Haplotype analysis of the polymorphic 40 Y-STR markers in Chinese populations

Forty Y-STR loci were analyzed in 1128 males from the following six Chinese ethnic populations: Han (n = 300), Hui (n = 244), Korean (n = 100), Mongolian (n = 100), Uighur (n = 284) and Tibetan (n = 100), utilizing two new generation multiplex Y-STR systems, AGCU Y24 STR and GFS Y24 STR genotyping kits, which allow for the genotyping of 24 loci from a single amplification reaction in each system. The lowest estimates of genetic diversity (below 0.5) correspond to markers DYS391 (0.441658) and DYS437 (0.496977), and the greatest diversity corresponds to markers DYS385a/b (0.969919) and DYS527a/b (0.94676). A considerable number of duplicate and off-ladder alleles were also revealed. Additionally, there were 1111 different haplotypes identified from the total 1128 samples, of which 1095 were unique. Notably, no shared haplotypes between populations were observed. The estimated overall haplotype diversity (HD) was 0.999085, and its discrimination capacity (DC) was 0.970745. An MDS plot based on the genetic distances between populations showed the genetic similarity of the southern Han population to the Northern populations of Hui, Korean, Mongolian and Uighur and a clear genetic departure of the Tibetan population from other populations. For the Y STR markers, population substructure correction was considered when calculating the rarity of the Y STR profile. However, because the haplotype based Fst values are extremely small within the present data (0.000153 with 40 Y-STRs), no substructure correction is required to estimate the rarity of a haplotype comprising 40 markers. In summary, the results of our study indicate that the 40 Y-STRs have a high level of polymorphism in Chinese ethnic groups and could therefore be a powerful tool for forensic applications and population genetic studies.     

Investigation of extended Y chromosome STR haplotypes in Sardinia

Y-chromosomal variation of selected single nucleotide polymorphisms (SNPs) and 32 short tandem repeat (STR) loci was evaluated in Sardinia in three open population groups (Northern Sardinia, n = 40; Central Sardinia, n = 56; Southern Sardinia, n = 91) and three isolates (Desulo, n = 34; Benetutti, n = 45, Carloforte, n = 42). The tested Y-STRs consisted of Yfiler^® Plus markers and the seven rapidly mutating (RM) loci not included in the YFiler^® Plus kit (DYF399S1, DYF403S1ab, DYF404S1, DYS526ab, DYS547, DYS612, and DYS626).As expected, inclusion of additional Y-STR loci increased haplotype diversity (h), though complete differentiation of male lineages was impossible even by means of RM Y-STRs (h = 0.99997).Analysis of molecular variance indicated that the three open populations were fairly homogeneous, whereas signs of genetic heterogeneity could be detected when the three isolates were also included in the analysis.Multidimensional scaling analysis showed that, even for extended haplotypes including RM Y-STR markers, Sardinians were clearly differentiated from populations of the Italian peninsula and Sicily. The only exception was represented by the Carloforte sample that, in accordance with its peculiar population history, clustered with Northern/Central Italian populations.The introduction of extended forensic Y-STR panels, including highly variable RM Y-STR markers, is expected to reduce the impact of population structure on haplotype frequency estimations. However, our results show that the availability of geographically detailed reference databases is still important for the assessment of the evidential value of a Y-haplotype match.     

MiniY-STR quadruplex systems with short amplicon lengths for analysis of degraded DNA samples

Two short amplicon Y-chromosomal short tandem repeat (miniY-STR) quadruplex systems for the eight Y-STR loci DYS522, DYS508, DYS632, DYS556, DYS570, DYS576, DYS504 and DYS540 were devised using newly designed primer sets. Among 224 samples from Japanese population, amplification product lengths detected in these Y-STR loci ranged from 95 to 147 bp, while 170 different haplotype were identified (discrimination capacity = 0.7589 and haplotype diversity = 0.9949). As a result of test on degraded DNA samples using the miniY-STR quadruplex systems, the systems proved to be an quite effective tools for analyzing degraded DNAs. We conclude that analyses of the miniY-STR quadruplex systems in addition to the commercial available Y-STR multiplex kits are highly useful for forensic practices of degraded DNA samples.     

Population data for 12 Y-chromosome STR loci in a sample from El Salvador

Haplotype, allele frequencies and population data of 12 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined from a sample of 150 unrelated male individuals from El Salvador, Central America. A total of 131 haplotypes were identified by the 12 Y-STR loci of which 118 were unique. The haplotype diversity (99.08%) and the proportion of different haplotypes (87.33%) were estimated. R_ST genetic distances were calculated between El Salvador and other populations from Southern and Central America, Europe and Africa. The highest R_ST genetic distances were found when comparing El Salvador with African populations (0.334 ? R_ST ? 0.395). The lowest non-significant distance was found in the comparison with Honduras. The observed genetic distances between El Salvador and Southern and Central Native groups presented a wide range of values (from 0.024 to 0.210) that can be explained by the differences in the proportion of European versus Amerindian contributions in these population groups. The Multi Dimensional Scaling (MDS) plot analysis, based on pairwise R_ST values, showed that the general population of El Salvador is closer to the European cluster (composed by European and South American general population samples from Brazil, Argentina, Colombia and Venezuela) than to the Southern/Central American cluster of Native and Mestizo populations.     

Y chromosome STR allelic and haplotype diversity in five ethnic Tamil populations from Tamil Nadu,India

We have analyzed 17 Y chromosomal STR loci in a population sample of 154 unrelated male individuals of the Tamil ethnic group residing in the state of Tamil Nadu, Southern India using AmpFlSTR® Yfiler? PCR amplification kit. The population samples consist of the following castes: Kongu Gounder (KOG), Nadar Hindu (NAH), Agamudayar (AGA), Parayar (PAR) and other Tamil individuals (MCT) of mixed castes. A total of 152 unique haplotypes were identified among the 154 individuals studied. The haplotype diversity was found to be 0.9935 or higher for all the five groups. The results of population pairwise Fst p values indicate no statistically significant differentiation between the five populations in this study, but the results were highly significant when compared with 12 other global populations (p < 0.05). Comparison of populations in this study with other national and global populations using Principal co-ordinate analysis (PCA) using Rst distance matrix indicates a delineation of all the Indian populations from other unrelated populations.     

Male lineage strata of Brazilian population disclosed by the simultaneous analysis of STRs and SNPs

Brazil has a large territory divided in five geographical regions harboring highly diverse populations that resulted from different degrees and modes of admixture between Native Americans, Europeans and Africans. In this study, a sample of 605 unrelated males was genotyped for 17 Y-STRs and 46 Y-SNPs aiming a deep characterization of the male gene pool of Rio de Janeiro and its comparison with other Brazilian populations. High values of Y-STR haplotype diversity (0.9999 ± 0.0001) and Y-SNP haplogroup diversity (0.7589 ± 0.0171) were observed. Population comparisons at both haplotype and haplogroup levels showed significant differences between Brazilian South Eastern and Northern populations that can be explained by differences in the proportion of African and Native American Y chromosomes. Statistical significant differences between admixed urban samples from the five regions of Brazil were not previously detected at haplotype level based on smaller size samples from South East, which emphasizes the importance of sample size to detected population stratification for an accurate interpretation of profile matches in kinship and forensic casework. Although not having an intra-population discrimination power as high as the Y-STRs, the Y-SNPs are more powerful to disclose differences in admixed populations. In this study, the combined analysis of these two types of markers proved to be a good strategy to predict population sub-structure, which should be taken into account when delineating forensic database strategies for Y chromosome haplotypes.     

Highly discriminatory capacity of the PowerPlex® Y23 System for the study of isolated populations

In order to evaluate the forensic utility of the new PowerPlex^® Y23 System, two Northern Spanish populations, the autochthonous Basque Country (N = 105) and Cantabria (N = 98), were typed. Two of the new markers incorporated in the panel, the rapid mutating loci DYS576 and DYS570, were among the most discriminative markers in both population datasets. In terms of the analysis of 23 Y-STRs, the two populations showed high haplotype diversities, with values slightly superior in the population of Cantabria (1 ± 0.0015) than in the Basque Country (0.9987 ± 0.0016). The comparison of the discrimination capacity obtained with the analysis of 23 Y-STRs and other available markers sets of 12 Y-STRs (PowerPlex^® Y System) or 17 Y-STRs (YFiler™), clearly demonstrated an improvement in the population of the Basque Country. Nevertheless, in Cantabria this augment was only seen when the number of markers was increased from 12 to 23, since the study of 17 Y-STRs was enough to differentiate all haplotypes. Therefore, this study shows that the improvement in forensic parameters by increasing the number of Y-STR markers analyzed is much more pronounced in the case of isolated populations such as the autochthonous population of the Basque Country, as it facilitates the differentiation among similar haplotypes. Moreover, by the use of the PowerPlex^® Y23 identification of population specific haplotypes increased in both populations. Ultimately, the analysis of 23 Y-STRs differentiated among the two geographically close populations of Basque Country and Cantabria. Indeed it showed significant differences between the Basque Country population and all European populations included, meanwhile Cantabria did exhibit significant proximity with the Iberian and the majority of European populations considered.     

Haplotype and mutation analysis for newly suggested Y-STRs in Korean father–son pairs

In this study, 363 Korean father–son haplotype transfers in 351 families were analyzed using an in-house multiplex PCR system for 14 Y-STRs (DYS385a/b, DYF387S1, DYS391, DYS449, DYS460, DYS481, DYS518, DYS533, DYS549, DYS570, DYS576, DYS627 and DYS643), that included 11 loci newly added to the PowerPlex Y23 system or the Yfiler Plus system. The Y-STRs showed gene diversity values ranging from 0.2499 to 0.9612; the multicopy Y-STR loci DYS385 and DYF387S1 had high gene diversity of 0.9612 and 0.9457, respectively. In addition, DYF387S1, which has two copies, showed three alleles in seven individuals, and micro-variant alleles were observed in 14 individuals at four loci (DYS448, DYS518, DYS570 and DYS627). Among 351 haplotypes for the 11 newly added Y-STRs, 350 different haplotypes were observed, with an overall haplotype diversity of 0.9999 and discrimination capacity of 99.72%. In 363 haplotype transfers from 351 pedigrees, 29 single-step mutations were observed at 11 Y-STRs. Locus-specific mutation rate estimates varied from 0.0 to 1.93 × 10⁻², with an average estimated mutation rate of 6.66 × 10⁻³. Two father–son pairs had mutations at two different loci in 11 Y-STRs. The number of pairs with mutations at multiple loci increased to five when the mutation event was investigated for haplotype transfer at 28 Y-STRs including 17 Yfiler loci and 11 Y-STRs examined in this study: four father–son pairs had mutations at two loci, and one pair had mutations at three loci. Overall, mutations were frequently observed at DYS449, DYS576 and DYS627 loci, which are known to be rapidly mutating Y-STRs. Mutation rate estimates at most loci were not significantly different from rates in other populations, but estimates for DYF387S1, DYS518 and DYS570 were considerably lower in the Korean population than in other populations.     

Genetic polymorphisms of 10 X-chromosome STR loci in Chinese Daur ethnic minority group

The population genetic data of 10 X-chromosomal short tandem repeats (STR) loci DXS101, DXS7130, DXS6804, DXS7133, DXS7132, DXS6799, DXS8378, DXS6789, DXS7423 and HPRTB were analyzed in samples of unrelated individuals from Chinese Daur population. Average heterozygosity of above 10 STR loci was 0.6489 and the DXS6789 was the most polymorphic. The exact test for female data showed no significant deviation from the Hardy–Weinberg equilibrium (P > 0.05). Allele frequencies between male and female samples were not significantly different in all examined loci. Further, the allelic frequencies of Daur ethnic population were compared with those of other populations, and most of loci were significantly different from each other (P = 0.05). Presented study is potential extension to a battery of autosomal systems in forensic application in the region, and enriches Chinese ethnical genetic informational resources.     

Non-random distribution of 17 Y-chromosome STR loci in different areas of Sardinia

Allele frequencies of 17 Y-chromosome short tandem repeat (STR) loci, included in the AmpFlSTR^® Y-FilerTM amplification kit, were analyzed for the first time in different samplings (N = 268) from Sardinia, Italy. Samples were collected from three isolated populations (N = 139) and three open populations (N = 129). A total of 230 unique haplotypes were detected; the observed haplotype diversity and discrimination capacity were 0.998 and 0.858, respectively. The data presented confirm that Sardinian population is well differentiated from other Italian and Mediterranean populations. Although regarded as a homogeneous population, substantial heterogeneity was detected when Sardinian isolated villages or microareas were analyzed. Our results highlights the importance of building a Sardinia-own database, organized by small areas, as a powerful tool for both forensic applications and population genetics studies.     

Identifying the most likely contributors to a Y-STR mixture using the discrete Laplace method

In some crime cases, the male part of the DNA in a stain can only be analysed using Y chromosomal markers, e.g. Y-STRs. This may be the case in e.g. rape cases, where the male components can only be detected as Y-STR profiles, because the fraction of male DNA is much smaller than that of female DNA, which can mask the male results when autosomal STRs are investigated. Sometimes, mixtures of Y-STRs are observed, e.g. in rape cases with multiple offenders. In such cases, Y-STR mixture analysis is required, e.g. by mixture deconvolution, to deduce the most likely DNA profiles from the contributors.We demonstrate how the discrete Laplace method can be used to separate a two person Y-STR mixture, where the Y-STR profiles of the true contributors are not present in the reference dataset, which is often the case for Y-STR profiles in real case work. We also briefly discuss how to calculate the weight of the evidence using the likelihood ratio principle when a suspect's Y-STR profile fits into a two person mixture. We used three datasets with between 7 and 21 Y-STR loci: Denmark (n = 181), Somalia (n = 201) and Germany (n = 3443). The Danish dataset with 21 loci was truncated to 15 and 10 loci to examine the effect of the number of loci. For each of these datasets, an out of sample simulation study was performed: A total of 550 mixtures were composed by randomly sampling two haplotypes, h₁ and h₂, from the dataset.We then used the discrete Laplace method on the remaining data (excluding h₁ and h₂) to rank the contributor pairs by the product of the contributors’ estimated haplotype frequencies. Successful separation of mixtures (defined by the observation that the true contributor pair was among the 10 most likely contributor pairs) was found in 42–52% of the cases for 21 loci, 69–75% for 15 loci and 92–99% for 10 loci or less depending on the dataset and how the discrete Laplace model was chosen. Y-STR mixtures with many loci are difficult to separate, but even haplotypes with 21 Y-STR loci can be separated.     

A novel multiplex assay amplifying 13 Y-STRs characterized by rapid and moderate mutation rate

As microsatellites located on Y chromosome mutate with different rates, they may be exploited in evolutionary studies, genealogical testing of a variety of populations and even, as proven recently, aid individual identification. Currently available commercial Y-STR kits encompass mostly low to moderately mutating loci, making them a perfect choice for the first two applications. Some attempts have been made so far to utilize Y-STRs to provide a discriminatory tool for forensic purposes. Although all 13 rapidly mutating Y-STRs were already multiplexed, no single assay based on single-copy markers allowing at least a portion of close male relatives to be differentiated from one another is available. To fill in the blanks, we constructed and validated an assay comprised of single-copy Y-STR markers only with a mutation rate ranging from 8 × 10⁻³ to 1 × 10⁻². Performance of the resulting combination of nine RM Y-STRs and four moderately mutating ones was tested on 361 father–son pairs and 1326 males from 9 populations revealing an overall mutation rate of 1.607 × 10⁻¹ for the assay as a whole. Application of the proposed 13 Y-STR set to differentiation of haplotypes present among homogenous population of Buryats resulted in a threefold increase of discrimination as compared with 10 Y-STRs from the PowerPlex^® Y.     

Haplotype diversity of 17 Y-chromosome STR loci in Han population from different areas of Sichuan Province,Southwest China

The distribution of 17 Y-chromosome short tandem repeat (STR) loci, included in the AmpFlSTR®Yfiler™ amplification kit, were analyzed in six different samplings (N = 878) from Sichuan, China. Haplotype diversity and discrimination capacity (DC) values were calculated. Pairwise Rst values were evaluated in AMOVA analysis and visualized through multidimensional scaling (MDS). A total of 547 unique haplotypes were detected. The observed haplotype diversity and discrimination capacity were 0.9995 and 0.7745, respectively. The homogeneity of Sichuan Han population was detected when microareas were analyzed. This population exhibited no significant genetic difference to both of the minorities in reference databases, Mongolian and Manchu, which had been through mass ethnic amalgamation with Sichuan Han population in history.     

Genetic variation of 17 autosomal STR loci in the Lahu population from Yunnan and phylogenetic structure exploration among 28 populations

This study evaluated the genetic variation of 17 autosomal short tandem repeat (STR) loci included in the PowerPlex® 18D Kit. Samples of 562 unrelated healthy Lahu individuals living in Yunnan Province in southwestern China were investigated. The data were analyzed to provide information on allele frequencies and other statistical parameters relevant to the forensic population. Of the 17 loci, 16 reached the Hardy–Weinberg equilibrium after Bonferroni correction. A total of 176 alleles were identified in 17 STR loci, and allele frequencies ranged from 0.000 890 to 0.578 292. The combined discrimination power (CPD) and probability of excluding paternity (CPE) of the 17 STR loci were 0.999 999 999 999 999 999 489 and 0.999 998 301 753 122. The genetic relationships among 28 populations were also estimated.     

Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans

Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif. Repeat motif and flanking region sequence variation have been described for major population groups, however, not for more isolated populations. Flanking region sequence variation in STR and single nucleotide polymorphism (SNP) loci in the Yavapai population was analyzed using the ForenSeq™ DNA Signature Prep Kit and STRait Razor v2s. Seven and 14 autosomal STRs and identity-informative single nucleotide polymorphisms (iiSNPs), respectively, had some degree of flanking region variation. Three and four of these identity-informative loci, respectively, showed ≥5% increase in expected heterozygosity. The combined length- and sequence-based random match probabilities (RMPs) for 27 autosomal STRs were 6.11 × 10⁻²⁶ and 2.79 × 10⁻²⁹, respectively. When combined with 94 iiSNPs (a subset of which became microhaplotypes) the combined RMP was 5.49 × 10⁻⁶³. Analysis of length-based and sequence-based autosomal STRs in STRUCTURE indicated that the Yavapai are most similar to the Hispanic population. While producing minimal increase in X- and Y-STR discrimination potential, access to flanking region data enabled identification of one novel X-STR and three Y-STR alleles relative to previous reports. Five ancestry-informative SNPs (aiSNPs) and two phenotype-informative SNPs (piSNPs) exhibited notable flanking region variation.     

Genetic variation of 15 autosomal microsatellite loci in a Tamil population from Tamil Nadu,Southern India

The genetic profiles for 15 autosomal microsatellite loci were analyzed in a Tamil population from Southern India to study the genetic diversities and relatedness of this population with other national and global populations. Statistical analyses of the data revealed all loci were within Hardy–Weinberg Equilibrium (HWE) expectations with the exception of the locus D5S818 (p = 0.011). A significantly greater inter-individual variation (Fst = 99%) observed within the individuals among the four subgroups in this study and low population differentiation (Fst = 1%) suggests relative genetic closeness of these four subgroups. This indicates that the populations in the southern region of India might have a common ancestry or probably experienced high gene flow during the period of their coexistence. The Neighbor Joining tree derived from genetic distances of samples from this study and other national and global populations show clustering of all the Indian populations in one branch of the tree while the African and Middle Eastern populations cluster in a separate branch. Principal Co-ordinate Analysis of the genetic distance data show clustering similar to the NJ tree.     

Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms

We analyzed 67 short tandem repeat polymorphisms from the non-recombining part of the Y-chromosome (Y-STRs), including 49 rarely studied simple single-copy (ss)Y-STRs and 18 widely used Y-STRs, in 590 males from 51 populations belonging to 8 worldwide regions (HGDP-CEPH panel). Although autosomal DNA profiling provided no evidence for close relationship, we found 18 Y-STR haplotypes (defined by 67 Y-STRs) that were shared by two to five men in 13 worldwide populations, revealing high and widespread levels of cryptic male relatedness. Maximal (95.9%) haplotype resolution was achieved with the best 25 out of 67 Y-STRs in the global dataset, and with the best 3–16 markers in regional datasets (89.6–100% resolution). From the 49 rarely studied ssY-STRs, the 25 most informative markers were sufficient to reach the highest possible male lineage differentiation in the global (92.2% resolution), and 3–15 markers in the regional datasets (85.4–100%). Considerably lower haplotype resolutions were obtained with the three commonly used Y-STR sets (Minimal Haplotype, PowerPlex Y^®, and AmpFlSTR^® Yfiler^®). Six ssY-STRs (DYS481, DYS533, DYS549, DYS570, DYS576 and DYS643) were most informative to supplement the existing Y-STR kits for increasing haplotype resolution, or – together with additional ssY-STRs – as a new set for maximizing male lineage differentiation. Mutation rates of the 49 ssY-STRs were estimated from 403 meiotic transfers in deep-rooted pedigrees, and ranged from ∼4.8 × 10⁻⁴ for 31 ssY-STRs with no mutations observed to 1.3 × 10⁻² and 1.5 × 10⁻² for DYS570 and DYS576, respectively, the latter representing the highest mutation rates reported for human Y-STRs so far. Our findings thus demonstrate that ssY-STRs are useful for maximizing global and regional resolution of male lineages, either as a new set, or when added to commonly used Y-STR sets, and support their application to forensic, genealogical and anthropological studies.     

Developmental validation of the PowerPlex® Y23 System: A single multiplex Y-STR analysis system for casework and database samples

The PowerPlex^® Y23 System combines the seventeen Y-STR loci in current commercially available Y-STR kits (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4) with six new highly discriminating Y-STR loci (DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643). These six new loci have higher gene diversities than most of the loci in other commercial Y-STR analysis kits, allowing for further distinction between unrelated male individuals. In addition, the inclusion of two rapidly mutating Y-STR loci may allow for the discrimination of related individuals. The PowerPlex^® Y23 System is designed to amplify DNA from purified extracts as well as direct amplification from substrates used to collect database samples (e.g. swabs and storage cards).Validation of the PowerPlex^® Y23 System includes all of the studies required by the FBI and SWGDAM. The results demonstrate that the PowerPlex^® Y23 System is a robust and reliable amplification kit capable of overcoming high concentrations of commonly encountered inhibitors such as hematin, humic acid, and tannic acid. Full profiles are consistently detected with 62.5 pg of male DNA, even in the presence of excessive amounts of female DNA, establishing the PowerPlex^® Y23 System as a sensitive method for Y-STR testing. Complete Y-STR profiles are detected from mixed samples with 62.5 pg of male DNA in a background of 400 ng of female DNA or 125 pg of male DNA mixed with 3000 ng of female DNA.     

Next generation sequencing of SNPs using the HID-Ion AmpliSeq™ Identity Panel on the Ion Torrent PGM™ platform

The HID-Ion AmpliSeq™ Identity Panel (the HID Identity Panel) is designed to detect 124-plex single nucleotide polymorphisms (SNPs) with next generation sequencing (NGS) technology on the Ion Torrent PGM™ platform, including 90 individual identification SNPs (IISNPs) on autosomal chromosomes and 34 lineage informative SNPs (LISNPs) on Y chromosome. In this study, we evaluated performance for the HID Identity Panel to provide a reference for NGS-SNP application, focusing on locus strand balance, locus coverage balance, heterozygote balance, and background signals. Besides, several experiments were carried out to find out improvements and limitations of this panel, including studies of species specificity, repeatability and concordance, sensitivity, mixtures, case-type samples and degraded samples, population genetics and pedigrees following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. In addition, Southern and Northern Chinese Han were investigated to assess applicability of this panel. Results showed this panel led to cross-reactivity with primates to some extent but rarely with non-primate animals. Repeatable and concordant genotypes could be obtained in triplicate with one exception at rs7520386. Full profiles could be obtained from 100 pg input DNA, but the optimal input DNA would be 1 ng–200 pg with 21 initial PCR cycles. A sample with ≥20% minor contributor could be considered as a mixture by the number of homozygotes, and full profiles belonging to minor contributors could be detected between 9:1 and 1:9 mixtures with known reference profiles. Also, this assay could be used for case-type samples and degraded samples. For autosomal SNPs (A-SNPs), F_ST across all 90 loci was not significantly different between Southern and Northern Chinese Han or between male and female samples. All A-SNP loci were independent in Chinese Han population. Except for 18 loci with H_e <0.4, most of the A-SNPs in the HID Identity Panel presented high polymorphisms. Forensic parameters were calculated as >99.999% for combined discrimination power (CDP), 0.999999724 for combined power of exclusion (CPE), 1.390 × 10¹¹ for combined likelihood ratio (CLR) of trios, and 2.361 × 10⁶ for CLR of motherless duos. For Y-SNPs, a total of 8 haplotypes were observed with the value of 0.684 for haplotype diversity. As a whole, the HID Identity Panel is a well-performed, robust, reliable and high informative NGS-SNP assay and it can fully meet requirements for individual identification and paternity testing in forensic science.     

Population and forensic data for three sets of forensic genetic markers in four ethnic groups from Iran: Persians,Lurs, Kurds and Azeris

A total of 255 individuals (Persians, Lurs, Kurds and Azeris) from Iran were typed for three sets of forensic genetic markers with the NGM SElect™, DIPplex^® and Argus X-12 kits. Statistically significant deviations (P ≤ 0.002) from Hardy–Weinberg expectations were observed for the insertion-deletion markers HLD97 and HLD93 after Holm–Šidák correction. Statistically significant (P < 0.05) levels of linkage disequilibrium were observed between markers within two of the four studied X-chromosomal linkage groups. AMOVA analyses of the three sets of markers did not show population structure when the individuals were grouped according to their ethnic group. The Iranian population grouped closely to populations living geographically near to Iran based on pairwise F_ST distances. The matching probabilities ranged from 1 in 3.2 × 10⁷ males by using haplotype frequencies of four X-chromosomal haplogroups to 1 in 3.4 × 10²¹ individuals for the 16 autosomal STRs.