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.

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs.

Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male-female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants ("DYS518~.2" alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.

Title: Developmental validation of Y-SNP pedigree tagging system: A panel via quick ARMS PCR.

The Y chromosomal short tandem repeats (Y-STRs) have been used widely to establish paternal relatedness and examine sub-structures in different geographical regions. However, the applications of Y-STRs showed their limitations when it comes to resolving the complicated relationships within close relatives or among unrelated individuals from different geographic areas. Here, we overcome these limitations by introducing a new strategy for Y-SNP multiplex typing using rapid ARMS (amplification-refractory mutation system) PCR. Newly developed Y-SNP Pedigree Tagging System is able to profile 24 Y-SNPs in a single reaction while the whole process takes 4-5 hours. The panel precisely defines the 11 haplogroups (E-M96, D-JST021355, N-M231, C-M130, O-P186, I-M170, IJ-M429, K-M9, QR-M45, G-M201, and IJK-M522) and 13 sub-haplogroups (D1a1a1-N1, D1a2a-P47, C2-M217, N1a1-M46, O1a-M119, O1b-M268, O1b2-M176, O2-M122, O2a1-KL1, O2a2-P201, O2a2b-P164, O2a2a1a2-M7 and O2a2b1a1-M117). This system could contribute to providing the haplogroup affiliation of unknown pedigree and resolving the sub-structures of East Asian populations. In this study, the multiplex system was validated for: ability to detect degraded DNA, sensitivity, species specificity, reproducibility/repeatability, stability, performance in different scenarios, mixture studies, PCR amplification conditions, and population surveys. The Y-SNP information showed a consistent pattern within 40 father-son or brother-brother pairs. The results of this multiplex system showed the different distribution patterns of male donors from two Chinese Han populations. In this study, we try to discriminate the suspect's pedigree on the level of Y-SNP haplogroups. These results show that Y-SNP Pedigree Tagging System is a robust and reliable amplification kit which can be used for male haplogroup determination.

[Study on the determinations of Ni, Fe, Mo, Mn and B in Ti/TiC composite material by atomic emission spectrometry].

The present paper describes the determination of trace Ni, Fe, Mo, Mn and B in Ti/TiC composite material using carbon powder, calcium carbonate, cupric oxide and beryllium oxide-as buffer by atomic emission spectrometry (ASE). Be 298.61 nm was selected as internal standard line. Sample separation and chemistry treatment were not requirel. The sample was directly loaded into ordinary electrode. The method is simple, rapid and accurate. The requirement of determination, and factors of influence were studied. A new method has developed for the determination of Ni, Fe, Mo, Mn and B. The analysis lines of Ni, Fe, Mo, Mn and B are 300.36, 248.33, 315.82, 260.57 and 249.68 nm respectively. The internal standard line of Be is 298.61 nm. The linear ranges of the determination of Ni, Fe, Mo, Mn and B are 0.003%-0.30%, 0.001%-0.20%, 0.003%-0.30%, 0.001%-0.20%, 0.001%-0.20% respectively. The detection limits of Ni, Fe, Mo, Mn and B are 0.003%; 0.001%, 0.003%, 0.001% and 0.001% respectively. The ranges of the recovery of Ni, Fe, Mo, Mn and B are 95.80%-104.8%, and the standard relative deviations (RSD) are less than 5.0% (n = 9). The method has been applied to the determination of Ni, Fe, Mo, Mn and B with satisfactory results.

[Atomic emission spectrometry determination of Au, Pt and Pd after separation and enrichment by hyperbranched polymer].

The present paper shows that the trace amount of gold, platinum and palladium in hydrochloric acid solution can be concentrated by hyperbranched polymer. The new reagent has a rapid adsorption rate and big concentrating capacity. The determination of trace Au, Pt and Pd in sample using carbon powder and strontium carbonate as buffer was carried out by atomic emission spectrometry(AES). Zirconium was selected as internal standard line. The sample was directly loaded into ordinary electrode. The method is simple, rapid and accurate. The condition of determination, and factors of influence were studied. The analysis line of Au, Pt and Pd is 312.3, 306.5 and 311.4 nm respectively. The internal standard line of Zr is 310.7 nm. The linear range of the determination of Au, Pt and Pd is 0-0. 20%, 0-0. 40% and 0-0. 20% respectively. The detection limit of Au, Pt and Pd is 0.010%, 0.0030% and 0.0030% respectively. The method has been applied to the determination of Au, Pt and Pd with satisfactory results.

[Determination of ten trace rare earth elements in the sample by atomic emission spectrometry].

This paper describes the determination of trace La, Ce, Pr, Nd, Sm, Gd, Tb, Dy, Yb and Lu in the sample, using carbon powder, potassium sulfate, barium sulfate, strontium sulfate, and scandium chloride as buffer, by atomic emission spectrometry (AES). Scandium was selected as internal standard line. Sample separation and chemical treatment were not required. The sample was directly loaded into ordinary electrode. The method is simple, rapid and accurate. The determination requirement and influence factors were studied. A new method was developed for the determination of ten rare earth elements, for which the detection limit is smaller than 0.030%, and the range of the recovery is 94%-105%. The results of these elements in standard sample are in agreement with certified values, and the RSD is smaller than 5% (n = 9). The method has been applied to the determination of ten rare earth elements with satisfactory results.

[Determination of trace zirconium and hafniumin sample by atomic emission spectrometry].

This paper describes the determination of trace Zr and Hf in the sample using carbon powder and titanium oxide as the buffer by Atomic Emission Spectrometry (AES). Titanium was selected for the internal standard line. Sample separation and chemical treatment were not required. The sample was directly loaded into an ordinary electrode. The method is simple, rapid and accurate. The conditions for the determination, and the factors of influence have been studied. A new method has been developed for the determination of zirconium and hafnium. The analytical lines of Zr and Hf were 327.3 and 286.6 nm respectively. The internal standard line of Ti was 308.8 nm. The linear range of the determination of Zr and Hf was 0-0.50% and 0-0.25% respectively. The detection limit of Zr and Hf was 0.0010% and 0.010% respectively. The range of the recovery of zirconium and hafnium was 96.67%-105.0%. The results for these elements in standard sample are in agreement with certified values with a precision of 3.61% RSD for Zr (n = 9), and 4.82% RSD for Hf (n = 9). The method has been applied to the determination of Zr and Hf with satisfactory results.