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

Yin, Caiyong; Ren, Yijie; Adnan, Atif; Tian, Junzhe; Guo, Kai; Xia, Mingxu; He, Ziwei; Zhai, Dian; Chen, Xueyun; Wang, Lei; Li, Xin; Qin, Xiaoqun; Li, Shilin; Li, Jin

doi:10.1016/j.fsigen.2020.102271

Cited by 11 publications

(8 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We considered the following 24 binary Y-SNP markers within the Y-SNP Pedigree Tagging System (Suzhou Microread Genetics, Suzhou, Jiangsu, China) [ 18 ]: E-M96, D-JST021355, N-M231, C-M130, O-P186, I-M170, IJ-M429, K-M9, QR-M45, G-M201, IJK-M522, 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. The nomenclature definition of these makers was strictly adopted according to the Y Chromosome Consortium (YCC) [ 6 , 7 ], International Society of Genetic Genealogy (ISOGG, website: ), Phylotree [ 19 ], and Y Chromosome Haplotype Reference Database (YHRD) [ 20 , 21 ].…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

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

Yin

et al. 2020

Genes

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Methodsmentioning

confidence: 99%

“…We considered the following 24 binary Y-SNP markers within the Y-SNP Pedigree Tagging System (Suzhou Microread Genetics, Suzhou, Jiangsu, China) [18]…”

Section: Typing Of 24 Y Haplogroup-determining Snp Markers and 27 Y-smentioning

confidence: 99%

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

Yin

et al. 2020

Genes

Self Cite

View full text Add to dashboard Cite

show abstract

“…We analyzed 24 Y-SNP markers using the Y-SNP pedigree marker system (Pedigree Tagging System (Suzhou Microread Genetics, Suzhou, Jiangsu, China)) [ 9 ], and the primary haplogroups included E-M96, D-JST021355, N-M231, C-M130, O-P186, I-M170, IJ-M429, K-M9, QR-M45, G-M201, and IJK-M522. Subhaplogroups included D1a1a1-N1, D1a2a-P47, O1a-M119, O1b-M268, O1b2-M176, O2-M122, O2a1-KL1, O2a2-P201, O2a2b-P164, O2a2a1a2-M7, O2a2b1a1-M117, C2-M217, and N1a1-M46.…”

Section: Methodsmentioning

confidence: 99%

Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs

Zhang

Zhen

Wang³

et al. 2022

Genes

Self Cite

View full text Add to dashboard Cite

Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of Pudong Han (n = 689) and Chongming Han (n = 530) in Shanghai. The haplotype diversity of the Y filer platinum genotyping system was the highest in the Han population in the Pudong area of Shanghai (0.99996) and Chongming Island (0.99997). The proportion of unique haplotypes was 97.10% (Pudong) and 98.49% (Chongming), respectively. The multidimensional scaling analysis and phylogenetic analysis were performed according to the genetic distance Rst, which was calculated based on the Y-STR gene frequency data. Moreover, we made a comparison on the frequency distribution analysis and principal component analysis of haplogroups in both populations. As a result, Shanghai Pudong Han, Chongming Island Han, and Jiangsu Han were determined to have a strong genetic affinity. The haplogroup distribution characteristics of the Pudong Han and Chongming Han populations were similar to those of the southern Han population. The results of haplotype network analysis showed that Jiangsu Wujiang Han and Jiangsu Changshu Han had more paternal genetic contributions to the formation of Shanghai Pudong Han and Chongming Island Han. Through the joint analysis of SNPs and STRs, this study deeply analyzed the paternal genetic structure of the Pudong Han and Chongming Han populations. The addition of Y-SNP haplogroups to forensic applications can provide information for pedigree investigation.

show abstract

“…The Y-chromosomal phylogeny has become an essential pillar of forensic pedigree searches and paternal ancestry inference. On this basis, several Y-SNP panels of different resolutions have been developed and validated in geographically and linguistically diverse populations [25][26][27][28][29][30][31]. Due to the popularity of the capillary electrophoresis (CE) platform, currently available dedicated Y-SNP genotyping tools developed based on this system have restrictions on the number of Y-SNPs analyzed simultaneously [26,28,29,32,33], hindering the dissection of paternal biogeographical ancestry at high resolution.…”

Section: Introductionmentioning

confidence: 99%

“…On this basis, several Y-SNP panels of different resolutions have been developed and validated in geographically and linguistically diverse populations [25][26][27][28][29][30][31]. Due to the popularity of the capillary electrophoresis (CE) platform, currently available dedicated Y-SNP genotyping tools developed based on this system have restrictions on the number of Y-SNPs analyzed simultaneously [26,28,29,32,33], hindering the dissection of paternal biogeographical ancestry at high resolution. Here, targeted NGS technologies are up-and-coming, which have the capability to sequence multiple targets and samples simultaneously and can take advantage of a large number of Y-SNPs for forensic investigations on a detailed level.…”

Section: Introductionmentioning

confidence: 99%

Multiple founding paternal lineages inferred from the newly-developed SNPSeqTyper 639 Y-SNP panel suggested the complex admixture and migration history of Chinese people

Wang

Chen

et al. 2022

Preprint

View full text Add to dashboard Cite

Non-recombining regions of the Y-chromosome are inherited male-specifically and recorded the evolutionary traces of male human populations. Recent whole Y-chromosome sequencing studies have identified previously unrecognized population divergence, expansion and admixture processes, which promotes a better understanding and application of the observed patterns of Y-chromosome genetic diversity. Here, we developed one highest-resolution Y-SNP panel for forensic pedigree search and paternal biogeographical ancestry inference, which included 639 phylogenetically informative SNPs (Y-SNPs). We genotyped these loci in 1033 Chinese male individuals from 33 ethnolinguistically diverse populations and identified 257 terminal Y-chromosomal lineages with frequency ranging from 0.010 (singleton) to 0.0687. We identified six dominant common founding lineages associated with different ethnolinguistic backgrounds, which included O2a2b1a1a1a1a1a1a1-M6539, O2a1b1a1a1a1a1a1-F17, O2a2b1a1a1a1a1b1a1b-MF15397, O2a2b2a1b1-A16609, O1b1a1a1a1b2a1a1-F2517 and O2a2b1a1a1a1a1a1-F155. The AMOVA and nucleotide diversity estimates revealed considerable differences and high genetic diversity among ethnolinguistically different populations. We constructed one representative phylogenetic tree among 33 studied populations based on the haplogroup frequency spectrum and sequence variations. Clustering patterns in principal component analysis and multidimensional scaling results showed a genetic differentiation between Tai-Kadai-speaking Li, Mongolic-speaking Mongolian and other Sinitic-speaking Han Chinese populations. Phylogenetic topology inferred from the BEAST and Network relationships reconstructed from the popART further showed the founding lineages from culturally/linguistically diverse populations, such as C2a/C2b was dominant in Mongolian people and O1a/O1b was dominant in island Li people. We also identified many lineages shared by more than two ethnolinguistically different populations with a high proportion, suggesting their extensive admixture and migration history. Our findings indicated that our developed high-resolution Y-SNP panel included major dominant Y-lineages of Chinese populations from different ethnic groups and geographical regions, which can be used as the primary and powerful tool for forensic practice. We should emphasize the necessity and importance of whole-sequencing of more ethnolinguistically different populations, which can help identify more unrecognized population-specific variations for the final promotion of Y-chromosome-based forensic applications.

show abstract

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

Cited by 11 publications

References 41 publications

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

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

Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs

Multiple founding paternal lineages inferred from the newly-developed SNPSeqTyper 639 Y-SNP panel suggested the complex admixture and migration history of Chinese people

Contact Info

Product

Resources

About