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学者姓名:朱波峰

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Forensic efficiencies of individual identification, kinship testing and ancestral inference in three Yunnan groups based on a self-developed multiple DIP panel SCIE Scopus
期刊论文 | 2023 , 13 | FRONTIERS IN GENETICS
SCOPUS Cited Count: 1
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Abstract :

Deletion/insertion polymorphism (DIP), as a short insertion/deletion sequence polymorphic genetic marker, has attracted the attention of forensic genetic scientist due to its lack of stutter, short amplicon and abundant ancestral information. In this study, based on a self-developed 43 autosomal deletion/insertion polymorphism (A-DIP) loci panel which could meet the forensic application purposes of individual identification, kinship testing and ancestral inference to some extent, we evaluated the forensic efficiencies of the above three forensic objectives in Chinese Yi, Hani and Miao groups of Yunnan province. The cumulative match probability (CPM) and combined probability of exclusion (CPE) of these three groups were 1.11433E-18, 8.24299E-19, 4.21721E-18; 0.999610217, 0.999629285 and 0.999582084, respectively. Average 96.65% full sibling pairs could be identified from unrelated individual pairs (as likelihood ratios > 1) using this DIP panel, whereas the average false positive rate was 3.69% in three target Yunnan groups. With the biogeographical ancestor prediction models constructed by extreme gradient boosting (XGBoost) and support vector machine (SVM) algorithms, 0.8239 (95% CI 0.7984, 0.8474) of the unrelated individuals could be correctly divided according to the continental origins based on the 43 A-DIPs which were large frequency distribution differentiations among different continental populations. The present results of principal component analysis (PCA), multidimensional scaling (MDS), neighbor joining (NJ) and maximum likelihood (ML) phylogenetic trees and STRUCTURE analyses indicated that these three Yunnan groups had relatively close genetic distances with East Asian populations.

Keyword :

deletion extreme gradient boosting full-sibling identification individual identification insertion polymorphism support vector machine

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GB/T 7714 Chen, Man , Lan, Qiong , Nie, Shengjie et al. Forensic efficiencies of individual identification, kinship testing and ancestral inference in three Yunnan groups based on a self-developed multiple DIP panel [J]. | FRONTIERS IN GENETICS , 2023 , 13 .
MLA Chen, Man et al. "Forensic efficiencies of individual identification, kinship testing and ancestral inference in three Yunnan groups based on a self-developed multiple DIP panel" . | FRONTIERS IN GENETICS 13 (2023) .
APA Chen, Man , Lan, Qiong , Nie, Shengjie , Hu, Liping , Fang, Yating , Cui, Wei et al. Forensic efficiencies of individual identification, kinship testing and ancestral inference in three Yunnan groups based on a self-developed multiple DIP panel . | FRONTIERS IN GENETICS , 2023 , 13 .
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Multiple genetic analyses for Chinese Hunan Han population via 46 A-STRs SCIE SSCI Scopus
期刊论文 | 2022 , 49 (2) , 156-163 | ANNALS OF HUMAN BIOLOGY
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Abstract :

Background Short tandem repeats (STRs) are important as common genetic markers in forensic identification and population genetics due to their highly polymorphic nature. Aims To explore genetic polymorphisms of the Chinese Hunan Han population and further dissect genetic relationships among the Hunan Han and other populations from China. Subjects and methods In this study, samples of 394 unrelated healthy individuals from the Chinese Hunan Han population were analysed using 46 autosomal-STRs (A-STRs). Thirteen previously reported populations (6378 individuals) from China were subsequently collected for population genetic analyses based on 23 shared A-STRs. Results In the Hunan Han population, a total of 452 alleles were detected in 46 A-STRs with allelic frequencies spanning from 0.0013 to 0.5571. Except for the Penta D locus in linkage disequilibrium, the combined power of discrimination and the combined power of exclusion for 45 A-STRs in the Hunan Han population were 0.999999999999999999999999999999999999999999999999510314 and 0.999999999999999726596, respectively. Results of interpopulation differentiation, principal component analysis, and phylogenetic relationship analyses uniformly showed that the Hunan Han have closer genetic affinities with Han populations from different Chinese regions and a geographically close ethnic minority group, namely the Hubei Tujia. Conclusion To summarise, these 46 A-STRs showed high polymorphism in the Chinese Hunan Han population for forensic practice.

Keyword :

Chinese Hunan Han population CODIS forensic genetics non-CODIS Short tandem repeat

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GB/T 7714 Zhang, Yunying , Fang, Yating , Chen, Man et al. Multiple genetic analyses for Chinese Hunan Han population via 46 A-STRs [J]. | ANNALS OF HUMAN BIOLOGY , 2022 , 49 (2) : 156-163 .
MLA Zhang, Yunying et al. "Multiple genetic analyses for Chinese Hunan Han population via 46 A-STRs" . | ANNALS OF HUMAN BIOLOGY 49 . 2 (2022) : 156-163 .
APA Zhang, Yunying , Fang, Yating , Chen, Man , Zhao, Ming , Xu, Hui , Zhao, Congying et al. Multiple genetic analyses for Chinese Hunan Han population via 46 A-STRs . | ANNALS OF HUMAN BIOLOGY , 2022 , 49 (2) , 156-163 .
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Allelic and haplotypic polymorphisms and paternal genetic analysis of Chinese Shaanxi Han population utilizing a multiplex Y-STR set SCIE SSCI Scopus
期刊论文 | 2022 | ANNALS OF HUMAN BIOLOGY
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Abstract :

BackgroundThe analysis of Y chromosomal genetic markers is of great significance in human genetic fields related to male individuals. The Han nationality is the most populous ethnic group. It is critical to investigate the Y-chromosome short tandem repeat (Y-STR) genetic informativeness of Han nationalities in different Chinese regions in order to gain a comprehensive understanding of their paternal genetic relationships and origin.AimTo assess the allelic and haplotypic polymorphisms of the novel AGCU Y SUPP STR amplification system containing seven Y-STRs in the maximal dataset of the Y-STR Haplotype Reference Database (YHRD) and 17 newly included Y-STRs, and explore the genetic relationships among the Shaanxi Han population and 12 reference populations from China.Subjects and methodsA total sample of 220 Han male subjects were obtained from the Shaanxi Province, China, and genotyped by the novel AGCU Y SUPP STR amplification system. Multiplex population genetic analyses derived from the same 16 Y-STR loci were carried out among the Shaanxi Han population and 12 reference populations from China.ResultsThe gene diversities (GD) ranged from the maximum value of 0.9609 (DYS385a,b) to the minimum value of 0.5441 (DYS531). Besides, 217 distinct haplotypes were detected wholly in 220 individuals, of which 214 (98.62%) were exclusive. The entire haplotype diversity (HD) and discrimination capacity (DC) were 0.9999 and 0.9864, respectively, while the haplotype match probability (HMP) was 0.0045. Among the reference populations, the obtained results of population genetic analyses revealed that the Shaanxi Han population had the largest genetic distance with the Guangxi Yao group, but the smallest genetic distance with the Hunan Tujia group.ConclusionsThese Y-STR loci in the AGCU Y SUPP STR amplification system were of high genetic polymorphisms and the amplification system could be used as a prospective complementary tool for forensic application and paternal genetics in the Shaanxi Han population.

Keyword :

AGCU Y SUPP STR amplification system genetic polymorphism haplotype diversity Shaanxi Han population Y-STR

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GB/T 7714 Xu, Hui , Zhao, Ming , Mei, Shuyan et al. Allelic and haplotypic polymorphisms and paternal genetic analysis of Chinese Shaanxi Han population utilizing a multiplex Y-STR set [J]. | ANNALS OF HUMAN BIOLOGY , 2022 .
MLA Xu, Hui et al. "Allelic and haplotypic polymorphisms and paternal genetic analysis of Chinese Shaanxi Han population utilizing a multiplex Y-STR set" . | ANNALS OF HUMAN BIOLOGY (2022) .
APA Xu, Hui , Zhao, Ming , Mei, Shuyan , Zhang, Yunying , Cai, Meiming , Lei, Fanzhang et al. Allelic and haplotypic polymorphisms and paternal genetic analysis of Chinese Shaanxi Han population utilizing a multiplex Y-STR set . | ANNALS OF HUMAN BIOLOGY , 2022 .
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Forensic Features and Genetic Structure Analyses of the Beijing Han Nationality Disclosed by a Self-Developed Panel Containing a Series of Ancestry Informative Deletion/Insertion Polymorphism Loci SCIE Scopus
期刊论文 | 2022 , 10 | FRONTIERS IN ECOLOGY AND EVOLUTION
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Abstract :

The utilization of the ancestry informative markers to disclose the ancestral composition of a certain population and explore the genetic affinities between diverse populations is beneficial to inferring the biogeographic ancestry of unknown individuals and assisting in case detection, as well as avoiding the impacts of population stratification during genome-wide association analysis studies. In the present study, we applied an in-house ancestry informative deletion/insertion polymorphic multiplex amplification system to investigate the ancestral compositions of the Beijing Han population and analyze the genetic relationships between the Beijing Han population and 31 global reference populations. The results demonstrated that 32 loci of this self-developed panel containing 39 loci significantly contributed to the inference of genetic information for the Beijing Han population. The results of multiple population genetics statistical analyses indicated that the ancestral component and genetic architecture of the Beijing Han population were analogous to the reference East Asian populations, and that the Beijing Han population was genetically close to the reference East Asian populations.

Keyword :

Beijing Han nationality deletion genetic characteristic genetic relationship insertion polymorphism population structure

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GB/T 7714 Xu, Hui , Fang, Yating , Zhao, Ming et al. Forensic Features and Genetic Structure Analyses of the Beijing Han Nationality Disclosed by a Self-Developed Panel Containing a Series of Ancestry Informative Deletion/Insertion Polymorphism Loci [J]. | FRONTIERS IN ECOLOGY AND EVOLUTION , 2022 , 10 .
MLA Xu, Hui et al. "Forensic Features and Genetic Structure Analyses of the Beijing Han Nationality Disclosed by a Self-Developed Panel Containing a Series of Ancestry Informative Deletion/Insertion Polymorphism Loci" . | FRONTIERS IN ECOLOGY AND EVOLUTION 10 (2022) .
APA Xu, Hui , Fang, Yating , Zhao, Ming , Lan, Qiong , Mei, Shuyan , Liu, Liu et al. Forensic Features and Genetic Structure Analyses of the Beijing Han Nationality Disclosed by a Self-Developed Panel Containing a Series of Ancestry Informative Deletion/Insertion Polymorphism Loci . | FRONTIERS IN ECOLOGY AND EVOLUTION , 2022 , 10 .
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Development and validation of a new multiplex Y-STR panel designed to increase the power of discrimination SCIE Scopus
期刊论文 | 2022 , 43 (18-19) , 1899-1910 | ELECTROPHORESIS
SCOPUS Cited Count: 1
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In an attempt to increase the discrimination capacity (DC) and reduce the adventitious match probability, a 6-dye multiplex Y-chromosomal short tandem repeat (Y-STR) panel named Y34plex was constructed that combined 25 Y-chromosomal markers (DYS456, DYS627, DYS390, DYS570, DYS635, DYS385a/b, DYS448, DYS437, DYS533, DYS449, DYS481, DYS392, DYS391, DYS389I, DYS460, YGATAH4, DYS438, DYS389II, DYS19, DYS458, DYF387S1a/b, DYS439, DYS393, DYS576, and DYS518) in widely used commercial kits, with nine highly polymorphic Y-STR loci (DYS557, DYS527a/b, DYS593, DYS444, DYS596, DYS643, DYS447, DYS549, and DYS645). The Y34plex is a promising type system to distinguish both unrelated and related male individuals due to the incorporation of rapidly mutated Y-STR loci. A validation study of the Y34plex was performed and followed the guidelines of the Scientific Working Group on DNA analysis methods. Results show that full Y-STR profiles were obtained from male/female DNA mixtures with 125 pg of male DNA in the presence of 50 ng of female DNA. The ability to tolerate polymerase chain reaction inhibitors commonly contained in forensic casework samples demonstrated the applicability and robustness of the Y34plex. Compared with the Yfiler Plus kit, the novel panel showed an increased power of discrimination in Chinese Wuxi Han population (n = 434). The overall haplotype diversity of the Y34plex was 0.999606, whereas DC value was 0.956221, which is suitable for use on forensic paternal investigation.

Keyword :

forensic DNA typing multiplex PCR amplification validation Y-STR

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GB/T 7714 Zhou, Yongsong , Cui, Wei , Wu, Buling et al. Development and validation of a new multiplex Y-STR panel designed to increase the power of discrimination [J]. | ELECTROPHORESIS , 2022 , 43 (18-19) : 1899-1910 .
MLA Zhou, Yongsong et al. "Development and validation of a new multiplex Y-STR panel designed to increase the power of discrimination" . | ELECTROPHORESIS 43 . 18-19 (2022) : 1899-1910 .
APA Zhou, Yongsong , Cui, Wei , Wu, Buling , Zhu, Bofeng . Development and validation of a new multiplex Y-STR panel designed to increase the power of discrimination . | ELECTROPHORESIS , 2022 , 43 (18-19) , 1899-1910 .
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Genetic Background of Kirgiz Ethnic Group From Northwest China Revealed by Mitochondrial DNA Control Region Sequences on Massively Parallel Sequencing SCIE Scopus
期刊论文 | 2022 , 13 | FRONTIERS IN GENETICS
SCOPUS Cited Count: 1
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The mitochondrial DNA (mtDNA) has been used to trace population evolution and apply to forensic identification due to the characteristics including lack of recombination, higher copy number and matrilineal inheritance comparing with nuclear genome DNA. In this study, mtDNA control region sequences of 91 Kirgiz individuals from the Northwest region of China were sequenced to identify genetic polymorphisms and gain insight into the genetic background of the Kirgiz ethnic group. MtDNA control region sequences of Kirgiz individuals presented relatively high genetic polymorphisms. The 1,122 bp sequences of mtDNA control region could differ among unrelated Kirgiz individuals, which suggested the mtDNA control region sequences have a good maternal pedigree tracing capability among different Kirgiz individuals. The neutrality test, mismatch distribution, Bayesian phylogenetic inference, Bayesian skyline analysis, and the median network analyses showed that the Kirgiz group might occurred population expansion, and the expansion could be observed at about similar to 53.41 kilo years ago (kya) when ancestries of modern humans began to thrive in Eurasia. The pairwise population comparisons, principal component analyses, and median network analyses were performed based on haplogroup frequencies or mtDNA control region sequences of 5,886 individuals from the Kirgiz group and the 48 reference populations all over the world. And the most homologous haplotypes were found between Kirgiz individuals and the East Asian individuals, which indicated that the Kirgiz group might have gene exchanges with the East Asian populations.

Keyword :

genetic polymorphism Kirgiz ethnic group massively parallel sequencing mitochondrial DNA control region population evolution

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GB/T 7714 Wang, Hongdan , Chen, Man , Chen, Chong et al. Genetic Background of Kirgiz Ethnic Group From Northwest China Revealed by Mitochondrial DNA Control Region Sequences on Massively Parallel Sequencing [J]. | FRONTIERS IN GENETICS , 2022 , 13 .
MLA Wang, Hongdan et al. "Genetic Background of Kirgiz Ethnic Group From Northwest China Revealed by Mitochondrial DNA Control Region Sequences on Massively Parallel Sequencing" . | FRONTIERS IN GENETICS 13 (2022) .
APA Wang, Hongdan , Chen, Man , Chen, Chong , Fang, Yating , Cui, Wei , Lei, Fanzhang et al. Genetic Background of Kirgiz Ethnic Group From Northwest China Revealed by Mitochondrial DNA Control Region Sequences on Massively Parallel Sequencing . | FRONTIERS IN GENETICS , 2022 , 13 .
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Forensic efficacy evaluation and genetic structure exploration of the Yunnan Miao group by a multiplex InDel panel SCIE Scopus
期刊论文 | 2022 , 43 (16-17) , 1765-1773 | ELECTROPHORESIS
SCOPUS Cited Count: 6
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Abstract :

The aim of the study was to better understand the genetic characteristics of the Miao group in China. Herein, genetic characteristics and forensic application values of 57 autosomal insertion-deletion (InDel) loci were investigated in 210 unrelated healthy individuals from the Chinese Yunnan Miao (YM) group. Meanwhile, the genetic differences in these InDels were compared among the YM group and 26 reference populations. The results of forensic statistical analyses showed that all 57 autosomal InDels were in accordance with the Hardy-Weinberg and linkage equilibria of pairwise loci in the Chinese YM group. Moreover, the combined probability of discrimination and probability of exclusion in the YM group were 0.9999999999999999999999801 and 0.999928, respectively, which indicated that the multiplex amplification including 57 autosomal InDels was suitable for forensic individual identification and paternity testing in the Chinese YM group. In addition, the results of allelic frequency distribution differential analyses, principal component analyses, phylogenetic tree reconstruction, and genetic structure analyses between the Chinese YM group and 26 reference populations revealed that the genetic similarities between the YM group and East Asian populations were more than that between the YM group and other geographical populations. This 57 autosomal InDels system can also effectively distinguish East Asian, European, and African populations.

Keyword :

genetic characteristic individual identification insertion-deletion locus Yunnan Miao group

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GB/T 7714 Chen, Xuebing , Nie, Shengjie , Hu, Liping et al. Forensic efficacy evaluation and genetic structure exploration of the Yunnan Miao group by a multiplex InDel panel [J]. | ELECTROPHORESIS , 2022 , 43 (16-17) : 1765-1773 .
MLA Chen, Xuebing et al. "Forensic efficacy evaluation and genetic structure exploration of the Yunnan Miao group by a multiplex InDel panel" . | ELECTROPHORESIS 43 . 16-17 (2022) : 1765-1773 .
APA Chen, Xuebing , Nie, Shengjie , Hu, Liping , Fang, Yating , Cui, Wei , Xu, Hui et al. Forensic efficacy evaluation and genetic structure exploration of the Yunnan Miao group by a multiplex InDel panel . | ELECTROPHORESIS , 2022 , 43 (16-17) , 1765-1773 .
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Genetic diversity analysis of forty-three insertion/deletion loci for forensic individual identification in Han Chinese from Beijing based on a novel panel SCIE Scopus
期刊论文 | 2022 , 23 (3) , 241-248 | JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B
SCOPUS Cited Count: 5
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GB/T 7714 Zhao, Congying , Yang, Jinlong , Xu, Hui et al. Genetic diversity analysis of forty-three insertion/deletion loci for forensic individual identification in Han Chinese from Beijing based on a novel panel [J]. | JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B , 2022 , 23 (3) : 241-248 .
MLA Zhao, Congying et al. "Genetic diversity analysis of forty-three insertion/deletion loci for forensic individual identification in Han Chinese from Beijing based on a novel panel" . | JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B 23 . 3 (2022) : 241-248 .
APA Zhao, Congying , Yang, Jinlong , Xu, Hui , Mei, Shuyan , Fang, Yating , Lan, Qiong et al. Genetic diversity analysis of forty-three insertion/deletion loci for forensic individual identification in Han Chinese from Beijing based on a novel panel . | JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B , 2022 , 23 (3) , 241-248 .
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Forensic Efficiency Estimation of a Homemade Six-Color Fluorescence Multiplex Panel and In-Depth Anatomy of the Population Genetic Architecture in Two Tibetan Groups SCIE Scopus
期刊论文 | 2022 , 13 | FRONTIERS IN GENETICS
WoS CC Cited Count: 1 SCOPUS Cited Count: 6
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Abstract :

The genetic information of the Chinese Tibetan group has been a long-standing research hotspot among population geneticists and archaeologists. Herein, 309 unrelated individuals from two Tibetan groups living in Qinghai Province, China (CTQ), and Tibet Autonomous Region, China (CTT), were successfully genotyped using a new homemade six-color fluorescence multiplex panel, which contained 59 autosomal deletion/insertion polymorphisms (au-DIPs), two mini short tandem repeats (miniSTRs), two Y-chromosomal DIPs, and one Amelogenin. The cumulative probability of matching and combined power of exclusion values for this new panel in CTQ and CTT groups were 1.9253E-27 and 0.99999729, as well as 1.5061E-26 and 0.99999895, respectively. Subsequently, comprehensive population genetic analyses of Tibetan groups and reference populations were carried out based on the 59 au-DIPs. The multitudinous statistical analysis results supported that Tibetan groups have close genetic affinities with East Asian populations. These findings showed that this homemade system would be a powerful tool for forensic individual identification and paternity testing in Chinese Tibetan groups and give us an important insight for further perfecting the genetic landscape of Tibetan groups.

Keyword :

deletion forensic efficiency estimation genetic architecture dissection insertion polymorphisms population genetics Tibetan group

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GB/T 7714 Liu, Yanfang , Cui, Wei , Jin, Xiaoye et al. Forensic Efficiency Estimation of a Homemade Six-Color Fluorescence Multiplex Panel and In-Depth Anatomy of the Population Genetic Architecture in Two Tibetan Groups [J]. | FRONTIERS IN GENETICS , 2022 , 13 .
MLA Liu, Yanfang et al. "Forensic Efficiency Estimation of a Homemade Six-Color Fluorescence Multiplex Panel and In-Depth Anatomy of the Population Genetic Architecture in Two Tibetan Groups" . | FRONTIERS IN GENETICS 13 (2022) .
APA Liu, Yanfang , Cui, Wei , Jin, Xiaoye , Wang, Kang , Mei, Shuyan , Zheng, Xingkai et al. Forensic Efficiency Estimation of a Homemade Six-Color Fluorescence Multiplex Panel and In-Depth Anatomy of the Population Genetic Architecture in Two Tibetan Groups . | FRONTIERS IN GENETICS , 2022 , 13 .
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Forensic and genetic landscape explorations of Chinese Kyrgyz group based on autosomal SNPs, Y-chromosomal SNPs and STRs SCIE Scopus
期刊论文 | 2022 , 832 | GENE
SCOPUS Cited Count: 1
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To assess the effect of population genetic polymorphism on forensic research, we investigated the genetic polymorphisms of Chinese Kyrgyz group (n = 98) and evaluated forensic application values in Chinese Kyrgyz group and other 26 reference populations at 90 autosomal SNPs, and then combined with 34 SNPs and 37 STRs on Y chromosome to reveal the genetic background of Kyrgyz group in autosomal and Y-chromosomal in-heritances, respectively. The 90 autosomal SNPs and 34 Y-chromosomal SNPs were sequenced base on next generation sequencing technology, and 37 Y-chromosomal STRs were analyzed by capillary electrophoresis platform. The results showed that cumulative power of discrimination and cumulative power of exclusion of 90 autosomal SNPs in the panel met the application need of forensic genetics in Kyrgyz group. The forensic ef-fectivenesses of the panel were high in all 27 populations, although there were genetic differences among these populations. The forensic effectiveness of the panel was relatively higher in the European populations, but relatively lower in the African populations. The population genetic results indicated that the Kyrgyz group had the relatively closer genetic relationships with the reference East Asian populations at autosomal SNPs, and there were gene exchanges between the Kyrgyz group and East Asian, European populations based on the analytical results of autosomal SNPs, Y-chromosomal SNPs and STRs.

Keyword :

Forensic genetic Next generation sequencing Population genetic polymorphism SNP Y-STR

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GB/T 7714 Fang, Yating , Mei, Shuyan , Zhang, Yunying et al. Forensic and genetic landscape explorations of Chinese Kyrgyz group based on autosomal SNPs, Y-chromosomal SNPs and STRs [J]. | GENE , 2022 , 832 .
MLA Fang, Yating et al. "Forensic and genetic landscape explorations of Chinese Kyrgyz group based on autosomal SNPs, Y-chromosomal SNPs and STRs" . | GENE 832 (2022) .
APA Fang, Yating , Mei, Shuyan , Zhang, Yunying , Teng, Rui , Tai, Yunchun , Zhu, Bofeng . Forensic and genetic landscape explorations of Chinese Kyrgyz group based on autosomal SNPs, Y-chromosomal SNPs and STRs . | GENE , 2022 , 832 .
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