Native American population data based on the Globalfiler ® autosomal STR loci

Genetic Polymorphism and Population Genetic Structure Analysis of 21 Autosomal STR Loci for a Han-Chinese Population from Luzhou of Southwest China

The Han nationality is an ancient and populous people, and different places in China may have their distinct group relationships. Luzhou area, as a crossroads of several provinces in Southwest China, lacks autosomal short tandem repeat (STR) research and population genetics research. In this study, 21 autosomal STR loci were evaluated in 1959 Han-Chinese individuals from Luzhou area. There was no substantial linkage disequilibrium (LD) among the 21 autosomal STR markers, and all markers were in Hardy-Weinberg equilibrium (HWE). The total discrimination power (TDP) and cumulative probability of exclusion (CPE) of the 21 autosomal STR loci were calculated to be 1-9.8505 × 10^-16 and 1-1.9406 × 10^-9, respectively. There were 333 alleles for 21 STRs with allelic frequencies ranging from 0.00026 to 0.51302, and the number of alleles ranged from 7 in locus TPOX to 29 in locus Penta E. According to the results of population comparison and population differentiation, historical influences, geographical distribution, cultural integration, and economic development may have an impact on the Luzhou Han population and other Chinese populations. These 21 STR loci were found to enrich autosomal STR information in forensic databases and provide highly informative polymorphisms for our forensic practice in China, including personal identification and parentage testing.

Use of Investigator 24plex GO! to analyse allele frequencies of 21 autosomal STRs in the population of Veracruz state, Mexico

BackgroundMexican population databases for autosomal STRs are scarce, and no previous studies have been performed with the Qiagen Investigator 24plex GO! Aim: To analyse the frequency of 21 autosomal short tandem repeat (STR) loci and forensic parameters in individuals from Veracruz state, Mexico. Subjects and methods: A total of 234 unrelated individuals were analysed with the Investigator 24plex GO! Kit, which includes the following autosomal STRs: TH01, D3S1358, vWA, D21S11, TPOX, D1S1656, D12S391, SE33, D10S1248, D22S1045, D19S433, D8S133879, D2S1338, D2S441, D18S51, FGA, D16S539, CSF1PO, D13S317, D5S818, and D7S820. Allele frequencies, forensic parameters, and relationships with neighbouring Mexican populations were estimated. Results: The STRs analysed were in Hardy-Weinberg Equilibrium (HWE). The combined matching probability and combined PE were 1.5266 E-24 and 0.999999988711, respectively. The D18S51 and SE33 loci presented the highest Ho (0.8974 and 0.8932) and PE (0.7902 and 0.7815), respectively. The highest PIC (0.9337) and PD (0.9894) values corresponded to SE33. Conversely, D22S1045 had the lowest PIC and PE (0.5533 y 0.3546, respectively). A population cluster among southern Mexican populations, which included non-differentiation between Guerrero and Veracruz states was detected. Conclusion: The forensic efficacy of the 21 STRs analysed by the Investigator 24plex GO! Kit was evaluated in the Veracruz state. Moreover, new population clusters that have not been yet been described and are related to geographic regions were identified, and these are in agreement with previously reported ancestral differences.

The Heart of Silk Road "Xinjiang," Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs

The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors almost 50 ethnic groups including the Uyghur (UGR: 45.84%), Han (HAN: 40.48%), Kazakh (KZK: 6.50%), Hui (HUI: 4.51%), Kyrgyz (KGZ: 0.86%), Mongol (MGL: 0.81%), Manchu (MCH: 0.11%), and Uzbek (UZK: 0.066%), which make it one of the most colorful regions with abundant cultural and genetic diversities. In our previous study, we established allelic frequency databases for 14 autosomal short tandem repeats (STRs) for four minority populations from XUARC (MCH, KGZ, MGL, and UZK) using the AmpFlSTR® Identifiler PCR Amplification Kit. In this study, we genotyped 2,121 samples using the GoldenEye™ 20A Kit (Beijing PeopleSpot Inc., Beijing, China) amplifying 19 autosomal STR loci for four major ethnic groups (UGR, HAN, KZK, and HUI). These groups make up 97.33% of the total XUARC population. The total number of alleles for all the 19 STRs in these populations ranged from 232 (HAN) to 224 (KZK). We did not observe any departures from the Hardy-Weinberg equilibrium (HWE) in these populations after sequential Bonferroni correction. We did find minimal departure from linkage equilibrium (LE) for a small number of pairwise combinations of loci. The match probabilities for the different populations ranged from 1 in 1.66 × 1023 (HAN) to 6.05 × 1024 (HUI), the combined power of exclusion ranged from 0.999 999 988 (HUI) to 0.999 999 993 (UGR), and the combined power of discrimination ranged from 0.999 999 999 999 999 999 999 983 (HAN) to 0.999 999 999 999 999 999 999 997 (UGR). Genetic distances, principal component analysis (PCA), STRUCTURE analysis, and the phylogenetic tree showed that genetic affinity among studied populations is consistent with linguistic, ethnic, and geographical classifications.

Streamlining the decision-making process for international DNA kinship matching using Worldwide allele frequencies and tailored cutoff log10LR thresholds

The identification of human remains belonging to missing persons is one of the main challenges for forensic genetics. Although other means of identification can be applied to missing person investigations, DNA is often extremely valuable to further support or refute potential associations. When reference DNA samples cannot be collected from personal items belonging to a missing person, a direct DNA identification cannot be carried out. However, identifications can be made indirectly using DNA from the missing person's relatives. The ranking of likelihood ratio (LR) values, which measure the fit of a missing person for any given pedigree, is often the first step in selecting candidates in a DNA database. Although implementing DNA kinship matching in a national environment is feasible, many challenges need to be resolved before applying this method to an international configuration. In this study, we present an innovative and intuitive method to perform international DNA kinship matching and facilitate the comparison of DNA profiles when the ancestry is unknown or unsure and/or when different marker sets are used. This straightforward method, which is based on calculations performed with the DNA matching software BONAPARTE, Worldwide allele frequencies and tailored cutoff log₁₀LR thresholds, allows for the classification of potential candidates according to the strength of the DNA evidence and the predicted proportion of adventitious matches. This is a powerful method for streamlining the decision-making process in missing person investigations and DVI processes, especially when there are low numbers of overlapping typed STRs. Intuitive interpretation tables and a decision tree will help strengthen international data comparison for the identification of reported missing individuals discovered outside their national borders.

Genetic differentiation between and within Northern Native American language groups: an argument for the expansion of the Native American CODIS database

The National Research Council recommends that genetic differentiation among subgroups of ethnic samples be lower than 3% of the total genetic differentiation within the ethnic sample to be used for estimating reliable random match probabilities for forensic use. Native American samples in the United States' Combined DNA Index System (CODIS) database represent four language families: Algonquian, Na-Dene, Eskimo-Aleut, and Salishan. However, a minimum of 27 Native American language families exists in the US, not including language isolates. Our goal was to ascertain whether genetic differences are correlated with language groupings and, if so, whether additional language families would provide a more accurate representation of current genetic diversity among tribal populations. The 21 short tandem repeat (STR) loci included in the Globalfiler® PCR Amplification Kit were used to characterize six indigenous language families, including three of the four represented in the CODIS database (i.e. Algonquian, Na-Dene, and Eskimo-Aleut), and two language isolates (Miwok and Seri) using major population genetic diversity metrics such as F statistics and Bayesian clustering analysis of genotype frequencies. Most of the genetic variation (97%) was found to be within language families instead of among them (3%). In contrast, when only the three of the four language families represented in both the CODIS database and the present study were considered, 4% of the genetic variation occurred among the language groups. Bayesian clustering resulted in a maximum posterior probability indicating three genetically distinct groups among the eight language families and isolates: (1) Eskimo, (2) Seri, and (3) all other language groups and isolates, thus confirming genetic subdivision among subgroups of the CODIS Native American database. This genetic structure indicates the need for an increased number of Native American populations based on language affiliation in the CODIS database as well as more robust sample sets for those language families. Supplemental data for this article is available online at https://doi.org/10.1080/20961790.2021.1963088 .

Estimating population genetics and forensic efficiency of the GlobalFiler PCR amplification kit in the population of Sardinia (Italy)

GlobalFiler is a new PCR amplification kit that includes 21 autosomal short tandem repeats and three sex-determining loci. In the present research, for the first time, the GlobalFiler kit was tested to analyze a sample of 500 unrelated individuals from 18 villages encompassing the entire area of Sardinia (Italy). We tested if the kit, which is a powerful tool in forensic studies, may also find application in the field of population genetics. In agreement with data from the literature on forensic parameters values, marker SE33 showed the highest degree of polymorphism, whereas TPOX was the least informative locus. Seventeen out of twenty-one autosomal markers included in the kit resulted highly polymorphic, and therefore Globalfiler turned out to be highly useful for forensic analysis in the Sardinian population. Moreover, our data suggest developing different STR databases in different populations, like Sardinians, to increase the statistical power of autosomal STR profiling. On the other hand, due to the presence of some very highly polymorphic markers, the efficiency of Globalfiler in detecting geographical variability is affected. Indeed, the differentiation previously observed between the Sardinian and Italian populations appeared greatly reduced and even the presence of genetic isolates, previously recorded when uniparental markers was not revealed.

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese

Modern East Asians derived from the admixture of aborigines and incoming farmers expanding from Yellow and Yangtze River Basins. Distinct genetic differentiation and subsequent admixture between Northeast Asians and Southeast Asians subsequently evidenced by the mitochondrial DNA, Y-chromosomal variations, and autosomal SNPs. Recently, population geneticists have paid more attention to the genetic polymorphisms and background of southern-Han Chinese and southern native populations. The genetic legacy of northern-Han remains uncharacterized. Thus, we performed this comprehensive population genetic analyses of modern and ancient genetic variations aiming to yield new insight into the formation of modern Han, and the genetic ancestry and phylogenetic relationship of the northern-Han Chinese population. We first genotyped 25 forensic associated markers in 3,089 northern-Han Chinese individuals using the new-generation of the Huaxia Platinum System. And then we performed the first meta-analysis focused on the genetic affinity between Asian Neolithic∼Iron Age ancients and modern northern-Han Chinese by combining mitochondrial variations in 417 ancient individuals from 13 different archeological sites and 812 modern individuals, as well as Y-chromosomal variations in 114 ancient individuals from 12 Neolithic∼Iron Age sites and 2,810 modern subjects. We finally genotyped 643,897 genome-wide nucleotide polymorphisms (SNPs) in 20 Shanxi Han individuals and combined with 1,927 modern humans and 40 Eurasian ancient genomes to explore the genetic structure and admixture of northern-Han Chinese. We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses. Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than with Uyghur and Tibetan. Genome-wide variations revealed that modern northern-Han derived their ancestry from Yakut-related population (25.2%) and She-related population (74.8%). Summarily, the genetic mixing that led to the emergence of a Han Chinese ethnicity occurred at a very early period, probably in Neolithic times, and this mixing involved an ancient Tibeto-Burman population and a local pre-Sinitic population, which may have been linguistically Altaic.

Genetic polymorphism and phylogenetic differentiation of the Huaxia Platinum System in three Chinese minority ethnicities

Short tandem repeats (STRs) with features of high polymorphism and abundant evolution information play a significant role in genetic applications such as human forensics, anthropology and population genetics. The Huaxia Platinum System was specifically exploited to allow coamplification of all markers in the expanded Combined DNA Index System and the Chinese National Database. Herein, in continuation of our previous studies, 493 unrelated individuals were firstly genotyped to investigate the efficacy of this novel system in three minority ethnicities of China (Hui, Tibetan and Uygur). Additionally, genetic relationships among our three investigated populations and other previously published populations were analyzed using pairwise genetic distances, multidimensional scaling (MDS), principal component analysis (PCA), cladogram and STRUCTURE. The combined match probabilities (CMP) for the Hui, Tibetan and Uygur groups were 1.6894 × 10⁻²⁷, 6.1666 × 10⁻²⁷ and 5.0655 × 10⁻²⁷, respectively, and the combined powers of exclusion (CPE) were 0.999999999646627, 0.999999999304935 and 0.999999999433994. Population comparison analysis manifested that the Hui and Tibetan populations had genetic affinities with the Han, Yi and Korean populations, while the Uygur group had a close relationship with the Kazakh population. The aforementioned results suggested that the Huaxia Platinum System is a polymorphic and effective tool that is appropriate for personal identification and population genetics.

Signs of continental ancestry in urban populations of Peru through autosomal STR loci and mitochondrial DNA typing

The human genetic diversity around the world was studied through several high variable genetic markers. In South America the demic consequences of admixture events between Native people, European colonists and African slaves have been displayed by uniparental markers variability. The mitochondrial DNA (mtDNA) has been the most widely used genetic marker for studying American mixed populations, although nuclear markers, such as microsatellite loci (STRs) commonly used in forensic science, showed to be genetically and geographically structured. In this work, we analyzed DNA from buccal swab samples of 296 individuals across Peru: 156 Native Amazons (Ashaninka, Cashibo and Shipibo from Ucayali, Huambiza from Loreto and Moche from Lambayeque) and 140 urban Peruvians from Lima and other 33 urban areas. The aim was to evaluate, through STRs and mtDNA variability, recent migrations in urban Peruvian populations and to gain more information about their continental ancestry. STR data highlighted that most individuals (67%) of the urban Peruvian sample have a strong similarity to the Amazon Native population, whereas 22% have similarity to African populations and only ~1% to European populations. Also the maternally-transmitted mtDNA confirmed the strong Native contribution (~90% of Native American haplogroups) and the lower frequencies of African (~6%) and European (~3%) haplogroups. This study provides a detailed description of the urban Peruvian genetic structure and proposes forensic STRs as a useful tool for studying recent migrations, especially when coupled with mtDNA.

Population genetic analysis of the Globalfiler STR loci in 3032 individuals from the Altay Han population of Xinjiang in northwest China

The genetic polymorphisms of 21 autosomal short tandem repeat (STR) loci included in the GlobalFiler™ PCR Amplification Kit were evaluated in 3032 unrelated individuals Altay Han of Xinjiang, northwest China. All of the loci reached the Hardy-Weinberg equilibrium. These loci were examined to determine allele frequencies and forensic statistical parameters. SE33 showed the greatest power of discrimination in Altay Han population, whereas TPOX showed the lowest. The combined discrimination power and probability of excluding paternity of the 21 autosomal STR loci were 0.999999999999999999999999889838 and 0.999999996664704, respectively. Both pairwise genetic distance and phylogenetic methods indicated that the Altay Han had the closest genetic relationship with the Han origin and Hui populations. The present results revealed that the GlobalFiler system had a high level of polymorphism in Altay Han population and hence could be a powerful tool for forensic application and population genetic study.

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.