The construction and application of a new 17-plex Y-STR system using universal fluorescent PCR

Liu, Jinding; Wang, Rongshuai; Shi, Jie; Cheng, Xiaojuan; Tang, Hao; Guo, Jiangling; Wang, Jiaqi; Liu, Zidong; Li, Wenyan; Fan, Haoliang; Yun, Keming; Yan, Jiangwei; Zhang, Gengqian

doi:10.1007/s00414-020-02291-3

Cited by 12 publications

(10 citation statements)

References 38 publications

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“…But in Kazakh populations from Xinjiang, Northwest China the discrimination capacity was 0.5950 (Shan et al, 2014a). The discrimination capacity in our Kazakh sample is also lower compared to some data from European and Asian populations for the same set of 15 Y-STR loci (Turrina et al, 2006;Roewer et al, 2007;Robino et al, 2008;Lacau et al, 2011;Liu et al, 2020). It should be borne in mind that diversity indices vary depending on the Y-STR genotyping systems used.…”

Section: Discussioncontrasting

confidence: 68%

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Genetic Relationship Among the Kazakh People Based on Y-STR Markers Reveals Evidence of Genetic Variation Among Tribes and Zhuz

et al. 2022

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Ethnogenesis of Kazakhs took place in Central Asia, a region of high genetic and cultural diversity. Even though archaeological and historical studies have shed some light on the formation of modern Kazakhs, the process of establishment of hierarchical socioeconomic structure in the Steppe remains contentious. In this study, we analyzed haplotype variation at 15 Y-chromosomal short-tandem-repeats obtained from 1171 individuals from 24 tribes representing the three socio-territorial subdivisions (Senior, Middle and Junior zhuz) in Kazakhstan to comprehensively characterize the patrilineal genetic architecture of the Kazakh Steppe. In total, 577 distinct haplotypes were identified belonging to one of 20 haplogroups; 16 predominant haplogroups were confirmed by SNP-genotyping. The haplogroup distribution was skewed towards C2-M217, present in all tribes at a global frequency of 51.9%. Despite signatures of spatial differences in haplotype frequencies, a Mantel test failed to detect a statistically significant correlation between genetic and geographic distance between individuals. An analysis of molecular variance found that ∼8.9% of the genetic variance among individuals was attributable to differences among zhuzes and ∼20% to differences among tribes within zhuzes. The STRUCTURE analysis of the 1164 individuals indicated the presence of 20 ancestral groups and a complex three-subclade organization of the C2-M217 haplogroup in Kazakhs, a result supported by the multidimensional scaling analysis. Additionally, while the majority of the haplotypes and tribes overlapped, a distinct cluster of the O2 haplogroup, mostly of the Naiman tribe, was observed. Thus, firstly, our analysis indicated that the majority of Kazakh tribes share deep heterogeneous patrilineal ancestries, while a smaller fraction of them are descendants of a founder paternal ancestor. Secondly, we observed a high frequency of the C2-M217 haplogroups along the southern border of Kazakhstan, broadly corresponding to both the path of the Mongolian invasion and the ancient Silk Road. Interestingly, we detected three subclades of the C2-M217 haplogroup that broadly exhibits zhuz-specific clustering. Further study of Kazakh haplotypes variation within a Central Asian context is required to untwist this complex process of ethnogenesis.

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Section: Discussioncontrasting

confidence: 68%

“…It should be borne in mind that diversity indices vary depending on the Y-STR genotyping systems used. As the number of marker sets increases, diversity indices also increase (Purps et al, 2014;Khubrani et al, 2018;Zhabagin et al, 2019;Liu et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Genetic Relationship Among the Kazakh People Based on Y-STR Markers Reveals Evidence of Genetic Variation Among Tribes and Zhuz

et al. 2022

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“…RM Y-STRs that showed high mutation rates or genetic diversities were chose from previous studies ( Huang et al, 2005 ; Lin et al, 2006 ; Ballantyne et al, 2010 , 2012 ; Zhang et al, 2014 ; Meng et al, 2019 ; Liu et al, 2020a ). Next, the primer pair for each RM Y-STR locus was designed using the Primer 3 online tool ( Untergasser et al, 2012 ) and was synthesized by the Sangon Biotech (Shanghai, China).…”

Section: Methodsmentioning

confidence: 99%

Developmental Validation of a Rapidly Mutating Y-STR Panel Labeled by Six Fluoresceins for Forensic Research

et al. 2022

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The male-specific region of the human Y chromosome is a useful genetic marker for genealogical searching, male inheritance testing, and male DNA mixture deconvolution in forensic studies. However, the Y chromosomal short tandem repeats (Y-STRs) are difficult to distinguish among related males due to their low/medium mutation rate. In contrast, rapidly mutating (RM) Y-STRs exhibit unusually high mutation rates and possess great potential for differentiating male lineages. In this study, we developed a novel Y-STRs multiplex amplification assay of 32 RM Y-STRs by fragment analysis using six dye-labeled technologies (FAM, HEX, TAMRA, ROX, VIG, and SIZ). The development and the validation of the kit were carried out in accordance with the Scientific Working Group guidelines on DNA Analysis Methods. Identical allelic profiles of the 32 RM Y-STRs using a DNA 9948 sample as the positive control could be observed at different concentrations of PCR reagents. Further, the RM Y-STRs did not show cross-reactions with other common animal species, and the developed assay could tolerate interferences from common PCR inhibitors and mixed DNA samples. More importantly, the kit showed relatively high sensitivity and could detect trace DNA samples. Genetic distributions of 32 RM Y-STRs in the Guizhou Han population revealed that these RM Y-STRs showed relatively high genetic diversities. In conclusion, the RM Y-STR assay developed here showed good species specificity, high sensitivity, tolerance to inhibitors, and sample compatibility, which can be viewed as a highly efficient tool with high discrimination capacity for forensic male differentiation.

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“…Therefore, the UAIS could supply additional information for the paternity tests. The Hainan Li, inhabiting in the south of Hainan island, is a relatively isolated minority group in China, which is beneficial to clarify the exquisite population structure and develop specific genetic markers for subpopulations in the forensic genetic field (Liu et al, 2020b;Fan et al, 2021a (mean He: 0.4666 ± 0.0560). Moreover, the CPE and CPD of the 57 A-InDels in the Hainan Li group was 0.999965 and 1-1.32 × 10 -23 , which demonstrated that the EAIS have good performances for individual identification and paternity test in the Hainan Li group (Table 2).…”

Section: Details Of the Novel Typing System And Distinct A-indel Setsmentioning

confidence: 99%

Systematic Evaluation of a Novel 6-dye Direct and Multiplex PCR-CE-Based InDel Typing System for Forensic Purposes

Fan

et al. 2022

Front. Genet.

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Insertion/deletion (InDel) polymorphisms, combined desirable characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), are considerable potential in the fields of forensic practices and population genetics. However, most commercial InDel kits designed based on non-Asians limited extensive forensic applications in East Asian (EAS) populations. Recently, a novel 6-dye direct and multiplex PCR-CE-based typing system was designed on the basis of genome-wide EAS population data, which could amplify 60 molecular genetic markers, consisting of 57 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels), and Amelogenin in a single PCR reaction and detect by capillary electrophoresis, simultaneously. In the present study, the DNA profiles of 279 unrelated individuals from the Hainan Li group were generated by the novel typing system. In addition, we collected two A-InDel sets to evaluate the forensic performances of the novel system in the 1,000 Genomes Project (1KG) populations and Hainan Li group. For the Universal A-InDel set (UAIS, containing 44 A-InDels) the cumulative power of discrimination (CPD) ranged from 1–1.03 × 10–14 to 1–1.27 × 10–18, and the cumulative power of exclusion (CPE) varied from 0.993634 to 0.999908 in the 1KG populations. For the East Asia-based A-InDel set (EAIS, containing 57 A-InDels) the CPD spanned from 1–1.32 × 10–23 to 1–9.42 × 10–24, and the CPE ranged from 0.999965 to 0.999997. In the Hainan Li group, the average heterozygote (He) was 0.4666 (0.2366–0.5448), and the polymorphism information content (PIC) spanned from 0.2116 to 0.3750 (mean PIC: 0.3563 ± 0.0291). In total, the CPD and CPE of 57 A-InDels were 1–1.32 × 10–23 and 0.999965, respectively. Consequently, the novel 6-dye direct and multiplex PCR-CE-based typing system could be considered as the reliable and robust tool for human identification and intercontinental population differentiation, and supplied additional information for kinship analysis in the 1KG populations and Hainan Li group.

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The construction and application of a new 17-plex Y-STR system using universal fluorescent PCR

Cited by 12 publications

References 38 publications

Genetic Relationship Among the Kazakh People Based on Y-STR Markers Reveals Evidence of Genetic Variation Among Tribes and Zhuz

Genetic Relationship Among the Kazakh People Based on Y-STR Markers Reveals Evidence of Genetic Variation Among Tribes and Zhuz

Developmental Validation of a Rapidly Mutating Y-STR Panel Labeled by Six Fluoresceins for Forensic Research

Systematic Evaluation of a Novel 6-dye Direct and Multiplex PCR-CE-Based InDel Typing System for Forensic Purposes

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