and haplotype frequencies reference database to facilitate the use of 19-X-STRs panel in routine forensic practice.     

NGMSElect™ and Investigator® Argus X-12 analysis in population samples from Albania,Iraq, Lithuania,Slovenia, and Turkey

The analysis of STRs is the main tool when studying genetic diversity in populations or when addressing individual identification in forensic casework. Population data are needed to establish reference databases that can be used in the forensic context. To that end, this work investigated five population samples from Albania, Iraq, Lithuania, Slovenia, and Turkey. Individuals were typed for 16 autosomal STRs and 12 X-chromosomal STRs using the NGMSElect™ and Investigator^® Argus X-12 kits, respectively. The aim of the study was to characterize the diversity of both STR kits in these population samples and to expand our forensic database.The results showed that all markers were polymorphic in the five populations studied. No haplotype was shared between the males analysed for X-STRs. No statistically significant deviations from Hardy–Weinberg equilibrium were observed for any of the genetic markers included in both the kits. Pairwise LD was only detected in X-STRs between markers located in the same linkage group. Power of discrimination values for males and females and the probability of exclusion in duos and trios were high for the populations in this study.     

Completion of a worldwide reference panel of samples for an ancestry informative Indel assay

The use of ancestry informative markers (AIMs) in forensic analysis is of considerable utility since ancestry inference can progress an investigation when no identification has been made of DNA from the crime-scene. Short-amplicon markers, including insertion deletion polymorphisms, are particularly useful in forensic analysis due to their mutational stability, capacity to amplify degraded samples and straightforward amplification technique. In this study we report the completion of H952 HGDP–CEPH panel genotyping with a set of 46 AIM-Indels. The study adds Central South Asian and Middle Eastern population data, allowing a comparison of patterns of variation in Eurasia for these markers, in order to enhance their use in forensic analyses, particularly when combined with sets of ancestry informative SNPs. Ancestry analysis using principal component analysis and Bayesian methods indicates that a proportion of classification error occurs with European–Middle East population comparisons, but the 46 AIM-Indels have the capability to differentiate six major population groups when European–Central South Asian comparisons are made. These findings have relevance for forensic ancestry analyses in countries where South Asians form much of the demographic profile, including the UK, USA and South Africa. A novel third allele detected in MID-548 was characterized – despite a low frequency in the HGDP–CEPH panel samples, it appears confined to Central South Asian populations, increasing the ability to differentiate this population group. The H952 data set was implemented in a new open access SPSmart frequency browser – forInDel: Forensic Indel browser.     

Evaluation of 12 Multi-InDel markers for forensic ancestry prediction in Asian populations

Various types of genetic markers have been applied to forensic ancestry inference. Biallelic markers, such as SNPs and InDels, have proven to be optimal choices except for the low information content provided by a single locus. Multi-InDel marker is defined as a specific DNA fragment with several InDel markers located tightly in the physical position. Previous research indicates that multi-InDel markers perform well in population analysis and ancestry inference because of higher degree of polymorphism and remarkable population differences. In this study, a panel consisting of 12 multi-InDel markers was employed to evaluate the general performance in forensic practice and the discrimination power for population analysis. Sample types encountered in routine forensic practice were genotyped to validate the feasibility of regular use. A population study was performed on a total of five Asian populations to verify the discrimination power. Moreover, a double-blind test for ancestry prediction was conducted to assess the predictive capability. In conclusion, these results revealed the significance of multi-InDel markers for population structure stratification. The present panel showed the potential as a valid complementary tool in forensic applications.     

Indel markers: genetic diversity of 38 polymorphisms in Brazilian populations and application in a paternity investigation with post mortem material

Aiming to evaluate the usefulness of 38 non-coding bi-allelic autosomal indels in genetic identification and kinship testing, three Brazilian population samples were studied: two from Rio de Janeiro (including a sample of individuals with self-declared African ancestry) and one Native American population of Terena from Mato Grosso do Sul. Based on the observed allele frequencies, parameters of forensic relevance were calculated. The combined power of discrimination of the 38 indels was high in all studied groups (PD≥0.9999999999997), although slightly lower in Native Americans. Genetic distance analysis showed significant differences between the allele frequencies in the Rio de Janeiro population and those previously reported for Europeans, Africans and Asians explained by its intermediate position between Europeans and Africans. As expected, the Terena sample was significantly different from all the other populations: Brazilians from Rio de Janeiro general population and with self-declared African ancestry, Europeans, Africans and East Asians. Finally, the performance of the 38-indel multiplex assay was tested in post-mortem material with positive results, supporting the use of short amplicon bi-allelic markers as an additional tool to STR analysis when DNA molecules are degraded.     

Analysis of 17 STR data on 5362 southern Portuguese individuals—an update on reference database

The main objective of this work consisted of the updating of allele frequencies and other relevant forensic parameters for the 17 autosomal STR loci provided by the combination of the two types of kits used routinely in our laboratory casework: AmpF/STR Identifiler^® and the Powerplex^® 16 Systems. This aim was of significant importance, given that the last study on these kits within the southern Portuguese population dates back to 2006, and, as a consequence, it was necessary to correct the deviation caused by population evolution over the last ten years so that they might be better applied to our forensic casework. For this reason genetic data from 5362 unrelated Caucasian Portuguese individuals from the south of Portugal who were involved in paternity testing casework from 2005 to 2014 was used. Of all the markers, TPOX proved to be the least polymorphic, and Penta E the most. Secondly, this up-to-date southern Portuguese population was compared not only with the northern and central Portuguese populations, but also with that of southern Portugal in 2006, along with populations from Spain, Italy, Greece, Romania, Morocco, Angola and Korea in order to infer information about the relatedness of these respective populations, and the variation of the southern Portuguese population over time.     

Phylogenetic analysis and forensic characteristics of 12 populations using 23 Y-STR loci

Genetic analysis of Y-STRs has the potential to be used to explore the complexity in population substructures and to perform forensic ancestry inference. In this study, 334 individuals from 12 populations were typed using the PowerPlex^® Y23 System (Promega, USA) to investigate their relationship. Population comparisons with other East Asian populations collated from YHRD (Y-STR Haplotype Reference Database) were also performed. Variant alleles, including seven intermediate alleles in 15 samples were observed, while the novel allele 11.3 at the DYS549 locus was confirmed by sequencing. Our results showed that the fraction of unique haplotypes differed among the 12 populations studied here. A close relationship was found between Chinese and other East Asian populations. The present study contributed to the enrichment of the forensic Y-chromosome databases with a high resolution 23 Y-STR marker set, which is informative in forensic casework, such as familial searching and estimating the geographical origin of the offender.     

Polish population data on 15 autosomal STRs of AmpFlSTR NGM PCR kit

The objective of the research was to provide a comprehensive database of autosomal microsatellite loci included in AmpFlSTR NGM PCR kit for a population of Poland considering possible genetic differentiation of a forensic interest. Fifteen STR markers were analyzed in 2041 unrelated individuals residing in eight geographically different regions. All the loci were found to be in Hardy–Weinberg equilibrium. The combined probability of match is 3.52 × 10⁻¹⁹ and the combined Power of Exclusion is 0.9999998. The F_ST estimate over all 15 STRs is 0.0051 for the Polish population. We established that a combined NGM database may be employed for a Polish population.     

The genetic structure of native Americans in North America based on the Globalfiler® STRs

Current forensic STR databases, such as CODIS, lack population genetic data on Native American populations. Information from a geographically diverse array of tribes is necessary to provide improved statistical estimates of the strength of associations with DNA evidence. The Globalfiler® STR markers were used to characterize the genetic structure of ten tribal populations from seven geographic regions in North America, including those not presently represented in forensic databases. Samples from the Arctic region, Baja California, California/Great Basin, the Southeast, Mexico, the Midwest, and the Southwest were analyzed for allele frequencies, observed and expected heterozygosities, and F-statistics. The tribal samples exhibited an F_ST or θ value above the conservative 0.03 estimate recommended by the National Research Council (NRC) for calculating random match probabilities among Native Americans. The greater differentiation among tribal populations computed here (θ = 0.04) warrants the inclusion of additional regional Native American samples into STR databases.     

Population study and mutation analysis for 28 short tandem repeat loci in southwest Chinese Han population

Short tandem repeat (STR) system is the most widely used genetic markers in modem forensic practice. Because of the relatively unstable molecular structure, STRs show a high mutation rate. In the current study, we report 169 mutation events of 13 CODIS and 15 non-CODIS STR loci that were found in 5569 cases of trios and duos paternity test. Our result indicated that locus-specific mutation rate varied among different populations, geometric means of the longest run of perfect repeats (LRPR) and heterozygosity. Along with previous published data, a forensic dataset for allele frequencies and locus-specific mutation rates of 13 CODIS and 15 non-CODIS STR loci from southwest Chinese Han population has been established. The mutation rate data have important implications in interpreting forensic individual identification and paternity testing.     

The multiethnic ancestry of Bolivians as revealed by the analysis of Y-chromosome markers

We have analyzed the specific male genetic component of 226 Bolivians recruited in five different regions (“departments”), La Paz, Cochabamba, Pando, Beni, and Santa Cruz. To evaluate the effect of geography on the distribution of genetic variability, the samples were also grouped into three main eco-geographical regions, namely, Andean, Sub-Andean, and Llanos. All the individuals were genotyped for 17 Y-STR and 32 Y-SNP markers. The average Y-chromosome Native American component in Bolivians is 28%, and it is mainly represented by haplogroup Q1a3a, while the average Y-chromosome European ancestry is 65%, and it is mainly represented by haplogroup R1b1-P25. The data indicate that there exists significant population sub-division in the country in terms of continental ancestry. Thus, the partition of ancestries in Llanos, Sub-Andean, and Andean regions is as follows (respectively): (i) Native American ancestry: 47%, 7%, and 19%, (ii) European ancestry: 46%, 86%, and 75%, and (iii) African ancestry: 7%, 7%, and 6%. The population sub-structure in the country is also well mirrored when inferred from an AMOVA analysis, indicating that among-population variance in the country reaches 9.74–11.15%. This suggests the convenience of using regional datasets for forensic applications in Bolivia, instead of using a global and single country database. By comparing the Y-chromosome patterns with those previously reported on the same individuals on autosomal SNPs and mitochondrial DNA (mtDNA), it becomes clear that Bolivians show a strong gender-bias.     

Using forensic microsatellites to decipher the genetic structure of linguistic and geographic isolates: A survey in the eastern Italian Alps

The study of geographically and/or linguistically isolated populations could represent a potential area of interaction between population and forensic genetics. These investigations may be useful to evaluate the suitability of loci which have been selected using forensic criteria for bio-anthropological studies. At the same time, they give us an opportunity to evaluate the efficiency of forensic tools for parentage testing in groups with peculiar allele frequency profiles. Within the frame of a long-term project concerning Italian linguistic isolates, we studied 15 microsatellite loci (Identifiler kit) comprising the CODIS panel in 11 populations from the north-eastern Italian Alps (Veneto, Trentino and Friuli Venezia Giulia regions). All our analyses of inter-population differentiation highlight the genetic distinctiveness of most Alpine populations comparing them either to each other or with large and non-isolated Italian populations. Interestingly, we brought to light some aspects of population genetic structure which cannot be detected using unilinear polymorphisms. In fact, the analysis of genotypic disequilibrium between loci detected signals of population substructure when all the individuals of Alpine populations are pooled in a single group. Furthermore, despite the relatively low number of loci analyzed, genetic differentiation among Alpine populations was detected at individual level using a Bayesian method to cluster multilocus genotypes. Among the various populations studied, the four linguistic minorities (Fassa Valley, Luserna, Sappada and Sauris) showed the most pronounced diversity and signatures of a peculiar genetic ancestry. Finally, we show that database replacement may affect estimates of probability of paternity even when the local database is replaced by another based on populations which share a common genetic background but which differ in their demographic history. These findings point to the importance of considering the demographic and cultural profile of populations in forensic applications, even in a context of substantial genetic homogeneity such as that of European populations.     

MATP polymorphisms in Germans and Japanese: the L374F mutation as a population marker for Caucasoids

Inference of the population and ancestry to which an individual belongs is important in forensic individualization and personal identification. In this study, five polymorphisms of the membrane-associated transporter protein (MATP) gene were investigated in German and Japanese populations. The L374F mutation was present at an allele frequency as high as 0.96 in the German population, whereas it was completely absent in the Japanese population. This extreme difference in allele frequency suggests that the L374F mutation is valuable as a population and ancestry informative marker for Caucasoids.