Developmental validation of a custom panel including 165 Y-SNPs for Chinese Y-chromosomal haplogroups dissection using the ion S5 XL system

Wang, Mengge; Wang, Zheng; He, Guanglin; Liu, Jing; Wang, Shouyu; Qian, Xiaoqing; Lang, Min; Li, Jienan; Xie, Mingkun; Li, Chengtao; Hou, Yiping

doi:10.1016/j.fsigen.2018.10.009

Cited by 26 publications

(27 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recently, MPS technology has attracted much interest in the field of forensic science. Multiple studies have been carried out to study various forensic markers using MPS technology . All of these studies imply that MPS holds promise for forensic applications.…”

Section: Introductionmentioning

confidence: 99%

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Wang

Liu

et al. 2020

Electrophoresis

Self Cite

View full text Add to dashboard Cite

Massively parallel sequencing (MPS) technologies have the ability to reveal sequence variations within STR alleles as well as their nominal allele lengths, which have traditionally been detected by CE instruments. Recently, Thermo Fisher Scientific has updated the MPS-STR panel, named the Precision ID GlobalFiler next-generation sequencing (NGS) STR Panel version 2, with primers redesigned to add two pentanucleotide tandem repeat loci and profile interpretation supported by the Converge software. Using the Ion Chef System, the Ion S5XL System, and the Converge software, genetic variations were characterized within STR repeat and flanking regions of 30 autosomal STR markers in 115 unrelated individuals from two Chinese population groups (58 Tibetans and 57 Hans). Nineteen STRs demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. In total, 390 alleles were identified by their sequences compared with 258 alleles that were identified by length. Of these 92 sequence variants found within the STR repeat regions, 40 variants were located in STR flanking regions. Additionally, the agreement of the results with CE data was evaluated, as was the ability of this new MPS panel to analyze case-type (11 samples) and artificially degraded samples (seven samples in triplicate). The results generated from this study illustrate that extensive sequence variation exists in commonly used STR markers in the selected population samples and indicate that this NGS STR panel has the potential to be used as an effective tool for human forensics.

show abstract

Section: Introductionmentioning

confidence: 99%

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Wang

Liu

et al. 2020

Electrophoresis

Self Cite

View full text Add to dashboard Cite

show abstract

“…The GD of rs771783753 ([CAT/-]) was reported to be 0.0641 in the Xinjiang Mongolian group [9], while in our study it was much higher (0.443484). The second indel rs759551978, an indel mutation [AGAT/-], representing haplogroup M117-O2a2b1a1, was reported to fail to obtain accurate genotyping after quality control when constructing a panel on the Ion S5 XL System (Thermo Fisher Scientific) [13]. But in this panel, it was successfully amplified.…”

mentioning

confidence: 99%

Developmental validation of the Yfiler Platinum PCR Amplification Kit for forensic genetic caseworks and databases

Song

Wang

et al. 2020

Electrophoresis

Self Cite

View full text Add to dashboard Cite

Y chromosome kits are successfully applied in cases where human biological material exists. With the development of genotyping ability, more Y chromosomal markers are needed for finer identification of male individuals and lineages. In this study, a developmental validation of a newly emerged Y chromosome kit that combines two different kinds of markers: 38 Y-STRs and 3 Y-indels are conducted. The results show that this kit has high sensitivity when there is a small amount of DNA (125 pg), more than one male (minor:major = 1:7), or a mixture of males and females (male:female = 125pg:1875pg), inhibited substances (800 μM hematin and more than 1600 ng/μL humic acid). The kit exhibits high precision level with a standard deviation of allele size no more than 0.14 nt. Locus DYS481 shows the largest stutter rate, with three stutters per true allele. Population samples are well identified (MP of 0.001106), and mutations can be observed in father-son pairs (46 mutations in 70 pairs, 10 in locus DYS627). Out of all the population samples, 13.2% belong to haplogroup M117-O2a2b1a1, with their ethnic group being Han Chinese. The results show that this kit can improve the performance of identifying male individuals, obtaining more unique haplotypes (increasing from 894 to 918 of 1000 male samples) and higher discrimination capacity (increasing from 0.942 to 0.955) in this study compared to previous widely used Yfiler Plus kit. Besides, it gives information about their paternal lineages in forensic genetic casework and genealogical database construction.

show abstract

“…Based on AmpFlSTR®Y ler TM plus and precise identi cation PrecisionID system (Ion Chef and Ion S5XL), 165 Y-SNP haplotype groups were constructed and detected [14], and likelihood was calculated by family search index (FSindex) to try to solve this problem. This study showed that the sample case 5 and case 6 had the same Y-STR typing 57/60 and 44/45 respectively.…”

Section: Discussionmentioning

confidence: 99%

Applied Research of Distinguishing Similar Y-STR Haplotypes by Y Chromosome Complete Sequencing

Yang

et al. 2021

Preprint

View full text Add to dashboard Cite

Background: To explore a technical method to distinguish similar Y-STR haplotypes and its value in deducing the differentiation the males in paternal line, we used a complete genome sequence of Y chromosome using streptavidin–biotin magnetic particle-based capture methodology (Y chromosome liquid phase probe capture next generation sequencing technique (NGS)) to detect male individuals with similar Y-STR haplotypes. Based on our independently developed mathematical model and the new topological structure of Y chromosome mutation sites as well as haplogroups and pedigree trees updated by the International Society of Genealogy (ISOGG) every year, we distinguished the coancestry of male individuals with similar Y-STR haplotypes and Results: Identifying differences between the judgment results of Y full sequencing and the pedigree survey results allowed for the estimation whether the individuals have close relation within 3~5 generations or not. Y chromosome liquid phase probe capture NGS technique could capture the 16M region and effectively analyze tens of thousands of Y-SNP loci. Among them, the coancestry obtained by analysis of 8 sample cases was consistent with the actual total case time obtained by family investigation. Conclusions: Detecting the Y-STR haplotype similarity between male individuals and conducting the previously reported mathematical model analysis by using Y chromosome liquid phase probe capture NGS technology can uncover the coancestry of the different male individuals. These results provide the foundation for further investigation of the similar Y-STR haplotype males in the Y-STR database.

show abstract

Developmental validation of a custom panel including 165 Y-SNPs for Chinese Y-chromosomal haplogroups dissection using the ion S5 XL system

Cited by 26 publications

References 39 publications

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Developmental validation of the Yfiler Platinum PCR Amplification Kit for forensic genetic caseworks and databases

Applied Research of Distinguishing Similar Y-STR Haplotypes by Y Chromosome Complete Sequencing

Contact Info

Product

Resources

About

Developmental validation of a custom panel including 165 Y-SNPs for Chinese Y-chromosomal haplogroups dissection using the ion S5 XL system

Cited by 26 publications

References 39 publications

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Developmental validation of the Yfiler Platinum PCR Amplification Kit for forensic genetic caseworks and databases

Applied Research of Distinguishing Similar Y-STR&nbsp;Haplotypes by Y Chromosome Complete Sequencing

Contact Info

Product

Resources

About

Applied Research of Distinguishing Similar Y-STR Haplotypes by Y Chromosome Complete Sequencing