Haplotypic polymorphisms and mutation rate estimates of 22 Y-chromosome STRs in the Northern Chinese Han father-son pairs

Improving the strategy to identify historical military remains: a literature review and Y-STR meta-analysis

The identification of historical military remains by Unrecovered War Casualties-Army (UWC-A) currently relies on Y-chromosome Short Tandem Repeat (Y-STR) testing when maternal relatives are not available, or when a mitochondrial DNA match does not provide sufficient certainty of identification. However, common Y-STR profiles (using Yfiler™) between sets of remains or families often prevent identification. To resolve these cases, an investigation of additional Y-DNA markers is needed for their potential inclusion into the DNA identification strategy. The number of genetic transmissions between missing soldiers and their living relatives needs to be considered to avoid false exclusions between paternal relatives. Analysis of 236 World War I/II (WWI/II) era pairs of relatives identified up to seven genetic transmissions between WWII soldiers and their living relatives, and nine for WWI. Previous Y-STR meta-analyses were published approximately 10 years ago when rapidly mutating markers were relatively new. This paper reports a contemporary literature review and meta-analysis of 35 studies (which includes 23 studies not previously used in meta-analysis) and 23 commonly used Y-STR's mutation rates to inform the inclusion of additional loci to UWC-A's DNA identification strategy. Meta-analysis found mutation data for a given Y-STR locus could be pooled between studies and that the mutation rates were significantly different between some loci (at P < 0.05). Based on this meta-analysis, we have identified two additional markers from PowerPlex® Y23 for potential inclusion in UWC-A's identification strategy. Further avenues for potential experimental exploration are discussed.

Key points

From 236 UWC-A pairs of relatives, we observed up to nine genetic transmissions between WWI soldiers and their living relatives, and seven for WWII.MedCalc® software for meta-analysis utilizing the Freeman-Tukey transformation was run, which analysed 35 published studies and 23 commonly used loci. Previous Y-STR mutation rate meta-analyses are now 10 years old; this paper includes 23 studies that were not included in previous meta-analyses.Through meta-analysis, we identify two markers from PowerPlex® Y23 for potential inclusion in UWC-A's historical remains identification strategy (alongside Yfiler™). We discuss potential next steps for experimental exploration of additional Y-DNA markers.

Genetic Polymorphism Analysis of 24 Y-STRs in a Han Chinese Population in Luzhou, Southwest China

Han is the largest of China's 56 ethnic groups and the most populous ethnic group in the world. The Luzhou region is located in southwest China, at the junction of three provinces. The unique historical factors contribute to the genetic polymorphism information. Short tandem repeats (STRs) are highly polymorphic, but the polymorphism of the Y chromosomal STRs (Y-STRs) loci in the Luzhou region is still unclear. It is of great significance to provide Y-STRs genetic data for the Han population from the Luzhou areas of southwest China. A total of 910 unrelated male individuals of the Han population from the Luzhou area were recruited, and 24 Y-STRs were analyzed. The population structure and phylogenetic relationships were compared with those of another 11 related Han populations. A total of 893 different haplotypes were achieved from 910 samples, of which 877 (98.21%) haplotypes were unique. Haplotype diversity and discrimination were 0.999956 and 0.981319, respectively. The lowest genetic diversity of DYS437 is 0.4321, and the highest genetic diversity of DYS385a/b is 0.9642. Pair-to-pair genetic distance and relative probability values indicate that Luzhou Han people are close to Sichuan Han people, Guangdong Han people, and Hunan Han people, which is consistent with geographical distribution, historical influence, and economic development. The 24 Y-STR markers of the southwest Luzhou Han population were highly polymorphic, which provided us with genetic polymorphism information and enriched the population genetic database. Therefore, it is of great value to our forensic applications and population genetics research.

The sequence of the repetitive motif influences the frequency of multistep mutations in Short Tandem Repeats

Microsatellites, or Short Tandem Repeats (STRs), are subject to frequent length mutations that involve the loss or gain of an integer number of repeats. This work aimed to investigate the correlation between STRs' specific repetitive motif composition and mutational dynamics, specifically the occurrence of single- or multistep mutations. Allelic transmission data, comprising 323,818 allele transfers and 1,297 mutations, were gathered for 35 Y-chromosomal STRs with simple structure. Six structure groups were established: ATT, CTT, TCTA/GATA, GAAA/CTTT, CTTTT, and AGAGAT, according to the repetitive motif present in the DNA leading strand of the markers. Results show that the occurrence of multistep mutations varies significantly among groups of markers defined by the repetitive motif. The group of markers with the highest frequency of multistep mutations was the one with repetitive motif CTTTT (25% of the detected mutations) and the lowest frequency corresponding to the group with repetitive motifs TCTA/GATA (0.93%). Statistically significant differences (α = 0.05) were found between groups with repetitive motifs with different lengths, as is the case of TCTA/GATA and ATT (p = 0.0168), CTT (p < 0.0001) and CTTTT (p < 0.0001), as well as between GAAA/CTTT and CTTTT (p = 0.0102). The same occurred between the two tetrameric groups GAAA/CTTT and TCTA/GATA (p < 0.0001) - the first showing 5.7 times more multistep mutations than the second. When considering the number of repeats of the mutated paternal alleles, statistically significant differences were found for alleles with 10 or 12 repeats, between GATA and ATT structure groups. These results, which demonstrate the heterogeneity of mutational dynamics across repeat motifs, have implications in the fields of population genetics, epidemiology, or phylogeography, and whenever STR mutation models are used in evolutionary studies in general.

Population genetic study of 17 Y-STR Loci of the Sorani Kurds in the Province of Sulaymaniyah, Iraq

Background

The Kurds as an ethnic group are believed to be a combination of earlier Indo-European tribes who migrated and inhabited a mountainous area thousands of years ago. However, as it is difficult to describe the precise history of their origin, it is necessary to investigate their population relationship with other geographical and ethnic groups.

Results

Seventeen Short Tandem Repeat markers on the Y chromosome (Y-STR) included in the AmpFLSTR™ Yfiler™ PCR Amplification Kit (Thermo Fisher Scientific, USA) were used to type DNA samples from the Sorani (Central) Kurdish population in Sulaymaniyah province. One hundred fifty-seven haplotypes were obtained from 162 unrelated male individuals. The highest and lowest gene diversities were DYS385a/b (GD = 0.848) and DYS392 (GD = 0.392), respectively. The haplotypes were used to predict the most likely haplogroups in the Sulaymaniyah population.

Conclusion

Haplogroup prediction indicated predominance (28%) of subclade J2 (44/157) in the Sorani Kurds, northeast of Iraq. The pairwise genetic distance results showed that the Kurdish group clustered along with Asian populations, whereas the furthest countries were Europeans and Africans.

Empirical Evidence on Enhanced Mutation Rates of 19 RM-YSTRs for Differentiating Paternal Lineages

Rapidly mutating Y-chromosomal short tandem repeats (RM Y STRs) with mutation rates ≥ 10⁻² per locus per generation are valuable for differentiating amongst male paternal relatives where standard Y STRs with mutation rates of ≤10⁻³ per locus per generation may not. Although the 13 RM Y STRs commonly found in commercial assays provide higher levels of paternal lineage differentiation than conventional Y STRs, there are many male paternal relatives that still cannot be differentiated. This can be improved by increasing the number of Y STRs or choosing those with high mutation rates. We present a RM Y STR multiplex comprising 19 loci with high mutation rates and its developmental validation (repeatability, sensitivity and male specificity). The multiplex was found to be robust, reproducible, specific and sensitive enough to generate DNA profiles from samples with inhibitors. It was also able to detect all contributor alleles of mixtures in ratios up to 9:1. We provide preliminary evidence for the ability of the multiplex to discriminate between male paternal relatives by analyzing large numbers of male relative pairs (536) separated by one to seven meioses. A total of 96 mutations were observed in 162 meioses of father–son pairs, and other closely related male pairs were able to be differentiated after 1, 2, 3, 4, 5, 6 and 7 meiosis in 44%, 69%, 68%, 85%, 0%, 100% and 100% of cases, respectively. The multiplex offers a noticeable enhancement in the ability to differentiate paternally related males compared with the 13 RM Y STR set. We envision the future application of our 19 RM Yplex in criminal cases for the exclusion of male relatives possessing matching standard Y STR profiles and in familial searching with unknown suspects. It represents a step towards the complete individualization of closely related males.

Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population

Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.

Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing

Short tandem repeats (STRs) are the preferred genetic markers in forensic DNA analysis, routinely measured by capillary electrophoresis (CE) method based on the fragment length features. While, the massive parallel sequencing (MPS) technology could simultaneously target a large number of intriguing forensic STRs, bypassing the intrinsic limitations of amplicon size separation and accessible fluorophores in CE, which is efficient and promising for enabling the identification of forensic biological evidence. Here, we developed a novel MPS-based Forensic Analysis System Multiplecues SetB Kit of 133-plex forensic STR markers (52 STRs and 81 Y-STRs) and one Y-InDel (M175) based on multiplex PCR and single-end 400 bp sequencing strategy. This panel was subjected to developmental validation studies according to the SWGDAM Validation Guidelines. Approximately 2185 MPS-based reactions using 6 human DNA standards and 8 male donors were conducted for substrate studies (filter paper, gauze, cotton swab, four different types of FTA cards, peripheral venous blood, saliva, and exfoliated cells), sensitivity studies (from 2 ng down to 0.0625 ng), mixture studies (two-person DNA mixtures), PCR inhibitor studies (seven commonly encountered PCR inhibitors), species specificity studies (11 non-human species), and repeatability studies. Results of concordance studies (413 Han males and 6 human DNA standards) generated by STRait Razor and in-house Python scripts indicated 99.98% concordance rate in STR calling relative to CE for STRs between 41,900 genotypes at 100 STR markers. Moreover, the limitations of present studies, the nomenclature rules and forensic MPS applications were also described. In conclusion, the validation studies based on ~ 2200 MPS-based and ~ 2500 CE-based DNA profiles demonstrated that the novel MPS-based panel meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities, and the STR nomenclature rules should be further regulated to integrate the inconformity between MPS-based and CE-based methods.

The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration

A sample of 606 Swiss individuals has been characterized for 27 Y-STR and 34 Y-SNPs, defining major European haplogroups. For the first time, a subsample from the southernmost part of Switzerland, the Italian speaking canton Ticino, has been included. The data reveals significant intra-national differences in the distribution of haplogroups R1b-U106, R1b-U152, I1 and J2a north and south of the alpine divide, with R1b-U152 being the most frequent haplogroup among all Swiss subpopulations, reaching 26 % in average and 53 % in the Ticino sample. In addition, a high percentage of haplogroup E1b1b-M35 in Eastern Switzerland corresponds well with data reported from Western Austria. In general, we detected a low level of differentiation between the subgroups north of the alpine divide. The dataset also revealed a variety of microvariants. Some of them were previously known to be associated with particular haplogroups. However, we discovered one microvariant in DYS533 that seems to be closely associated with haplogroup I2-P215 (xM223). This association had not yet been reported to date. The concordance study with two STR-kits suggests that the DYS533 microvariant is due to an InDel in the flanking regions of the marker. One individual carried a large deletion, frequently detected in people of East Asian ancestry, encompassing the amelogenin locus. To our knowledge, this is the first time that such a deletion has been observed within European haplogroup R1b-U152. This is the first comprehensive Y chromosomal dataset for Switzerland, demonstrating significant population substructure due to an intra-national geographical barrier.

Analyzing genetic polymorphism and mutation of 44 Y-STRs in a Chinese Han population of Southern China

Short tandem repeat on the non-recombining part of chromosome Y with paternally inheritable capability is a valuable tool in the studies of forensic genetics, population genetics and anthropology. The mutation rate of Y-STR is an important parameter in the applications. A total of 629 haplotypes at 44 Y-STR markers were found in 629 unrelated males of our population. Mutation rates at 44 Y-STR loci ranged from 0 (CI: 0-5.70 × 10^-3) to 40.63 × 10^-3 (25.90 × 10^-3-57.2 × 10^-3) in our population. A higher mutation rate was noted at DYS612, DYS449, DYS547, DYS518, DYS576, DYS627, DYF403S1b, DYF387S1, DYS385a/b, DYS527a/b, DYF404S1, DYF403S1a and DYF399S1 in this population. The Y-STR set showed a higher discrimination capacity in forensic applications, and the present study provided reference data for the application of forensic and population genetics.