Genetic variation and forensic efficiency of autosomal insertion/deletion polymorphisms in Chinese Bai ethnic group: phylogenetic analysis to other populations

Yang, Chunhua; Yin, Caiyong; Shen, Chunmei; Guo, Yuxin; Dong, Qi; Yan, Jiangwei; Wang, Hongdan; Zhang, Yu-Dang; Meng, Hao-Tian; Jin, Rui; Chen, Feng; Zhu, Bofeng

doi:10.18632/oncotarget.17137

Cited by 11 publications

(10 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The genetic distances (D A distance) were calculated among Yao, Kelao, and Zhuang samples, and the 20 referenced groups included Beijing Han (Wei et al, 2014), Guangdong Han ( Li et al, 2013), Shanghai Han (Wang et al, 2014), Yi (Liang et al, 2013), Bai (Yang et al, 2017), Xibe (Meng et al, 2015), South Korean (Seong et al, 2014), Tibet Tibetan (Wei et al, 2014), Qinghai Tibetan (Wei et al, 2014), She (Martin et al, 2013), Kazak (Wei et al, 2014), Uigur (Wei et al, 2014), Danes (Friis et al, 2012), Hungarian (Kis et al, 2012), Basque (Martin et al, 2013), Central Spanish (Martin et al, 2013), Uruguaya (Saiz et al, 2014), Jalisco Mexican (Martinez-Cortes et al, 2016), Nigeria (Du et al, 2017), Vietnamese (Du et al, 2017). The result of D A distances was illustrated in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The Investigator DIPplex kit was the first commercial kit developed by Qiagen (Qiagen, Hilden, Germany) for the indel marker. This kit contains 30 autosomal indels and amelogenin, and it has been used to perform systematic investigations on worldwide populations of African (Hefke, Davison & D’Amato, 2015), Asian (Wang et al, 2014; Li et al, 2013; Liang et al, 2013; Meng et al, 2015; Seong et al, 2014; Wei et al, 2014; Yang et al, 2017), European (Friis et al, 2012; Kis et al, 2012; Martin et al, 2013), and American (Saiz et al, 2014) origins. However, very few studies have reported about how indels can be used in comprehending the genetic variation of ethnic minority groups (Zhuang, Yao, and Kelao) in the Guangxi Zhuang Autonomous Region, China.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations

Feng

Yao

et al. 2019

PeerJ

View full text Add to dashboard Cite

Aim In this study, we used a series of diallelic genetic marker insertion/deletion polymorphism (indel) to investigate three populations of Yao, Kelao, and Zhuang groups in the Guangxi region of China and to evaluate their efficiency in forensic application. Result No deviations for all 30 loci were observed from the Hardy–Weinberg equilibrium after Bonferroni correction (p > 0.05/30 = 0.0017). The allele frequencies of the short allele (DIP-) for the above three populations were in the range of 0.0520–0.9480, 0.0950–0.8780, and 0.0850–0.915, respectively. The observed heterozygosity of the 30 loci for the three populations was in the ranges 0.0802–0.5802, 0.1908–0.6053, and 0.1400–0.5600, respectively. The cumulative power of exclusion and combined discrimination power for Yao, Kelao, and Zhuang groups were (0.9843 and 0.9999999999433), (0.9972 and 0.9999999999184), and (0.9845 and 0.9999999999608), respectively. The DA distance, principal component analysis, and cluster analysis indicated a clear regional distribution. In addition, Zhuang groups had close genetic relationships with the Yao and Kelao populations in the Guangxi region. Conclusion This study indicated that the 30 loci were qualified for personal identification; moreover, they could be used as complementary genetic markers for paternity testing in forensic cases for the studied populations.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations

Feng

Yao

et al. 2019

PeerJ

View full text Add to dashboard Cite

show abstract

“…Population data of 30 DIPs in different continental populations were obtained from previous studies [8, 9, 11, 12, 14, 15, 19–28]. Totally 26 populations were selected for the following study.…”

Section: Methodsmentioning

confidence: 99%

“…In this study, previously reported population data of 30 DIPs in different continental populations [8, 9, 11, 12, 14, 15, 19–28] were gathered and analyzed to solve the three issues. First, we explored whether some DIP loci, like HLD125, HLD99, and HLD118, identified in previous studies [14, 23] were suitable for ancestry analyses of different continental populations.…”

Section: Introductionmentioning

confidence: 99%

Autosomal deletion/insertion polymorphisms for global stratification analyses and ancestry origin inferences of different continental populations by machine learning methods

Jin

Zhang

et al. 2021

Electrophoresis

View full text Add to dashboard Cite

A lot of population data of 30 deletion/insertion polymorphisms (DIPs) of the Investigator DIPplex kit in different continental populations have been reported. Here, we assessed genetic distributions of these 30 DIPs in different continental populations to pinpoint candidate ancestry informative DIPs. Besides, the effectiveness of machine learning methods for ancestry analysis was explored. Pairwise informativeness (In) values of 30 DIPs revealed that six loci displayed relatively high In values (>0.1) among different continental populations. Besides, more loci showed high population‐specific divergence (PSD) values in African population. Based on the pairwise In and PSD values of 30 DIPs, 17 DIPs in the Investigator DIPplex kit were selected to ancestry analyses of African, European, and East Asian populations. Even though 30 DIPs provided better ancestry resolution of these continental populations based on the results of PCA and population genetic structure, we found that 17 DIPs could also distinguish these continental populations. More importantly, these 17 DIPs possessed more balanced cumulative PSD distributions in these populations. Six machine learning methods were used to perform ancestry analyses of these continental populations based on 17 DIPs. Obtained results revealed that naïve Bayes manifested the greatest performance; whereas, k nearest neighbor showed relatively low performance. To sum up, these machine learning methods, especially for naïve Bayes, could be used as the valuable tool for ancestry analysis.

show abstract

“…To comprehensively explore the patterns of genetic affinity between our studied populations and worldwide reference populations, we merged our newly obtained population data with those of 61 worldwide populations. The final database used in the population comparison study included 6483 East Asian individuals from 38 populations [4,5,[8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26], 494 South Asians from three populations [27][28][29], 300 Vietnamese of Southeast Asia [30], 194 West Asians from two populations [31], 621 African individuals from five populations [27,30,32], 984 European individuals from eight populations [4,[31][32][33][34][35] and 1 071 South Americans from eight populations [36,38]. The detailed geographical regions and population sizes of these included populations are submitted in Supplementary Table S1.…”

Section: Reference Databasementioning

confidence: 99%

Population Genetics and Forensic Efficiency of 30 InDel Markers in Four Chinese Ethnic Groups Residing in Sichuan

Wang

et al. 2020

Forensic Sciences Research

View full text Add to dashboard Cite

Sichuan Province is located at the transitional junction regions of the Qinghai-Tibet Plateau and the low-altitude plains. It also serves as the corridor of Sino-Tibetan-speaking population migration and expansion since neolithic expansion of Proto-Tibeto-Burman populations from Middle/Upper Yellow River during Majiayao period (3300-2000 BC). However, the population structure and the corresponding genetic diversity of forensic-related markers in this region remain unclear. Thus, we genotyped 30 insertion-deletion (InDel) markers in 444 samples from four ethnic groups (Han, Tibetan, Hui and Yi) from Sichuan Province using the Investigator V R DIPplex kit to explore the characteristics of population genetics and forensic genetic focuses. All the loci were found to be in Hardy-Weinberg Equilibrium (HWE) after applying a Bonferroni correction and no pairwise loci showed prominent linkage disequilibrium. The combined matching probability (CMP) and the combined power of discrimination (CPD) are larger than 1.8089 Â 10 À11 and 0.99999999995, respectively. Principal component analysis, Multi-Dimensional Scaling Plots and Neighbour-Joining tree among 65 worldwide populations indicated that Sichuan Hui and Han are genetically close to Hmong-Mien and Tai-Kadai-speaking populations, and Sichuan Tibetan and Yi bear a strong genetic affinity with Tibeto-Burmanspeaking populations. The model-based genetic structure further supports the genetic affinity between the studied populations and linguistically close populations. KEY POINTSForensic parameters of 30 insertion-deletions (InDels) in 444 individuals from four populations are reported, which showed abundant genetic affinity and diversity among populations and high value in personal identification. Genetic similarities existed between the studied populations and ethnically, linguistically close populations. Sichuan Hui and Han are genetically close to Hmong-Mien and Tai-Kadai-speaking populations. Sichuan Tibetan and Yi bear a strong genetic affinity with Tibeto-Burman-speaking populations. ARTICLE HISTORY

show abstract

Genetic variation and forensic efficiency of autosomal insertion/deletion polymorphisms in Chinese Bai ethnic group: phylogenetic analysis to other populations

Cited by 11 publications

References 43 publications

Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations

Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations

Autosomal deletion/insertion polymorphisms for global stratification analyses and ancestry origin inferences of different continental populations by machine learning methods

Population Genetics and Forensic Efficiency of 30 InDel Markers in Four Chinese Ethnic Groups Residing in Sichuan

Contact Info

Product

Resources

About