Technical note: developmental validation of a novel 41-plex Y-STR system for the direct amplification of reference samples

Fan, Guangyao; Pan, Lipeng; Tang, Peizhi; Zhou, Yijun; Liu, Mengnan; Luo, Xiangmin

doi:10.1007/s00414-020-02326-9

Cited by 20 publications

(9 citation statements)

References 28 publications

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“…A total of 41 Y-STRs and three Y-InDels were selected, including 17 loci from the Yfiler kit [ 15 ] (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4), nine RM Y-STR loci [ 20 ] (DYS449, DYS518, DYS570, DYS576, DYS627, DYF387S1a/b, and DYF404S1a/b), 15 low-medium mutating loci [ 12 , 20 ] (DYS549, DYS481, DYS533, DYS447, DYS527a/b, DYS460, DYS444, DYS643, DYS557, DYS596, DYS388, DYS522, DYS593, and DYS645), and rs199815934, rs759551978, and rs771783753. The system contains all loci from Yfiler [ 15 ], PowerPlex Y23 [ 17 ], and the Yfiler Plus PCR Amplification kit [ 18 ], compatible with the current worldwide mainstream Y-STR loci.…”

Section: Methodsmentioning

confidence: 99%

Internal validation of an improved system for forensic application: a 41-plex Y-STR panel

Chai

Tao

et al. 2023

Forensic Sciences Research

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Y-chromosome short tandem repeats (Y-STRs) have a unique role in forensic investigation. However, low-medium mutating Y-STRs cannot meet the requirements for male lineage differentiation in inbred populations, while rapidly mutating (RM) high-resolution Y-STRs might cause unexpected exclusion of paternal lineages. Thus, combining Y-STRs with low and high mutation rates help to distinguish male individuals and lineages in family screening and analysis of genetic relationships. In this study, a novel 6-dye, 41-plex Y-STR panel was developed and validated, which included 17 loci from the Yfiler kit, 9 RM Y-STR loci, 15 low-medium mutating Y-STR loci, and three Y-InDels. Developmental validation was performed for this panel, including size precision testing, stutter analysis, species specificity analysis, male specificity testing, sensitivity testing, concordance evaluation, PCR inhibitors analysis, and DNA mixture examination. The results demonstrated that the novel 41-plex Y-STR panel, developed in-house, was time efficient, accurate and reliable. It showed good adaptability to directly amplify a variety of case-type samples. Further, adding multiple Y-STR loci significantly improved the system’s ability to distinguish related males, making it highly informative for forensic applications. In addition, the data obtained was compatible with the widely used Y-STR kits, facilitating the search and construction of population databases. Moreover, the addition of Y-Indels with short amplicons improves analyses of degraded samples.

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Section: Methodsmentioning

confidence: 99%

Internal validation of an improved system for forensic application: a 41-plex Y-STR panel

Chai

Tao

et al. 2023

Forensic Sciences Research

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“…A total of 26 reference populations were selected in this study, including Jiangsu Wujiang Han [ 16 ], Jiangsu Changshu Han [ 17 ], Jiangsu Nantong Han [ 26 , 27 ] ( n = 1336), Jiangsu Changzhou Han [ 28 ] ( n = 2597), other Jiangsu Han [ 29 ] ( n = 377), Anhui Han [ 30 ] ( n = 3110), Guangdong Han [ 31 ] ( n = 1827), Guangxi Han ( n = 105), Guizhou Han [ 32 ] ( n = 658), Jiangxi Han ( n = 1325), Liaoning Han [ 33 ] ( n = 3544), Fujian Han ( n = 857), Zhejiang Ningbo Han ( n = 925), Shanghai Han [ 18 ] ( n = 777), Sichuan Han [ 34 ] ( n = 337), Zhejiang Han [ 35 , 36 ] ( n = 2039), Ningxia Hui [ 37 , 38 ] ( n = 78), Yunnan Bai ( n = 133), Hainan Li [ 39 , 40 ] ( n = 497), Inner Mongolian [ 41 ] ( n = 466), Qinghai Tibetans [ 42 , 43 ] ( n = 590), Yunnan Yi [ 44 , 45 ] ( n = 452), Nagasaki, Japanese [ 46 ] ( n = 133), Okinawa Japanese [ 47 ] ( n = 55), South Korean [ 48 ] ( n = 272), and African Americans [ 49 , 50 ] ( n = 1800). Pairwise genetic distance (Rst) matrices for the 28 reference populations were calculated by the “AMOVA” online tool on the YHRD website ( , accessed on 21 September 2021).…”

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

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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.

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“…Following the technical instructions in previous research (Fan et al 2021), 41 Y-STR loci and 3 Y-chromosome insertion/deletion markers were coamplified by the SureID PathFinder Plus Kit. PCR was performed on GeneAmp PCR System 9700 Thermal Cycler (Applied Biosystems, Foster City, CA, USA).…”

Section: Methodsmentioning

confidence: 99%

Y-STR Haplotypic Polymorphisms for the Hakka Population in West China and Phylogenic Comparison with Other Chinese Populations

Liu,

Peng,

Song

et al. 2021

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The Hakka, who have undergone a series of great migrations, are usually identified with people who speak the Hakka language or share at least same Hakka ancestry. As the largest Hakka dialect island in West China, the Dongshan region was closely linked with the great migration wave of Hakka. However, the paternal genetic profiles of Dongshan Hakka have never been revealed. In the present study, 41 Y-chromosomal short tandem repeat (Y-STR) loci included in the SureID PathFinder Plus Kit were analyzed in 353 unrelated male individuals (171 Hakka and 182 Han) of Sichuan Province, China. By analyzing 166 different haplotypes among Dongshan Hakka and 176 different haplotypes among Sichuan Han males, haplotype diversity was calculated as 0.9997, with a discrimination capacity of 0.9708, for the Hakka population, and 0.9996 and 0.9670 for the Sichuan Han population, respectively. Most of the Y-STR loci were highly informative in both populations except DYS645. The genetic relationships were evaluated by comparing the Hakka population with 11 other groups that are relevant to Hakka migration routes. The results of the multidimensional scaling plot and phylogenetic tree indicate that the Dongshan Hakka population was closely related to Han nationalities from Anhui, Jiangxi, and Fujian Provinces.

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Technical note: developmental validation of a novel 41-plex Y-STR system for the direct amplification of reference samples

Cited by 20 publications

References 28 publications

Internal validation of an improved system for forensic application: a 41-plex Y-STR panel

Internal validation of an improved system for forensic application: a 41-plex Y-STR panel

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

Y-STR Haplotypic Polymorphisms for the Hakka Population in West China and Phylogenic Comparison with Other Chinese Populations

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