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学者姓名：朱波峰
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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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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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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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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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Abstract ：
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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Abstract ：
Single nucleotide polymorphism (SNP) possesses a promising application in forensic individual identification due to its wide distribution in the human genome and the ability to carry out the genotyping of degraded biological samples by designing short amplicons. Some commonly used individual identification SNPs are less polymorphic in East Asian populations. In order to improve the individual identification efficiencies in East Asian populations, SNP genetic markers with relatively higher polymorphisms were selected from the 1,000 Genome Project phase III database in East Asian populations. A total of 111 individual identification SNPs (II-SNPs) with the observed heterozygosity values greater than 0.4 were screened in East Asian populations, and then, the forensic efficiencies of these selected SNPs were also evaluated in Chinese Inner Mongolia Manchu group. The observed heterozygosity and power of discrimination values at 111 II-SNPs in the Inner Mongolia Manchu group ranged from 0.4011 to 0.7005, and 0.5620 to 0.8025, respectively, and the average value of polymorphism information content was greater than 0.3978. The cumulative match probability and combined probability of exclusion values at II-SNPs were 7.447E(-51) and 1-4.17E(-12) in the Inner Mongolia Manchu group, respectively. The accumulative efficiency results indicated that the set of II-SNPs could be used as a potential tool for forensic individual identification and parentage testing in the Manchu group. The sequencing depths ranged from 781x to 12374x. And the mean allele count ratio and noise level were 0.8672 and 0.0041, respectively. The sequencing results indicated that the SNP genetic marker detection based on the massively parallel sequencing technology for SNP genetic markers had high sequencing performance and could meet the sequencing requirements of II-SNPs in the studied group.
Keyword ：
Chinese Inner Mongolia Manchu group forensic genetics individual identification massively parallel sequencing SNP
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| GB/T 7714 | Zhao, Congying , Xu, Hui , Fang, Yating et al. Systematic selections and forensic application evaluations of 111 individual identification SNPs in the Chinese Inner Mongolia Manchu group [J]. | FRONTIERS IN GENETICS , 2022 , 13 . |
| MLA | Zhao, Congying et al. "Systematic selections and forensic application evaluations of 111 individual identification SNPs in the Chinese Inner Mongolia Manchu group" . | FRONTIERS IN GENETICS 13 (2022) . |
| APA | Zhao, Congying , Xu, Hui , Fang, Yating , Zhao, Ming , Lan, Qiong , Chen, Man et al. Systematic selections and forensic application evaluations of 111 individual identification SNPs in the Chinese Inner Mongolia Manchu group . | FRONTIERS IN GENETICS , 2022 , 13 . |
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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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Abstract ：
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 x 10(-14) to 1-1.27 x 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 x 10(-23) to 1-9.42 x 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 x 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.
Keyword ：
1000 Genomes Project East Asian population Hainan Li group Human identification InDel Intercontinental population differentiation PCR-CE
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| GB/T 7714 | Fan, Haoliang , He, Yitong , Li, Shuanglin et al. Systematic Evaluation of a Novel 6-dye Direct and Multiplex PCR-CE-Based InDel Typing System for Forensic Purposes [J]. | FRONTIERS IN GENETICS , 2022 , 12 . |
| MLA | Fan, Haoliang et al. "Systematic Evaluation of a Novel 6-dye Direct and Multiplex PCR-CE-Based InDel Typing System for Forensic Purposes" . | FRONTIERS IN GENETICS 12 (2022) . |
| APA | Fan, Haoliang , He, Yitong , Li, Shuanglin , Xie, Qiqian , Wang, Fenfen , Du, Zhengming et al. Systematic Evaluation of a Novel 6-dye Direct and Multiplex PCR-CE-Based InDel Typing System for Forensic Purposes . | FRONTIERS IN GENETICS , 2022 , 12 . |
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Abstract ：
Background Ancestry informative markers are regarded as useful tools for inferring the ancestral information of an individual, which have been widely used in the criminal investigations and population genetic studies. Previously, a multiplex amplification panel containing 39 AIM-InDel loci was constructed. This study aims to investigate the genetic polymorphisms of these 39 AIM-InDel loci in Yunnan Hani and Miao ethnic groups, and to uncover their genetic affinities with reference populations based on the AIM-InDel markers. Materials and methods In this research, 39 AIM-InDel profiles of 203 unrelated Miao individuals and 203 unrelated Hani individuals in Yunnan province of China were acquired. Additionally, we evaluated the genetic polymorphisms of 39 InDel loci in Yunnan Miao and Hani groups. Moreover, the genetic relationships among Yunnan Miao, Hani and reference populations were also clarified based on Nei's genetic distances, pairwise fixation indexes, principal component analyses, phylogenetic analyses, and STRUCTURE analyses. Results Genetic diversity analyses demonstrated that these InDel loci showed varying degrees of genetic polymorphisms, and could be utilized in forensic identifications in Yunnan Miao and Hani groups. The results of principal component analyses, phylogenetic analyses and Structure analyses revealed that Yunnan Miao and Hani groups had closer genetic relationships with East Asian populations, especially with the populations from Southern China. This research enriched the genetic data of Chinese ethnic minority, and provided ancestral information of Yunnan Miao and Hani groups from the perspective of population genetics.
Keyword ：
Ancestry informative marker InDel Population genetics Yunnan Hani group Yunnan Miao group
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| GB/T 7714 | Cui, Wei , Nie, Shengjie , Fang, Yating et al. Insights into AIM-InDel diversities in Yunnan Miao and Hani ethnic groups of China for forensic and population genetic purposes [J]. | HEREDITAS , 2022 , 159 (1) . |
| MLA | Cui, Wei et al. "Insights into AIM-InDel diversities in Yunnan Miao and Hani ethnic groups of China for forensic and population genetic purposes" . | HEREDITAS 159 . 1 (2022) . |
| APA | Cui, Wei , Nie, Shengjie , Fang, Yating , Chen, Man , Zhao, Ming , Lan, Qiong et al. Insights into AIM-InDel diversities in Yunnan Miao and Hani ethnic groups of China for forensic and population genetic purposes . | HEREDITAS , 2022 , 159 (1) . |
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Abstract ：
Ancestry informative markers (AIMs) are useful to infer individual biogeographical ancestry and to estimate admixture proportions of admixed populations or individuals. Although a growing number of AIM panels for forensic ancestry origin analyses were developed, they may not efficiently infer the ancestry origins of most populations in China. In this study, a set of 52 ancestry informative deletion/insertion polymorphisms (AIDIPs) were selected with the aim of effectively differentiate continental and partial Chinese populations. All of the selected markers were successfully incorporated into a single multiplex PCR panel, which could be conveniently and efficiently detected on capillary electrophoresis platforms. Genetic distributions of the same 50 AIDIPs in different continental populations revealed that most loci showed high genetic differentiations between East Asian populations and other continental populations. Population genetic analyses of different continental populations indicated that these 50 AIDIPs could clearly discriminate East Asian, European, and African populations. In addition, the 52 AIDIPs also exhibited relatively high cumulative discrimination power in the Eastern Han population, which could be used as a supplementary tool for forensic investigation. Furthermore, the Eastern Han population showed close genetic relationships with East Asian populations and high ancestral components from East Asian populations. In the future, we need to investigate genetic distributions of these 52 AIDIPs in Chinese Han populations in different regions and other ethnic groups, and further evaluate the power of these loci to differentiate different Chinese populations.
Keyword ：
AIDIP ancestry informative marker deletion Eastern Han forensic ancestry analysis insertion polymorphism
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| GB/T 7714 | Zhou, Yongsong , Jin, Xiaoye , Wu, Buling et al. Development and Performance Evaluation of a Novel Ancestry Informative DIP Panel for Continental Origin Inference [J]. | FRONTIERS IN GENETICS , 2022 , 12 . |
| MLA | Zhou, Yongsong et al. "Development and Performance Evaluation of a Novel Ancestry Informative DIP Panel for Continental Origin Inference" . | FRONTIERS IN GENETICS 12 (2022) . |
| APA | Zhou, Yongsong , Jin, Xiaoye , Wu, Buling , Zhu, Bofeng . Development and Performance Evaluation of a Novel Ancestry Informative DIP Panel for Continental Origin Inference . | FRONTIERS IN GENETICS , 2022 , 12 . |
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