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Feng Y, Wang T, Yang Y, You J, He K, Zhang H, Wang Q, Yang M, Huang J, Ren Z, Jin X. Genetic features and phylogenetic relationship analyses of Guizhou Han population residing in Southwest China via 38 X-InDels. PeerJ 2023; 11:e14964. [PMID: 36915656 PMCID: PMC10007965 DOI: 10.7717/peerj.14964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
Background The insertion/deletion polymorphism (InDel), an ideal forensic genetic marker with a low spontaneous mutation rate and small amplification product fragments, is widely distributed in the genome, combining the advantages of STR and SNP genetic markers. The X-chromosome has high application value in complex paternity testing, and it is an excellent system for evaluating population admixture and studying evolutionary anthropology. However, further research is needed on the population genetics of X-chromosome InDels (X-InDels). Methods In this article, a system composed of 38 X-InDel loci was utilized to analyse and evaluate the forensic parameters of the Guizhou Han population in order to explore its forensic application efficiency. Results The results showed that expected heterozygosities spanned from 0.0189 to 0.5715, and the cumulative power of discrimination of the 32 X-InDels and three linkage blocks was 0.9999999954 and 0.999999999999741 for males and females, respectively. The combined mean exclusion chance of these loci for trios and duos is 0.999999 and 0.999747, respectively. Multiple methods like principal component analysis, Fst genetic distance, and phylogenetic reconstruction were employed for dissecting the genetic structure of the Guizhou Han population by comparing it with previously reported populations. As expected, the studied Han population displayed relatively close genetic affinities with the East Asian populations. At the same time, there were obvious genetic differentiations between the Guizhou Han population and other continental populations that were discerned, especially for the African populations. Conclusions This study further verified the applicability of 38 X-InDels for human personal identification and kinship analyses of Han Chinese, and also showed the application potential of X-InDels in population genetics.
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Affiliation(s)
- Yuhang Feng
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China, Academy of Forensic Science, Shanghai, China.,Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Ting Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yunteng Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jiangtao You
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Kun He
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiaoye Jin
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China, Academy of Forensic Science, Shanghai, China.,Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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The discovery BPD (D-BPD) program: study protocol of a prospective translational multicenter collaborative study to investigate determinants of chronic lung disease in very low birth weight infants. BMC Pediatr 2019; 19:227. [PMID: 31279333 PMCID: PMC6612113 DOI: 10.1186/s12887-019-1610-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/02/2019] [Indexed: 01/21/2023] Open
Abstract
Background Premature birth is a growing and serious public health problem affecting more than one of every ten infants worldwide. Bronchopulmonary dysplasia (BPD) is the most common neonatal morbidity associated with prematurity and infants with BPD suffer from increased incidence of respiratory infections, asthma, other forms of chronic lung illness, and death (Day and Ryan, Pediatr Res 81: 210–213, 2017; Isayama et la., JAMA Pediatr 171:271–279, 2017). BPD is now understood as a longitudinal disease process influenced by the intrauterine environment during gestation and modulated by gene-environment interactions throughout the neonatal and early childhood periods. Despite of this concept, there remains a paucity of multidisciplinary team-based approaches dedicated to the comprehensive study of this complex disease. Methods The Discovery BPD (D-BPD) Program involves a cohort of infants < 1,250 g at birth prospectively followed until 6 years of age. The program integrates analysis of detailed clinical data by machine learning, genetic susceptibility and molecular translation studies. Discussion The current gap in understanding BPD as a complex multi-trait spectrum of different disease endotypes will be addressed by a bedside-to-bench and bench-to-bedside approach in the D-BPD program. The D-BPD will provide enhanced understanding of mechanisms, evolution and consequences of lung diseases in preterm infants. The D-BPD program represents a unique opportunity to combine the expertise of biologists, neonatologists, pulmonologists, geneticists and biostatisticians to examine the disease process from multiple perspectives with a singular goal of improving outcomes of premature infants. Trial registration Does not apply for this study. Electronic supplementary material The online version of this article (10.1186/s12887-019-1610-8) contains supplementary material, which is available to authorized users.
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Genetic diversities and phylogenetic analyses of three Chinese main ethnic groups in southwest China: A Y-Chromosomal STR study. Sci Rep 2018; 8:15339. [PMID: 30337624 PMCID: PMC6193932 DOI: 10.1038/s41598-018-33751-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/05/2018] [Indexed: 01/25/2023] Open
Abstract
Short tandem repeats (STRs) located on the Y chromosome with the properties of male-specific inheritance and haploidy are widely used in forensics to analyze paternal genealogies and match male trace donors to evidence. Besides, Y-chromosomal haplotypes play an important role in providing breathtaking insights into population genetic history. However, the genetic diversity and forensic characteristics of Y-STRs in Guizhou main ethnic groups (Hans, Miaos and Bouyeis) remain uncharacterized. Here, we obtained Y-chromosomal 23-marker haplotypes in three Guizhou populations and submitted the first batch of Y-STR haplotype data to the YHRD. The HD in the aforementioned three populations are 0.99990, 0.99983, and 0.99979, respectively, and DC values are 0.9902, 0.9908, and 0.97959, respectively. Subsequently, genetic differentiation between our newly studied populations and reference groups along ethnic/administrative divisions, as well as national/continental boundaries were investigated via AMOVA, MDS, and phylogenetic relationship reconstruction. Significant genetic differentiations from our subjects and other groups are identified in ethnically, linguistically and geographically diverse populations, including most prominently Tibetans and Uyghurs among 30 mainland Chinese populations, Taiwanese groups and others among 58 Asian populations, as well as African groups and others among 89 worldwide populations. Qiannan Bouyei has a close genetic relationship with Guangxi Zhuang, and Zunyi Han and Qiandongnan Miao have close genetic affinity with Hunan Han and Guizhou Shui, respectively. Collectively, this new-generation Y-STR amplification system can be used as a supplementary tool in forensic identification and male parentage testing and even pedigree search.
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Yuasa I, Akane A, Yamamoto T, Matsusue A, Endoh M, Nakagawa M, Umetsu K, Ishikawa T, Iino M. Japaneseplex: A forensic SNP assay for identification of Japanese people using Japanese-specific alleles. Leg Med (Tokyo) 2018; 33:17-22. [PMID: 29705644 DOI: 10.1016/j.legalmed.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 02/15/2018] [Accepted: 04/23/2018] [Indexed: 11/17/2022]
Abstract
It is sometimes necessary to determine whether a forensic biological sample came from a Japanese person. In this study, we developed a 60-locus SNP assay designed for the differentiation of Japanese people from other East Asians using entirely and nearly Japanese-specific alleles. This multiplex assay consisted of 6 independent PCR reactions followed by single nucleotide extension. The average number and standard deviation of Japanese-specific alleles possessed by an individual were 0.81 ± 0.93 in 108 Koreans from Seoul, 8.87 ± 2.89 in 103 Japanese from Tottori, 17.20 ± 3.80 in 88 Japanese from Okinawa, and 0 in 220 Han Chinese from Wuxi and Changsha. The Koreans had 0-4 Japanese-specific alleles per individual, whereas the Japanese had 4-26 Japanese-specific alleles. Almost all Japanese were distinguished from the Koreans and other people by the factorial correspondence and principal component analyses. The Snipper program was also useful to estimate the degree of Japaneseness. The method described here was successfully applied to the differentiation of Japanese from non-Japanese people in forensic cases. This Japanese-specific SNP assay was named Japaneseplex.
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Affiliation(s)
- Isao Yuasa
- Division of Legal Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan.
| | - Atsushi Akane
- Department of Legal Medicine, Kansai Medical University, Hirakata, Japan
| | - Toshimichi Yamamoto
- Department of Legal Medicine and Bioethics, Nagoya University School of Medicine, Nagoya, Japan
| | - Aya Matsusue
- Department of Forensic Medicine, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Minoru Endoh
- Division of Legal Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
| | - Mayumi Nakagawa
- Department of Pathobiological Science and Technology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kazuo Umetsu
- Department of Forensic Medicine, Yamagata University School of Medicine, Yamagata, Japan
| | - Takaki Ishikawa
- Department of Legal Medicine, Osaka City University Medical School, Osaka, Japan
| | - Morio Iino
- Division of Legal Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
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A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese. Eur J Hum Genet 2013; 22:248-53. [PMID: 23714748 DOI: 10.1038/ejhg.2013.111] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/10/2013] [Accepted: 04/16/2013] [Indexed: 12/19/2022] Open
Abstract
Population stratification acts as a confounding factor in genetic association studies and may lead to false-positive or false-negative results. Previous studies have analyzed the genetic substructures in Han Chinese population, the largest ethnic group in the world comprising ∼20% of the global human population. In this study, we examined 5540 Han Chinese individuals with about 1 million single-nucleotide polymorphisms (SNPs) and screened a panel of ancestry informative markers (AIMs) to facilitate the discerning and controlling of population structure in future association studies on Han Chinese. Based on genome-wide data, we first confirmed our previous observation of the north-south differentiation in Han Chinese population. Second, we developed a panel of 150 validated SNP AIMs to determine the northern or southern origin of each Han Chinese individual. We further evaluated the performance of our AIMs panel in association studies in simulation analysis. Our results showed that this AIMs panel had sufficient power to discern and control population stratification in Han Chinese, which could significantly reduce false-positive rates in both genome-wide association studies (GWAS) and candidate gene association studies (CGAS). We suggest this AIMs panel be genotyped and used to control and correct population stratification in the study design or data analysis of future association studies, especially in CGAS which is the most popular approach to validate previous reports on genetic associations of diseases in post-GWAS era.
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Qu HQ, Li Q, Lu Y, Fisher-Hoch SP, McCormick JB. Translational genomic medicine: common metabolic traits and ancestral components of Mexican Americans. J Med Genet 2012; 49:544-5. [PMID: 22717649 PMCID: PMC3419327 DOI: 10.1136/jmedgenet-2012-100966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Hui-Qi Qu
- The University of Texas School of Public Health, Brownsville Regional Campus, Brownsville, Texas, USA
| | - Quan Li
- Endocrine Genetics Lab, The McGill University Health Center (Montreal Children’s Hospital), Montréal, Québec, Canada
| | - Yang Lu
- The University of Texas School of Public Health, Brownsville Regional Campus, Brownsville, Texas, USA
| | - Susan P Fisher-Hoch
- The University of Texas School of Public Health, Brownsville Regional Campus, Brownsville, Texas, USA
| | - Joseph B McCormick
- The University of Texas School of Public Health, Brownsville Regional Campus, Brownsville, Texas, USA
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