A 16-plex Y-SNP typing system based on allele-specific PCR for the genotyping of Chinese Y-chromosomal haplogroups

Zhou, Zhihan; Zhou, Yuxiang; Li, Jinliang; Qian, Jin; Liu, Baonian; Yang, Qinrui; Shao, Chengchen; Li, Hui; Sun, Kuan; Tang, Qiqun; Xie, Jianhui

doi:10.1016/j.legalmed.2020.101720

“…In this study, the abasic site was designed 5–9 nt away from the 3′ end of primers and could be introduced into primary nascent strands to change the exponential amplification into a linear fashion. In previous studies, a mismatch was commonly added at the 3rd nt of primers at the 3′ end for allele-specific SNP typing [ 29 , 30 ]. Therefore, it is still permissible to optimize the location of the abasic site in primers to improve the amplification efficiency.…”

Section: Discussionmentioning

confidence: 99%

Investigation of Linear Amplification Using Abasic Site-Containing Primers Coupled to Routine STR Typing for LT-DNA Analysis

Qian

¹

,

Li

²

,

Zhou

³

et al. 2022

Genes

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Obtaining a full short tandem repeat (STR) profile from a low template DNA (LT-DNA) still presents a challenge for conventional methods due to significant stochastic effects and polymerase slippage. A novel amplification method with a lower cost and higher accuracy is required to improve the DNA amount. Previous studies suggested that DNA polymerases without bypass activity could not perform processive DNA synthesis beyond abasic sites in vitro and our results showed a lack of bypass activity for Phusion, Pfu and KAPA DNA polymerases in this study. Based on this feature, we developed a novel linear amplification method, termed Linear Aamplification for double-stranded DNA using primers with abasic sites near 3′ end (abLAFD), to limit the replication error. The amplification efficiency was evaluated by qPCR analysis with a result of approximately a 130-fold increase in target DNA. In a LT-DNA analysis, the abLAFD method can be employed as a pre-PCR. Similar to nested PCRs, primer sets used for the abLAFD method were designed as external primers suitable for commercial multiplex STR amplification assays. The practical performance of the abLAFD method was evaluated by coupling it to a routine PP21 STR analysis using 50 pg and 25 pg DNA. Compared to reference profiles, all abLAFD profiles showed significantly recovered alleles, increased average peak height and heterozygote balance with a comparable stutter ratio. Altogether, our results support the theory that the abLAFD method is a promising strategy coupled to STR typing for forensic LT-DNA analysis.

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“…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 639-plex Y-SNP panel suggested the complex admixture and migration history of Chinese people

He

¹

,

Wang

²

,

Miao³

et al. 2023

Preprint

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Non-recombining regions of the Y-chromosome recorded the evolutionary traces of male human populations and are inherited haplotype-dependently and male-specifically. 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-chromosome Single Nucleotide Polymorphisms (Y-SNP) panel targeted for uniparental genealogy reconstruction 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

“…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

He

¹

,

Wang

²

,

Chen

³

et al. 2022

Preprint

0

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

A 16-plex Y-SNP typing system based on allele-specific PCR for the genotyping of Chinese Y-chromosomal haplogroups

Cited by 10 publications

References 27 publications

Investigation of Linear Amplification Using Abasic Site-Containing Primers Coupled to Routine STR Typing for LT-DNA Analysis

Investigation of Linear Amplification Using Abasic Site-Containing Primers Coupled to Routine STR Typing for LT-DNA Analysis

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

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

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