Characterisation of three Amerindian populations from Hidalgo State (Mexico) by 15 STR-PCR polymorphisms

The purpose of this study is to report allele frequency data of three ethnic Amerindian population samples: the Otomi (Hña-hñu) from eastern Sierra Madre and Ixmiquilpan valley and the Huasteco from La Huasteca. These groups were characterised by 15 STR-PCR polymorphisms (HumTH01, HumvWA, D18S51, HumTPOX, D19S433, D16S539, D13S317, D8S1179, D7S820, D5S818, HumFGA, CSF1PO, D2S1338, D3S1358 and D21S11). No significant deviations in observed allelic frequencies from Hardy-Weinberg equilibrium were found for all the studied systems. From the forensic point of view, the heterozygosity value, power of discrimination and the a priori chance of exclusion were calculated.     

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.     

Haplotype frequencies of eight Y-chromosome STR loci in Barcelona (North-East Spain)

Haplotype frequencies for eight Y-chromosomal short tandem repeat (STR) loci were determined in ¶a population sample from Barcelona (NE Spain). After PCR amplification and denaturing PAGE electrophoresis, DYS19, DYS388, DYS389 I/II, DYS390, DYS391, DYS392 and DYS393 loci were typed. Complete eight ¶Y-chromosomal STRs haplotypes could be formed for 223 subjects, among which 137 different haplotypes were observed. The most common haplotype was shared by 13% of the sample, while 108 haplotypes were unique. The discrimination capacity was 61.5% and the gene diversity was 0.978. From the forensic point of view the combined polymorphisms provide a high diagnostic efficiency.     

Genetic polymorphisms of 20 autosomal STR loci in the Han population of Zhangzhou City,Southeastern China

China harbors 56 ethnic groups and Han is the largest population. It is informative and useful to explore the available population genetic characteristics of Chinese Han population from Fujian Province, Southeast China. In our study, we explored the genetic characteristics of 20 autosomal Short tandem repeat (STR) loci in 1555 unrelated Chinese Han individuals from Zhangzhou City, Southeastern China using the SureID® 21G Human STR Identification Kit. Moreover, phylogenetic analysis was performed between the Zhangzhou Han population and other relevant populations based on the shared autosomal STR genotyping. The neighbor-joining tree and multidimensional scaling analysis were analyzed based on the Nei’s standard genetic distance. We found 262 alleles among 1555 unrelated individuals and the corresponding allele frequencies ranged from 0.5521 to 0.0003. The combined power of discrimination and exclusion of the 20 autosomal STR loci were 0.99999999999999999999999943 and 0.999999996166537, respectively. Population comparison revealed that the Zhangzhou Han population were lining up together with the southern Han populations in China while showed significant differences from other China populations. Our results found that the 20 autosomal STR loci in Zhangzhou Han population are meaningful for forensic medicine and human genetic. The genetics characteristic of Zhangzhou Han population is similar with the southern Han population in China.     

Genetic polymorphism and population structure of Torghut Mongols and comparison with a Mongolian population 3000 kilometers away

Mongolians played a pivotal role in shaping the culture and genetic architecture of modern Eurasia through the rapid expansion of the Mongol Empire in the 13th century. While the historical aspects of the Mongolian Empire are well documented, research on the genetic variations among Mongolian populations is still insufficient. In this study, we examined the genetic diversity of 70 Torghut Mongols residing in the Ili region of China compared with 88 Jalaid Mongols residing 3000 km away. Over 200 forensically relevant genetic markers, including autosomal short tandem repeats (A-STRs), X chromosomal STRs (X-STRs), Y chromosomal STRs (Y-STRs), identity-informative single nucleotide polymorphisms (iiSNPs), ancestry-informative SNPs (aiSNPs), and phenotype-informative SNPs (piSNPs), were genotyped to uncover the genetic polymorphism of the Torghut Mongols. The STR genotyping results showed that 80 alleles (39 A-STRs, 25 Y-STRs, and 16 X-STRs; 14.4% of 554 alleles) identified in Torghut Mongols were not identified in Jalaid Mongols, while 155 alleles (84 A-STRs, 59 Y-STRs and 12 X-STRs; 24.6% of 630 alleles) identified in Jalaid Mongols were not observed in Torghut Mongols. Calculation of the forensic parameters demonstrated that the STRs and SNPs analyzed here could be employed in forensic applications. Interpopulation comparisons via principal component analysis (PCA), phylogenetic tree, and STRUCTURE analysis showed that the two Mongolian populations were closely related by their genetic background, although genetic differences were also discovered. When both the sequence-based A-STRs and iiSNPs were included in the STRUCTURE analysis, the Torghut population was more similar to the Uyghur population than to Jalaid Mongols, indicating certain population structure differences between the two Mongolian populations. The Y-DNA haplogroup prediction showed that although haplogroup C (C2-M217) was dominant in both Mongolian populations, haplogroup O2-M122 was rarely presented in Torghut Mongols, which differentiated the Torghut Mongols from the other Mongolian populations. This study not only uncovered the genetic features of the two Mongolian tribes, providing valuable frequency data for forensic applications, but the genetic patterns of the two Mongolian populations also provide a genetic evidence that the Torghut Mongols may have developed via the gradual intermixing of nomadic groups of Mongol and Turkic origin, as recorded in historical records. This study also highlighted the importance of building regional reference databases that consider both ethnic and geographic location information, instead of a more universal reference database, for forensic applications.     

Amplification and detection of the VNTR locus D4S95 in a Japanese population

The D4S95-VNTR locus was amplified and the polymorphism analysed in a population sample of 169 randomly selected Japanese individuals. A total of 14 alleles containing 850–1360 base pairs were distinguished by agarose gel electrophoresis. The distribution of alleles was symmetrical with respect to one peak at 1030 bp. The mean exclusion chance and discrimination power were calculated as 0.604 and 0.876 respectively.     

Evaluation of an extended set of 15 candidate STR loci for paternity and kinship analysis in an Austrian population sample

We investigated 15 polymorphic short tandem repeat (STR) loci (D1S1656, D7S1517, D8S306, D8S639, D9S304, D10S2325, D11S488, D12S391, D14S608, D16S3253, D17S976, D18S1270, D19S253, D20S161, and D21S1437) which are not included in the standard sets of forensic loci. The markers were selected according to the complexity of the polymorphic region: Of the 15 investigated loci, 7 loci showed a simple repeat structure (D9S304, D10S2325, D14S608, D16S3253, D18S1270, D19S253, and D21S1437), 3 loci (D7S1517, D12S391, and D20S161) consisted of compound repeat units, and 5 loci (D1S1656, D8S306, D8S639, D11S488, and D17S976) showed a more complex polymorphic region partly including different repeat blocks and incomplete repeat units, which resulted in a relatively high proportion of intermediate alleles. A population study on a sample of 270 unrelated persons from Austria was carried out. We did not observe significant deviations from Hardy–Weinberg expectations. The combined probability of exclusion for the 15 loci was 0.99999998. In combination with the conventional set of STR markers included in commercially available kits (no linkage was observed between these 15 loci and the Powerplex 16 System loci), these markers are approved as highly discriminating forensic tools, also suitable for the analysis of difficult paternity and kinship constellations. Electronic Supplementary Material Supplementary material is available for this article at     

Forensic genetic polymorphisms of 16 X-STR loci in the Yunnan Miao population and their relationship to other Chinese groups

Allele frequencies for 16 X-chromosomal STR (X-STR) loci were obtained from a sample set of 440 unrelated Yunnan Miao individuals in China. A total of 117 alleles were observed in this group, with allele frequencies ranging from 0.0016 to 0.7565. The most informative marker for the studied population was DXS10134, with a polymorphism information content (PIC) of 0.8499, and the least polymorphic locus was DXS6810 (PIC = 0.3071). The power of discrimination (PD) varied from 0.4046 (DXS6800) to 0.8642 (DXS10134) in males and from 0.6188 (DXS6800) to 0.9673 (DXS10134) in females. The combined PDM and PDF were 0.999999989975990 and 0.999999999999949, respectively. The combined MECD and MECT were 0.999983301904059 and 0.999999915883733, respectively. Furthermore, population genetic structure investigation between the Yunnan Miao and 20 other populations using principal component analysis (PCA), multidimensional scaling plot (MDS), and neighboring-joining (NJ) phylogenetic tree analyses illustrated significant genetic difference between the Yunnan Miao and the other populations. This study is the first to provide X chromosome genetic polymorphism data of the Miao population in Yunnan Province and can be used as a supplementary reference to enrich the national database.     

Autosomal SNPs study of a population sample from North of Portugal and a sample of immigrants from the Eastern Europe living in Portugal

The use of autosomal single nucleotide polymorphisms (SNPs) for forensic research has been widely discussed in recent years, mainly because SNPs have important advantages compared to short tandem repeats (STRs).In this study a total of 131 non related individuals from the North of Portugal and 85 immigrant individuals from the Eastern Europe, mainly Ukrainians, equally non related and residing in Portugal, were typed for 52 loci included in the in the SNP for ID 52plex with the SNaPshot™ assay.     

Sequence polymorphisms of forensic Y-STRs revealed by a 68-plex in-house massively parallel sequencing panel

Sequence polymorphisms of Y chromosome short tandem repeat (Y-STR) markers can be unveiled using next generation sequencing (NGS). Compared to capillary electrophoresis, NGS has the advantage of distinguishing between some alleles of the same length. Here, a 68-plex in-house panel covering 67 Y-STR loci and the sex determinant Amelogenin locus, was developed. The accuracy of this panel was 100% concordant with three standard reference samples. The sensitive was as low as 250 pg. A total of 466 length-based alleles, 806 sequence-based alleles, and 149 haplotypes were observed across 149 Chinese Han individuals. The total haplotype diversity and discrimination capacity was 1.0000 in detected samples. The DYS710 locus possessed the highest diversity by sequence among these Y-STRs, with 109 sequence-based alleles observed. Micro-variant alleles with the same length were observed in 39 Y-STR loci, with their sequence variations mainly attributable to repeat pattern variations. While the number of sequence-based alleles identified for DYS447, DYS449, DYS710, DYS720 and DYF387S1a/b was approximately three times that of their length-based alleles, flanking sequence variations were observed in 18 alleles. In addition, 201 sequence-based alleles in 42 loci were newly discovered. This significantly expanded the knowledge of human Y-STR sequence polymorphisms. Collectively, the 68-plex panel provided reliable Y-STR results as well as higher resolution for paternal lineage analysis.     

The Bubi population of Equatorial Guinea characterised by HUMTH01, HUMVWA31A, HUMCSF1PO, HUMTPOX, D3S1358, D8S1179, D18S51 and D19S253 STR polymorphisms

Allele frequencies for eight STR loci (HUMTH01, HUMVWA31A, HUMCSF1PO, HUMTPOX, D3S1358, D8S1179, D18S51, D19S253) have been analysed in the Bubi population of Bioko Island, Equatorial Guinea. For all loci, no deviation from Hardy-Weinberg equilibrium was found. Data obtained were compared with that of Caucasian and African populations. Significant differences were found for all systems between all the black populations compared and the Caucasoid population. Similarities were observed between the Bubi and Zimbabweans, and also with African American populations. Also, more affinities were observed between Zimbabweans and Ugandans and Ovambos than between these groups and the Bubi population. From these comparisons it is suggested that in Africa, as in other continents, there is a certain genetic heterogeneity. Received: 9 May 2000 / Accepted: 19 September 2000     

Genetic diversity at 15 microsatellite loci among the Adi Pasi population of Adi tribal cluster in Arunachal Pradesh, India

Genetic polymorphisms at 15 tetrameric short tandem repeat (STR) loci were studied in 203 healthy individuals of Adi Pasi population from Arunachal Pradesh, India. All the loci analyzed were highly polymorphic and there was no significant deviation from the Hardy-Weinberg equilibrium (HWE) excepting D8S1179 and D18S51. Other forensic useful statistical parameters were also calculated and the 15 microsatellite markers selected for this study were found to be suitable for human identification and population genetic studies.     

Applicability of the SNPforID 52-plex panel for human identification and ancestry evaluation in a Brazilian population sample by next-generation sequencing

SNP analysis is of paramount importance in forensic genetics. The development of new technologies in next-generation sequencing allowed processing a large number of markers in various samples simultaneously. Although SNPs are less informative than STRs, they present lower mutation rates and perform better when using degraded samples. Some SNP systems were developed for forensic usage, such as the SNPforID 52-plex, from the SNPforID Consortium, containing 52 bi-allelic SNPs for human identification. In this paper we evaluated the informativeness of this system in a Brazilian population sample (n = 340). DNA libraries were prepared using a customized HaloPlex Target Enrichment System kit (Agilent Technologies, Inc.) and sequenced in the MiSeq Personal Sequencer platform (Illumina Inc.). The methodology presented here allowed the analysis of 51 out of 52 SNPforID markers. Allele frequencies and forensic parameters were estimated, revealing high informativeness: the combined match probability and power of exclusion were 6.48 × 10⁻²¹ and 0.9997, respectively. Population admixture analysis indicates high European contribution (more than 70%) and low Amerindian contribution (less than 10%) in our population, while individual admixture analyses were consistent with the majority of individuals presenting high European contribution. This study demonstrates that the 52-plex kit is suitable for forensic cases in a Brazilian population, presenting results comparable with those obtained using a 16 STR panel.