80 results on '"Jiangwei Yan"'
Search Results
2. Application of Microbiome in Forensics
- Author
-
Jun Zhang, Wenli Liu, Halimureti Simayijiang, Ping Hu, and Jiangwei Yan
- Subjects
Computational Mathematics ,Genetics ,Molecular Biology ,Biochemistry - Abstract
Recent advances in next-generation sequencing technology and improvements in bioinformatics have expanded the scope of microbiome analysis as a forensic tool. Microbiome research is concerned with the study of the compositional profile and diversity of microbial flora as well as the interactions between microbes, hosts, and the environment. It has opened up many new possibilities for forensic analysis. In this review, we discuss various applications of microbiomes in forensics, including identification of individuals, geolocation inference, post-mortem interval (PMI) estimation, and others.
- Published
- 2022
3. A recombinase polymerase amplification (RPA) combined with strip visualization method for RNA-based presumptive tests of saliva and vaginal secretion
- Author
-
Jinding, Liu, Xiuying, Zhang, Yao, Liu, Jiajia, Fan, Mingming, Zhang, Huan, Yu, Wenyan, Li, Jing, Li, Zeqin, Li, Jiangwei, Yan, and Gengqian, Zhang
- Subjects
Male ,Recombinases ,Genetics ,Humans ,RNA ,Female ,RNA, Messenger ,Salivary Proteins and Peptides ,Nucleic Acid Amplification Techniques ,Sensitivity and Specificity ,Aged ,Body Fluids ,Pathology and Forensic Medicine - Abstract
Identifying the origin of body fluids is a critical step in a forensic investigation. One widely used method to identify human body fluids is based on the color visualization of immune antigen detection strips for detecting hemoglobin in blood and prostate-specific antigen in semen. It is highly imperative to construct an easy-to-perform, mRNA-based method for the point-of-care identification of other human body fluids, such as saliva and vaginal secretion. Here, we established specific strips with the mRNA markers STATH (for saliva) and SPINK5 (for vaginal secretion) via reverse transcription recombinase polymerase amplification (RT-RPA) and lateral flow dipstick (LFD) assays (RT-RPA-LFD). RT-RPA could be accomplished in a single tube at a wide temperature range of 30-42 ℃ within 10-25 min if we do not count time for RNA extraction. The diluted RPA products were added onto the LFD strip pad to visually observe the color change of the Control/Test line. The tissue specificity and detection limit of the assays were evaluated using the optimized reaction conditions of RPA at 37 ℃ for 15 min. The positive signals of STATH were observed both in saliva and nasal secretions. SPINK5 was positive in a template-dependent manner in 4 out of 30 female urine samples in addition to vaginal secretion and menstrual blood samples. Cross-reactions were not detected in semen, skin swabs, sweat, or male urine. Both assays were capable of detecting aged samples, which were stored for 180 days (saliva) or 300 days (vaginal secretion) at room temperature. Moreover, saliva or vaginal secretion was successfully detected in all kinds of mixtures made from various body fluids. Overall, the rapid strip test method by the RT-RPA-LFD assay is simple, time-saving and highly sensitive for estimating the tissue origin of saliva and vaginal secretion. This method for the rapid RNA-based presumptive tests of the tissue type of body fluids is easy to perform prior to a multiplex mRNA analysis, which can demonstrate more reliable saliva or vaginal secretion identification.
- Published
- 2023
4. Distinguishing between Monozygotic Twins' Blood Samples Through Immune Repertoire Sequencing
- Author
-
Deping Meng, Peng Zhou, Min Li, Jie Xu, Linchao Lu, Yilin Guo, Chunjiang Yu, Yuliu Xu, Xiaoqun Xu, Chen Fang, and Jiangwei Yan
- Subjects
Genetics ,Pathology and Forensic Medicine - Published
- 2022
5. Multiple methods used for type detection of uniparental disomy in paternity testing
- Author
-
Xiao Wang, Hongliang Su, Tingting Sun, Man Chen, Wenyan Ren, Jiangwei Yan, Keming Yun, Gengqian Zhang, Yaming Chen, and Jinding Liu
- Subjects
Adult ,Male ,congenital, hereditary, and neonatal diseases and abnormalities ,Genotype ,Paternity ,Single-nucleotide polymorphism ,Multiple methods ,Biology ,Polymorphism, Single Nucleotide ,Pathology and Forensic Medicine ,symbols.namesake ,Gene Frequency ,INDEL Mutation ,medicine ,Humans ,SNP ,Genetic Testing ,Child ,Genotyping ,Genetics ,Uniparental Disomy ,medicine.disease ,DNA Fingerprinting ,Uniparental disomy ,Molecular Diagnostic Techniques ,Mendelian inheritance ,symbols ,Microsatellite ,Female ,Microsatellite Repeats - Abstract
Uniparental disomy (UPD) has attracted more attention recently in paternity testing, though it is an infrequent genetic event. Although short tandem repeat (STR) profiling has been widely used in paternity testing, it is not sufficient to use STR only to judge the genetic relationship, because the existence of UPD will inevitably affect the results of genotyping. Compared with complete UPD, segmental UPD is more difficult to detect because it does not affect all genotypes on the same chromosome. It is necessary to determine the type of UPD with multiple methods because a single method is not sufficient. Therefore, it is advisable to detect UPD in paternity testing with multiple methods. In this study, after autosomal STR profiling was used, we found that there were several gene loci on the same chromosome that did not conform to Mendelian genetic law, thus we highly suspected the existence of UPD and performed X-STR profiling immediately. Then whole-genome single nucleotide polymorphism (SNP) array analysis was performed to identify the type, and the results provided straightforward evidence for distinguishing complete from segmental UPD. Lastly, we used deletion insertion polymorphism (DIP)-SNP SNaPshot assay and Miseq FGx sequencing (for SNP and STR) to determine whether the mutation source is maternal uniparental disomy (mUPD) or paternal uniparental disomy (pUPD). To avoid false exclusion of kinship, it is vital to determine the type of UPD in paternity testing and effective strategies based on multiple methods to detect the type of UPD are provided in this study.
- Published
- 2019
6. Estimating the time since deposition (TsD) in saliva stains using temporal changes in microbial markers
- Author
-
Jiaqi, Wang, Xiaojuan, Cheng, Jun, Zhang, Zidong, Liu, Feng, Cheng, Jiangwei, Yan, and Gengqian, Zhang
- Subjects
RNA, Ribosomal, 16S ,Genetics ,Humans ,Forensic Medicine ,Coloring Agents ,Saliva ,Biomarkers ,Pathology and Forensic Medicine - Abstract
Determining the time since deposition (TsD) of traces could be helpful in the investigation of criminal offenses. However, there are no reliable markers and models available for the inference of short-term TsD. The goal of this study was to investigate the potential of the succession pattern of human salivary microbial communities to serve as an efficiency TsD prediction tool in the resolution of the forensic cases. Saliva stains exposed to indoor conditions up to 20 days were collected and analyzed by 16S rRNA profiling using high-throughput sequencing technique. Noticeable differences in microbial composition were observed between different time points, and the indoor exposure time of saliva stains were inversely correlated with alpha diversity estimates across the measured time period. The sequencing results were used to identify TsD-dependent bacterial indicators to regress a generalized random forest model, resulting in a mean absolute deviation (MAD) of 1.41 days. Furthermore, a simplified TsD predictive model was also developed utilizing Enhydrobacter, Paenisporosarcina, and Janthinobacterium by quantitative PCR (qPCR) with a MAD of 1.32 days, and then forensic practice assessment were also performed by using mock samples with a MAD of 3.53 days. In conclusion, this study revealed significant changes in salivary microbial abundance as the prolongation of TsD. It demonstrated that the microbial biomarkers could be invoked as a "clock" for TsD estimation in human dried saliva stains.
- Published
- 2022
7. Development of a new 17 Y-STRs system using fluorescent-labelled universal primers and its application in Shanxi population in China
- Author
-
Xiaojuan Cheng, Jiangwei Yan, Ting Hao, Jinding Liu, Rongshuai Wang, Keming Yun, Jiangling Guo, and Gengqian Zhang
- Subjects
education.field_of_study ,Population ,Haplotype ,Population genetics ,Computational biology ,Biology ,humanities ,Pathology and Forensic Medicine ,Forensic identification ,Multiplex polymerase chain reaction ,Genetics ,Microsatellite ,Identification (biology) ,education ,Genotyping - Abstract
Y-chromosomal short tandem repeats (Y-STRs) polymorphisms are useful in forensic identification, population genetics and constructing of human structures. Increasing the number of Y-STRs and their polymorphism will drastically narrow down the matching number of genealogy populations or pedigrees when searching against a forensic DNA databank. In this study, we develop a system containing 17 complementary Y-STRs that are compatible and reinforce the current commercially available Y-STR kits. This system was constructed by multiplex PCR with expected size of 126bp-400bp using home-made universal primers labeled by different fluorescence (DYS715, DYS709, DYS716, DYS713, DYS607, DYS718, DYS723, DYS708, DYS714, DYS712, DYS717, DYS721, DYS605, DYS719, DYS726, DYS598 and DYS722). The genetic data were obtained from 394 individuals in Shanxi province, China. The Y-STR system has 131 haplotypes and high discrimination power is 1. In conclusion, our study provides a robust, sensitive and cost-effective genotyping method for human identification, which is beneficial for narrowing the searching scope when applying to the genealogy searching with Y-STR DNA databank.
- Published
- 2019
8. MicroRNA profile analysis for discrimination of monozygotic twins using massively parallel sequencing and real-time PCR
- Author
-
Jiangwei Yan, Chunrui Yu, Huijuan Wu, Zhang Xiaoli, Jing Zhao, Qian Jialin, Liu Xu, Yaran Yang, Jingjing Zhang, Liu Wenli, Yunwang Cao, and Chen Fang
- Subjects
Adult ,Male ,0301 basic medicine ,Adolescent ,Computational biology ,Biology ,Real-Time Polymerase Chain Reaction ,Pathology and Forensic Medicine ,law.invention ,Young Adult ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,law ,microRNA ,Genetics ,Humans ,030216 legal & forensic medicine ,Child ,Polymerase chain reaction ,Massive parallel sequencing ,Sequence Analysis, RNA ,High-Throughput Nucleotide Sequencing ,Twins, Monozygotic ,MicroRNA Profile ,Middle Aged ,MicroRNAs ,genomic DNA ,030104 developmental biology ,Real-time polymerase chain reaction ,chemistry ,Microsatellite ,Female ,DNA - Abstract
In general, it is extremely problematic to discriminate between monozygotic twins (MZTs), who share the same genomic DNA sequence, using traditional DNA-based identification methods such as short tandem repeat profiling. MicroRNAs (miRNAs) have shown potential in forensic applications owing to their low molecular weight, abundant and tissue-specific expression. In this study, we utilized massively parallel sequencing technology to perform genome-wide profiling of miRNAs in the blood from four pairs of healthy MZTs. On average, 158 miRNAs were detected in each individual and 14% of which were differentially expressed within each pair of MZTs. The miRNAs with the most significant differences in expression between the twins were confirmed using real-time polymerase chain reaction. Our results demonstrated that miRNAs have potential for use as molecular markers in MZTs discrimination.
- Published
- 2019
9. Retraction Note to: Revisiting the male genetic landscape of China: a multi-center study of almost 38,000 Y-STR haplotypes
- Author
-
Michael Nothnagel, Guangyao Fan, Fei Guo, Yongfeng He, Yiping Hou, Shengping Hu, Jiang Huang, Xianhua Jiang, Wook Kim, Kicheol Kim, Chengtao Li, Hui Li, Liming Li, Shilin Li, Zhao Li, Weibo Liang, Chao Liu, Di Lu, Haibo Luo, Shengjie Nie, Meisen Shi, Hongyu Sun, Jianpin Tang, Lei Wang, Chuan-Chao Wang, Dan Wang, Shao-Qing Wen, Hongyan Wu, Weiwei Wu, Jiaxin Xing, Jiangwei Yan, Shi Yan, Hongbing Yao, Yi Ye, Libing Yun, Zhaoshu Zeng, Lagabaiyila Zha, Suhua Zhang, Xiufen Zheng, Sascha Willuweit, and Lutz Roewer
- Subjects
Genetics ,Genetics (clinical) - Published
- 2021
10. Predicting the postmortem interval of burial cadavers based on microbial community succession
- Author
-
Gengqian Zhang, Feng Liu, Qi Xiaoqin, Zhang Jun, Linyu Shi, Wang Mengchun, Jiarong Zhang, Xiaomeng Zhang, Jianbo Ren, Jiangwei Yan, and Tingting Yang
- Subjects
0301 basic medicine ,Forensic Genetics ,Veterinary medicine ,Burial ,Mean absolute error ,Ecological succession ,Biology ,Polymerase Chain Reaction ,Pathology and Forensic Medicine ,Rats, Sprague-Dawley ,03 medical and health sciences ,0302 clinical medicine ,RNA, Ribosomal, 16S ,Genetics ,Cadaver ,Animals ,030216 legal & forensic medicine ,Soil Microbiology ,Skin ,Microbiota ,Rectum ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Pmi estimation ,030104 developmental biology ,Microbial population biology ,Postmortem Changes ,Models, Animal - Abstract
Previous studies have demonstrated that microbial community succession during the decomposition of cadavers could be used to estimate the postmortem interval (PMI). However, the vast majority of the existing studies focused on exposed cadavers. In fact, burial cadavers are common scenarios for forensic investigations. In this study, the microbial communities from gravesoil, rectum and skin of burial SD rat cadavers during decomposition were characterized using 16S rRNA gene high-throughput sequencing. We predicted PMI based on the microbial community succession. Obvious differences in microbial community structures were observed between different stages of decomposition. Later decay stages had a lower alpha diversity compared to earlier decay stages. Significant linear relationships between similarities of the microbial communities and postmortem intervals were observed, manifesting regular succession over the course of decomposition. Furthermore, we combined random forest models with postmortem microbial features to predict PMI. The model explained 86.83%, 84.55% and 81.67% of the variation in the microbial community, with a mean absolute error of 1.82, 2.06 and 2.13 days within 60 days of decomposition for gravesoil, rectum and skin of burial cadavers, respectively. Overall, our results suggested that postmortem microbial community data could serve as a potential forensic tool to estimate accurate PMI of burial cadavers.
- Published
- 2020
11. Non-pathological complete paternal uniparental isodisomy of chromosome 2 revealed in a maternity testing case
- Author
-
He Ren, Jiangwei Yan, Zhiyong Liu, Feng Cheng, Chuguang Chen, Jing Zhao, Jian Jiang, Chen Li, Wei Chen, Tong Chen, and Man Chen
- Subjects
Genetics ,Daughter ,media_common.quotation_subject ,Chromosome ,030209 endocrinology & metabolism ,Single-nucleotide polymorphism ,030204 cardiovascular system & hematology ,Biology ,medicine.disease ,Uniparental disomy ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,Uniparental Isodisomy ,Genetic marker ,medicine ,Microsatellite ,Pathological ,media_common - Abstract
We present a duo paternity test case to assess the biological relationship between a woman and her female child. After analyzing 57 autosomal and 19 X-chromosomal short tandem repeat loci, mother-daughter exclusions were discovered at four loci, which were all located on chromosome 2. Further testing of whole-genome single nucleotide polymorphisms confirmed that the daughter had complete uniparental disomy (UPD) of chromosome 2. This study presents a cautionary case demonstrating that hasty decisions of parentage exclusion should not be made when genetic markers on the same chromosome do not conform to Mendel's laws due to UPD.
- Published
- 2018
12. Tri-allelic patterns of STRs and partially homologous non-sister chromatid crossover observed in a parentage test
- Author
-
Chuguang Chen, Jiangwei Yan, Huiyong Jiao, Haiyan Zhou, Yunwang Cao, Yaran Yang, Bin Ni, He Ren, Wei Chen, and Yanmei Huang
- Subjects
Male ,0301 basic medicine ,DNA Copy Number Variations ,Aneuploidy ,Paternity ,Chromatids ,Biology ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Homologous chromosome ,Humans ,Sister chromatids ,Alleles ,Genetics ,Chromosome ,Karyotype ,medicine.disease ,Molecular biology ,Issues, ethics and legal aspects ,Genetics, Population ,030104 developmental biology ,030220 oncology & carcinogenesis ,Female ,Chromatid ,Trisomy ,Chromosome 21 ,Microsatellite Repeats - Abstract
A maternity testing case is reported, in which the child showed tri-allelic patterns in two short tandem repeat (STR) loci. The genotypes of Penta D of the mother and the child were 9,13 and 9,10,13, respectively. Those of D21S11 were 32.2,35 and 29,35, respectively, but intensity ratio of alleles 29 and 35 of the child was 1:2. These results suggested the copy number variations (CNVs) or trisomy of chromosome 21. By further examination using STR-based chromosome aneuploidy detection kit, three alleles were detected in D21S1411, LFG21 and Penta D, and 2 alleles with intensity ratio of 1:2 were observed in D21S2502, D21S1435, D21S11 and D21S1246. Karyotype and whole-genome SNP array analyses showed that the child had a free trisomy 21. In addition, partially homologous non-sister chromatid crossover occurred at the region 19181770-39499178 on the long arm of chromosome 21.
- Published
- 2018
13. Identification of coding region SNPs from specific and sensitive mRNA biomarkers for the deconvolution of the semen donor in a body fluid mixture
- Author
-
Jinding Liu, Zidong Liu, Jie Shi, Jiangling Guo, Gengqian Zhang, Wenyan Li, Xiuying Zhang, Jiangwei Yan, Jiaqi Wang, Xiaojuan Cheng, Feng Liu, Jing Li, Jintao Li, and Ting Hao
- Subjects
Forensic Genetics ,Genetic Markers ,Male ,0301 basic medicine ,L-Iditol 2-Dehydrogenase ,Saliva ,Context (language use) ,Semen ,Biology ,Seminal Vesicle Secretory Proteins ,Polymerase Chain Reaction ,Polymorphism, Single Nucleotide ,Pathology and Forensic Medicine ,03 medical and health sciences ,fluids and secretions ,0302 clinical medicine ,Multiplex polymerase chain reaction ,Genetics ,Humans ,Coding region ,RNA, Messenger ,030216 legal & forensic medicine ,Creatine Kinase ,Homeodomain Proteins ,Body fluid ,Transglutaminases ,Electrophoresis, Capillary ,Nuclear Proteins ,Prostate-Specific Antigen ,Molecular biology ,Reverse transcription polymerase chain reaction ,genomic DNA ,030104 developmental biology ,Cervix Mucus ,Female ,Kallikreins ,Multiplex Polymerase Chain Reaction ,Blood Chemical Analysis ,Transcription Factors - Abstract
mRNA markers provide a very promising method for the identification of human body fluids or tissues in the context of forensic investigations. Previous studies have shown that different body fluids can be distinguished from each other according to their specific mRNA biomarkers. In this study, we evaluated eight semen-specific mRNA markers (KLK3, NKX3–1, CKB, KLK2, PRAC1, SEMG1, TGM4, and SORD) that encompass 12 coding single nucleotide polymorphisms (cSNPs) to identify the semen contributor in a mixed stain. Five highly specific and sensitive mRNA markers for blood, menstrual blood, saliva, vaginal secretions, and skin were also incorporated into the PCR system as body fluid-positive controls. Reverse transcription polymerase chain reaction (RT-PCR), multiplex PCR and SNaPshot mini-sequencing assays were established for the identification of semen-specific mRNA. The amplicon size ranged from 133 to 337 bp. The semen-specific system was examined against blood, menstrual blood, saliva, vaginal secretions, and skin swabs. The eight mRNA biomarkers were semen-specific and could be successfully typed in laboratory-generated mixtures composed of different body fluids supplemented with 1 ng of semen cDNA. This system possessed a high sensitivity that ranged from 1:10–1:100 for detecting trace amounts of semen in semen-containing body fluid mixtures. Additionally, our results demonstrated that the cSNPs polymorphisms included in the mRNA markers were concordant with genomic DNA (gDNA). Despite the presence of other body fluids, the system exhibited high sensitivity and specificity to the semen in the mixture. In future studies, we will add other cSNPs from the semen-specific genes using massively parallel sequencing to further improve our system.
- Published
- 2021
14. Chinese Xibe population genetic composition according to linkage groups of X-chromosomal STRs: population genetic variability and interpopulation comparisons
- Author
-
Ting Mei, Yuxin Guo, Qian Dong, Chun-Mei Shen, Hao-Tian Meng, Yu-Dang Zhang, Jianfeng Shi, Bofeng Zhu, Yao-Shun Liu, Jiangwei Yan, and Guang Yang
- Subjects
Male ,0301 basic medicine ,China ,Aging ,Genetic Linkage ,Physiology ,Epidemiology ,Population ,Biology ,03 medical and health sciences ,0302 clinical medicine ,Gene Frequency ,Genetics ,Humans ,030216 legal & forensic medicine ,Genetic variability ,Allele ,education ,Phylogeny ,Linkage (software) ,Chromosomes, Human, X ,education.field_of_study ,Haplotype ,Public Health, Environmental and Occupational Health ,030104 developmental biology ,Haplotypes ,Population data ,Microsatellite ,Female ,Genetic composition ,Microsatellite Repeats - Abstract
The Xibe population is one of China's officially recognised populations and is now distributed separately from west to east in the northern part of China. X-chromosomal short tandem repeats have a special inheritance pattern, and could be used as complements in forensic application, especially for complex or deficiency cases.This study obtained the allelic and haplotypic frequencies of 19 X-STR loci in the Xibe population from Xinjiang Uygur Autonomous Region, China, and studied the genetic differentiations between the Xibe and other populations.The combined power of discrimination in females and males and mean exclusion chances in deficiency cases, normal trios and duo cases was at least 0.999 999 994. In the haplotypic study, the Xibe population showed a more similar pattern of haplotype distribution with Asian populations than populations from other continents, while allelic study also indicated a closer relationship between the Xibe and Asian populations.The 19 X-STR loci would be useful in forensic application in the studied population. The Xibe population showed a closer genetic relationship with Asian populations in the study, and more population data would be necessary for more detailed genetic relationship studies.
- Published
- 2017
15. Genetic diversity and haplotypic structure of Chinese Kazak ethnic group revealed by 19 STRs on the X chromosome
- Author
-
Li-Ping Zhang, Qian Dong, Jiangwei Yan, Yuxin Guo, Bofeng Zhu, Jian-Gang Chen, Ting Mei, Yu-Dang Zhang, Hao-Tian Meng, Jing Chen, and Yao-Shun Liu
- Subjects
Forensic Genetics ,Genetic Markers ,Male ,0301 basic medicine ,China ,Population ,Population genetics ,Locus (genetics) ,Biology ,Linkage Disequilibrium ,03 medical and health sciences ,0302 clinical medicine ,Asian People ,Gene Frequency ,Ethnicity ,Genetics ,Humans ,030216 legal & forensic medicine ,Allele ,education ,Alleles ,Phylogeny ,X chromosome ,Chromosomes, Human, X ,Genetic diversity ,education.field_of_study ,Polymorphism, Genetic ,Genetic Variation ,General Medicine ,humanities ,Pedigree ,Forensic identification ,Genetics, Population ,030104 developmental biology ,Haplotypes ,Microsatellite ,Female ,Microsatellite Repeats - Abstract
X-chromosomal short tandem repeats (X-STRs) have been widely used in forensic practices involving complicated ties of kinship over the past years, and also play an increasingly important role in population genetics. To study the genetic polymorphisms of 19 STR loci on X chromosome in Chinese Kazak ethnic group, we investigated the allelic and haplotypic frequencies of the 19 loci in 300 (149 males and 151 females) unrelated healthy individuals from Ili Kazak Autonomous Prefecture, Xinjiang Uigur Autonomous Region of China after having evaluated the forensic application value of these loci in forensic sciences, and then compared the population distinctions between the Kazak group and other reference groups. We observed a total of 240 alleles at these X-STR loci with the corresponding allelic frequencies ranging from 0.0017 to 0.5917. In the study, the highest polymorphism was found at DXS10135 locus. The combined power of discrimination in females was 0.999999999999999999999985 and in males 0.999999999999968. The present study indicates that the 19 X-STR loci are very useful for both forensic identification cases and kinship analyses involving a female offspring.
- Published
- 2017
16. RETRACTED ARTICLE: Revisiting the male genetic landscape of China: a multi-center study of almost 38,000 Y-STR haplotypes
- Author
-
Meisen Shi, Lagabaiyila Zha, Suhua Zhang, Wook Kim, Zhaoshu Zeng, Libing Yun, Xianhua Jiang, Dan Wang, Yiping Hou, Zhao Li, Haibo Luo, Liming Li, Shao-Qing Wen, Yongfeng He, Michael Nothnagel, Jia-xin Xing, Shilin Li, Hui Li, Weibo Liang, Chengtao Li, Kicheol Kim, Jianpin Tang, Xiufen Zheng, Shi Yan, Weiwei Wu, Jiang Huang, Yi Ye, Hongyan Wu, Sheng-Ping Hu, Hong-Bing Yao, Di Lu, Fei Guo, Sascha Willuweit, Lei Wang, Lutz Roewer, Guangyao Fan, Chao Liu, Shengjie Nie, Hongyu Sun, Chuan-Chao Wang, and Jiangwei Yan
- Subjects
0301 basic medicine ,Mainland China ,education.field_of_study ,Haplotype ,Population ,Ethnic origin ,Biology ,Y chromosome ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Genetic distance ,Evolutionary biology ,Genetic variation ,Genetics ,030216 legal & forensic medicine ,China ,education ,Genetics (clinical) - Abstract
China has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography. While some studies reported a genetic distinction between Northern and Southern Han Chinese, others showed a more clinal picture of small differences within China. Here, we investigated the distribution of Y chromosome variation along administrative as well as ethnic divisions in the mainland territory of the People's Republic of China, including 28 administrative regions and 19 recognized Chinese nationalities, to assess the impact of recent demographic processes. To this end, we analyzed 37,994 Y chromosomal 17-marker haplotype profiles from the YHRD database with respect to forensic diversity measures and genetic distance between groups defined by administrative boundaries and ethnic origin. We observed high diversity throughout all Chinese provinces and ethnicities. Some ethnicities, including most prominently Kazakhs and Tibetans, showed significant genetic differentiation from the Han and other groups. However, differences between provinces were, except for those located on the Tibetan plateau, less pronounced. This discrepancy is explicable by the sizeable presence of Han speakers, who showed high genetic homogeneity all across China, in nearly all studied provinces. Furthermore, we observed a continuous genetic North-South gradient in the Han, confirming previous reports of a clinal distribution of Y chromosome variation and being in notable concordance with the previously observed spatial distribution of autosomal variation. Our findings shed light on the demographic changes in China accrued by a fast-growing and increasingly mobile population.
- Published
- 2017
17. The application of next-generation sequencing to validate D12S391 microvariation
- Author
-
Li Jia, He Ren, Jiangwei Yan, Jin-jie Liu, Shuai Sun, Qing-xia Zhang, Yi Zhao, Ya-Cheng Liu, and Chong Chen
- Subjects
Genetics ,lcsh:Public aspects of medicine ,Mutation ,Locus (genetics) ,next-generation sequencing ,lcsh:RA1-1270 ,Allele ,Biology ,STR ,Law ,DNA sequencing ,Pathology and Forensic Medicine - Abstract
Objective: In a paternity case, the D12S391 locus was reported as a mismatch. To confirm the existence of mutations and mutations come from father or mother. Methods: STR and next-generation sequencing technology were used to validate the sequence. Results: NGS showed the loss of one adenine between the 19.3 allele of the child and allele 20 of the mother. Conclusion: The NGS can be applied in the paternity to validate the mutation.
- Published
- 2018
18. Comparison of CE- and MPS-based analyses of forensic markers in a single cell after whole genome amplification
- Author
-
Man Chen, Jiangwei Yan, Zhiyong Liu, Qingwei Fan, Jingjing Zhang, Tong Chen, Jing Zhao, and Feng Cheng
- Subjects
0301 basic medicine ,Forensic Genetics ,Genetic Markers ,Male ,Genotype ,Single-nucleotide polymorphism ,Biology ,Polymorphism, Single Nucleotide ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,Genetics ,Humans ,030216 legal & forensic medicine ,Allele ,Genotyping ,Whole Genome Amplification ,Blood Cells ,Genome, Human ,Multiple displacement amplification ,Electrophoresis, Capillary ,High-Throughput Nucleotide Sequencing ,Molecular biology ,SNP genotyping ,030104 developmental biology ,Microsatellite ,Female ,Nucleic Acid Amplification Techniques ,Microsatellite Repeats - Abstract
Whole genome amplification (WGA) allows for multiple genetic analyses with low template DNA, such as DNA derived from a single cell. WGA could increase the amount of input DNA from the pg to the μg level. However, there are no studies comparing the performance of forensic markers with DNA from a single cell after WGA evaluated on both capillary electrophoresis (CE) and massively parallel sequencing (MPS) platforms. In this study, cell lines consisting of female cultured B-lymphoblastoid cells and karyocytes from male venous blood were segregated into one, two, three and five cells. Including the references with the bulk cells, all samples were generated by WGA with the multiple displacement amplification (MDA) strategy in triplicate and genotyped on CE and MPS platforms. Allele balance, stutter ratio, accuracy, repeatability and concordance of short tandem repeat (STR) markers were used to evaluate the genotyping performance on both platforms. Additionally, the sequence coverage ratio (SCR) and SNP genotypes were evaluated for sequence information generated from the MPS. Heterozygous loci showed high allele balance, with an overall average allele balance ratio larger than 0.79 on the CE and 0.75 on the MPS platforms for the venous blood cell samples; the cultured B-lymphoblastoid cell samples had ratios of 0.62 and 0.70, respectively. The stutter ratio of every source and cell number from both cell line samples were very close, ranging from 5.3%-7.2% for autosomal STRs and approximately 10 % of Y chromosomal STRs on the CE platform. The average stutter, allele, and sequence-based and length-based noise ratios were 6.6 %, 88 %, 4.7 % and 0.7 %, respectively, in the single male cell sample. SNPs also showed high consistency and intralocus balance. Our study indicated that WGA with MDA strategy works relatively well of STR and SNP genotyping with low copy number samples on CE and MPS, even with one-cell sample.
- Published
- 2019
19. Multistep microsatellite mutation at D18S51 locus in a parentage testing case
- Author
-
He Ren, Chen Li, Yang Meng, Yacheng Liu, Yaran Yang, and Jiangwei Yan
- Subjects
0301 basic medicine ,Genetics ,Paternity Index ,Biological Father ,Locus (genetics) ,Biology ,Pathology and Forensic Medicine ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Genotype ,Str loci ,Microsatellite ,030216 legal & forensic medicine ,Allele - Abstract
Mutations of short tandem repeats (STRs) loci might cause allelic mismatchs between the child and the parents, which entangled the forensic inference in paternity testing. Most of the reported microsatellite mutations are confined to single-step mutations, and multistep mutations were rarely reported and only account for a very limited number of STR mutation events in previously studied cases. Here we reported a paternity case with a mismatch in locus D18S51. The genotypes of the alleged father, the mother and the child in D18S51 locus were 14/23, 15/16, and 15/20, respectively. Examination of 38 autosomal STR loci revealed no mismatches, and the paternity index is above 1.58E+15. These results suggested that the alleged father is the biological father of the child that a rare three-steps mutation had occurred in the paternal allele of D18S51.
- Published
- 2017
20. Allele and haplotype diversity of new multiplex of 19 ChrX-STR loci in Han population from Guanzhong region (China)
- Author
-
Guang Yang, Yuxin Guo, Bofeng Zhu, Yu-Dang Zhang, Rui-Zhe Huang, Jiangwei Yan, Qian Dong, Hao-Tian Meng, Chun-Mei Shen, Ting Mei, and Yao-Shun Liu
- Subjects
Forensic Genetics ,Male ,0301 basic medicine ,China ,Clinical Biochemistry ,Population ,Locus (genetics) ,Biology ,Biochemistry ,Analytical Chemistry ,03 medical and health sciences ,0302 clinical medicine ,Humans ,Multiplex ,030216 legal & forensic medicine ,Allele ,Han population ,education ,Alleles ,Genetics ,Chromosomes, Human, X ,education.field_of_study ,Polymorphism, Genetic ,Haplotype ,Genetics, Population ,030104 developmental biology ,Haplotypes ,Genetic Loci ,Microsatellite ,Female ,Microsatellite Repeats - Abstract
X-chromosomal short tandem repeats (X-STRs) have been proved to be useful for some deficiency paternity cases in recent years. Here, we studied the genetic polymorphisms of 19 X-STR loci (DXS10148-DXS10135-DXS8378, DXS10159-DXS10162-DXS10164, DXS7132-DXS10079-DXS10074-DXS10075, DXS6809-DXS6789, DXS7424-DXS101, DXS10103-HPRTB-DXS10101 and DXS7423-DXS10134) in 252 male and 222 female individuals from Guanzhong Han population, China. No deviation for all 19 loci was observed from the Hardy-Weinberg equilibrium. The polymorphism information content values of the panel of 19 loci were more than 0.5 with the exception of the locus DXS7423. The combined power of discrimination were 0.9999999999999999999994340 in females and 0.9999999999997662 in males, respectively; and the combined mean exclusion chances were 0.999999993764 in duos and 0.999999999997444 in trios, respectively. The haplotype diversities for all the seven clusters of linked loci were more than 0.9. The results showed that the panel of 19 X-STR loci were powerful for forensic applications in Guanzhong Han population. Locus by locus population comparisons showed significant differences at more than seven loci between Guanzhong Han population and the groups from North America, Europe and Africa.
- Published
- 2016
21. Development of a rapid 21-plex autosomal STR typing system for forensic applications
- Author
-
Jiangwei Yan, Xu Liu, Meibo Xu, Chen Jing, Yuexin Lv, Feng Chen, Huijuan Wu, Yang Meng, Yaran Yang, Zailiang Yu, and Caiyong Yin
- Subjects
0301 basic medicine ,Genetics ,STR multiplex system ,Clinical Biochemistry ,Biology ,Biochemistry ,DNA extraction ,Analytical Chemistry ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Multiplex polymerase chain reaction ,Microsatellite ,Str typing ,030216 legal & forensic medicine ,Typing ,National standard ,Genotyping - Abstract
DNA-STR genotyping technology has been widely used in forensic investigations. Even with such success, there is a great need to reduce the analysis time. In this study, we established a new rapid 21-plex STR typing system, including 13 CODIS loci, Penta D, Penta E, D12S391, D2S1338, D6S1043, D19S433, D2S441 and Amelogenin loci. This system could shorten the amplification time to a minimum of 90 min and does not require DNA extraction from the samples. Validation of the typing system complied with the Scientific Working Group on DNA Analysis Methods (SWGDAM) and the Chinese National Standard (GA/T815-2009) guidelines. The results demonstrated that this 21-plex STR typing system was a valuable tool for rapid criminal investigation.
- Published
- 2016
22. Precision methylome characterization ofMycobacterium tuberculosiscomplex (MTBC) using PacBio single-molecule real-time (SMRT) technology
- Author
-
Liya Yue, Lingna Lv, Cuidan Li, Xinmiao Jia, Guan Liu, Suting Chen, Mengxing Dong, Yu Kang, Lingxiang Zhu, Hairong Huang, Baoli Zhu, Jun Zhong, Fei Chen, Jing Fu, Jingfa Xiao, Jiangwei Yan, Xiuli Zhang, Bing Zhang, Qian Li, and Meng Lei
- Subjects
0301 basic medicine ,Minisatellite Repeats ,Biology ,Polymorphism, Single Nucleotide ,Genome ,Mycobacterium ,Evolution, Molecular ,Mycobacterium tuberculosis ,03 medical and health sciences ,Genetics ,DNA Modification Methylases ,Molecular Biology ,Gene ,Phylogeny ,Mycobacterium bovis ,Sequence Analysis, DNA ,Genomics ,Methylation ,DNA Methylation ,biology.organism_classification ,030104 developmental biology ,Mycobacterium tuberculosis complex ,DNA methylation ,Genome, Bacterial - Abstract
Tuberculosis (TB) remains one of the most common infectious diseases caused by Mycobacterium tuberculosis complex (MTBC). To panoramically analyze MTBC's genomic methylation, we completed the genomes of 12 MTBC strains (Mycobacterium bovis; M. bovis BCG; M. microti; M. africanum; M. tuberculosis H37Rv; H37Ra; and 6 M. tuberculosis clinical isolates) belonging to different lineages and characterized their methylomes using single-molecule real-time (SMRT) technology. We identified three (m6)A sequence motifs and their corresponding methyltransferase (MTase) genes, including the reported mamA, hsdM and a newly discovered mamB. We also experimentally verified the methylated motifs and functions of HsdM and MamB. Our analysis indicated the MTase activities varied between 12 strains due to mutations/deletions. Furthermore, through measuring 'the methylated-motif-site ratio' and 'the methylated-read ratio', we explored the methylation status of each modified site and sequence-read to obtain the 'precision methylome' of the MTBC strains, which enabled intricate analysis of MTase activity at whole-genome scale. Most unmodified sites overlapped with transcription-factor binding-regions, which might protect these sites from methylation. Overall, our findings show enormous potential for the SMRT platform to investigate the precise character of methylome, and significantly enhance our understanding of the function of DNA MTase.
- Published
- 2015
23. Haplotypic polymorphisms and mutation rate estimates of 22 Y-chromosome STRs in the Northern Chinese Han father–son pairs
- Author
-
Jiangwei Yan, Jing Zhao, Yacheng Liu, Feng Cheng, Chuguang Chen, Yan Shi, Man Chen, Chong Chen, Wei-ni Wang, Chen Li, Yaran Yang, and Tong Chen
- Subjects
0301 basic medicine ,Male ,Mutation rate ,China ,Science ,Population ,Locus (genetics) ,Biology ,Y chromosome ,Article ,03 medical and health sciences ,Fathers ,0302 clinical medicine ,Asian People ,Mutation Rate ,Humans ,030216 legal & forensic medicine ,Allele ,education ,Alleles ,Genetics ,education.field_of_study ,Multidisciplinary ,Chromosomes, Human, Y ,Polymorphism, Genetic ,Haplotype ,Forensic identification ,030104 developmental biology ,Genetics, Population ,Haplotypes ,Mutation ,Microsatellite ,Medicine ,Microsatellite Repeats - Abstract
Y chromosome Short tandem repeats (Y-STRs) analysis has been widely used in forensic identification, kinship testing, and population evolution. An accurate understanding of haplotype and mutation rate will benefit these applications. In this work, we analyzed 1123 male samples from Northern Chinese Han population which including 578 DNA-confirmed father-son pairs at 22 Y-STRs loci. A total of 537 haplotypes were observed and the overall haplotype diversity was calculated as 1.0000 ± 0.0001. Except that only two haplotypes were observed twice, all the rest of the 535 were unique. Furthermore, totally 47 mutations were observed during 13,872 paternal meiosis. The mutation rate for each locus estimates ranged from 0.0 to 15.6 × 10−3 with an average mutation rate 3.4 × 10−3 (95% CI 2.5–4.5 × 10−3). Among the 22 loci, DYS449, DYS389 II and DYS458 are the most prone to mutations. This study adds to the growing data on Y-STR haplotype diversity and mutation rates and could be very useful for population and forensic genetics.
- Published
- 2018
24. Genetic polymorphisms and association of KIR-HLA system of Chinese Henan Han population and an extensive KIR gene diversity study between populations distributed worldwide
- Author
-
Bofeng Zhu, Yuxin Guo, Chunmei Shen, Tie-niu Song, Jiangwei Yan, Caiyong Yin, Xiaoye Jin, Zhan-Qi Feng, and Hongdan Wang
- Subjects
Genetics ,Oncology ,media_common.quotation_subject ,Human leukocyte antigen ,Han population ,Biology ,Gene ,Diversity (politics) ,media_common - Published
- 2018
25. A 472-SNP panel for pairwise kinship testing of second-degree relatives
- Author
-
Huijuan Wu, Shao-Kang Mo, Zhen Li, Jiangwei Yan, Ming Ni, Zi-Lin Ren, Yacheng Liu, Yaran Yang, Shengqi Wang, Xiaochen Bo, and Jingjing Zhang
- Subjects
0301 basic medicine ,Genetic Markers ,China ,Genotype ,Single-nucleotide polymorphism ,Biology ,Polymorphism, Single Nucleotide ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,Asian People ,Gene Frequency ,Genetics ,SNP ,Humans ,030216 legal & forensic medicine ,Allele frequency ,Genotyping ,Likelihood Functions ,Massive parallel sequencing ,DNA Fingerprinting ,humanities ,Pedigree ,030104 developmental biology ,DNA profiling ,Microsatellite ,Human genome ,Multiplex Polymerase Chain Reaction ,Microsatellite Repeats - Abstract
Kinship testing based on genetic markers, as forensic short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), has valuable practical applications. Paternity and first-degree relationship can be accurately identified by current commonly-used forensic STRs and reported SNP markers. However, second-degree and more distant relationships remain challenging. Although ∼105-106 SNPs can be used to estimate relatedness of higher degrees, genome-wide genotyping and analysis may be impractical for forensic use. With rapid growth of human genome data sets, it is worthwhile to explore additional markers, especially SNPs, for kinship analysis. Here, we reported an autosomal SNP panel consisted of 342 SNP selected from >84 million SNPs and 131 SNPs from previous systems. We genotyped these SNPs in 136 Chinese individuals by multiplex amplicon Massively Parallel Sequencing, and performed pairwise gender-independent kinship testing. The specificity and sensitivity of these SNPs to distinguish second-degree relatives and the unrelated was 99.9% and 100%, respectively, compared with 53.7% and 99.9% of 19 commonly-used forensic STRs. Moreover, the specificity increased to 100% by the combined use of these STRs and SNPs. The 472-SNP panel could also greatly facilitate the discrimination among different relationships. We estimated that the power of ∼6.45 SNPs were equivalent to one forensic STR in the scenario of 2nd-degree relative pedigree. Altogether, we proposed a panel of 472 SNP markers for kinship analysis, which could be important supplementary of current forensic STRs to solve the problem of second-degree relative testing.
- Published
- 2017
26. Evaluation of the protective capabilities of nucleosome STRs obtained by large-scale sequencing
- Author
-
Chunnan Dong, Shujin Li, Lihong Fu, Jiangwei Yan, Yadong Yang, Xiaojing Zhang, and Bin Cong
- Subjects
Genetics ,education.field_of_study ,Clinical Biochemistry ,Population ,Biology ,Biochemistry ,DNA sequencing ,Analytical Chemistry ,chemistry.chemical_compound ,DNA profiling ,chemistry ,Nucleosome ,Microsatellite ,education ,Large-Scale Sequencing ,Gene ,DNA - Abstract
Partial DNA profiles are often obtained from degraded forensic samples and are hard to analyze and interpret. With in-depth studies on degraded DNA, an increasing number of forensic scientists have focused on the intrinsic structural properties of DNA. In theory, nucleosomes offer protection to the bound DNA by limiting access to enzymes. In our study, we performed large-scale DNA sequencing on nucleosome core DNA of human leucocytes. Five nucleosome short tandem repeats (STRs) were selected (including three forensic common STRs (i.e. TPOX, TH01, and D10S1248) and two unpublished STRs (i.e. AC012568.7 and AC007160.3)). We performed a population genetic investigation and forensic genetic statistical analysis of these two unpublished loci on 108 healthy unrelated individuals of the HeBei Han population in China. We estimated the protective capabilities of five selected nucleosome loci and MiniFiler™ loci with artificial degraded DNA and case samples. We also analyzed differences between sequencing results and software predicted results. Our findings showed that nucleosome STRs were more likely to be detected than MiniFiler™ loci. They were well protected from degradation by nucleosomes and could be candidates for further nucleosome multiplex construction, which would increase the chances of obtaining a better balanced profile with fewer allelic drop-outs.
- Published
- 2015
27. Forensic evaluation and population genetic study of 30 insertion/deletion polymorphisms in a Chinese Yi group
- Author
-
Ze-Long Yang, Bofeng Zhu, Rui Jin, Chun-Mei Shen, Hong Dan Wang, Yu-Dang Zhang, Bo Wang, Ya-Ni Li, Jiangwei Yan, Hao-Tian Meng, and Li-Xia Ma
- Subjects
Genetics ,education.field_of_study ,Phylogenetic tree ,Clinical Biochemistry ,Population ,Locus (genetics) ,Biology ,Biochemistry ,Analytical Chemistry ,Forensic science ,Insertion deletion ,Allele ,Indel ,education ,Allele frequency - Abstract
Insertion/deletion polymorphisms have become a research hot spot in forensic science due to their tremendous potential in recent years. In the present study, we investigated 30 indel loci in a Chinese Yi ethnic group. The allele frequencies of the short allele of the 30 indel loci were in the range of 0.1025–0.9221. The power of discrimination values were observed ranging from to 0.2630 (HLD111 locus) to 0.6607 (HLD70 locus) and probability of exclusion values ranged from 0.0189 (HLD111 locus) to 0.2343 (HLD56 locus). The combined power of discrimination and power of exclusion for 30 loci in the studied Yi group were 0.99999999995713 and 0.97746, respectively, which showed tremendous potential for forensic personal identification in the Yi group. Moreover, the DA distances, phylogenetic tree, principal component analysis, and cluster analysis showed the Yi group had close genetic relationships with the Tibetan, South Korean, Chinese Han, and She groups.
- Published
- 2015
28. Genetic diversities of 20 novel autosomal STRs in Chinese Xibe ethnic group and its genetic relationships with neighboring populations
- Author
-
Jiangwei Yan, Li-Ping Zhang, Bofeng Zhu, Yu-Dang Zhang, Chun-Hua Yang, Hua Wu, Wen-Juan Liu, Yan Wang, Hao-Tian Meng, Jian-Gang Chen, and Hongdan Wang
- Subjects
Male ,Genetics ,Principal Component Analysis ,Polymorphism, Genetic ,Phylogenetic tree ,Ethnic group ,Locus (genetics) ,Genetic relationship ,General Medicine ,Biology ,Linkage Disequilibrium ,Loss of heterozygosity ,Genetic distance ,Str loci ,Cluster Analysis ,Humans ,Female ,Allele ,Phylogeny ,Microsatellite Repeats - Abstract
In the present study, we investigated the genetic polymorphisms of 20 novel STR loci and one previously studied locus in the Xibe ethnic group from China, as well as its genetic relationships with neighboring populations. Totally 226 unrelated healthy Xibe individuals were involved in the study. At least 5 alleles were observed for each locus, with the minimum and maximum allelic frequencies of 0.0022 and 0.5221, respectively. We obtained the lowest and highest observed heterozygosity and expected heterozygosity at locus D1S1627 and D19S433, respectively. The values of combined power of discrimination and probability of exclusion of all the 21 STR loci were 0.99999999999999999997310 and 0.999998650, respectively. Analyses of interpopulation differentiation, principal component analysis, genetic distance and phylogenetic tree revealed the relationships between Xibe group and its neighboring groups, showing that the studied Xibe group had a close genetic relationship with the Mongolian group. The present results indicated that these 21 STR loci had high genetic polymorphisms in the studied Xibe group, and were capable for the paternity testing and individual identification in forensic application.
- Published
- 2015
29. Developmental validation of the AGCU 21+1 STR kit: A novel multiplex assay for forensic application
- Author
-
Rui Jin, Wen-Juan Liu, Du Wei'an, Xiao-Hua Bie, Bofeng Zhu, Jiangwei Yan, Hao-Tian Meng, Yu-Dang Zhang, Chun-Hua Yang, Chun-Mei Shen, Guang Yang, and Hongdan Wang
- Subjects
Genetics ,STR multiplex system ,Clinical Biochemistry ,Str loci ,Microsatellite ,Locus (genetics) ,Multiplex ,Dna index ,Biology ,Biochemistry ,Analysis method ,Analytical Chemistry - Abstract
In this study, we describe the developmental validation assay performed on a novel designed STR multiplex system, AGCU 21+1 STR kit. This kit contains a sex-determining locus amelogenin and 21 noncombined DNA index system STR loci, that are, D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435, and D5S2500. The 21+1 kit was validated by a series of tests including optimized PCR conditions, sensitivity, precision and accuracy, stutter ratio, DNA mixture, inhibitors, and species specificity according to the revised validation guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Our results in this study show that the kit is a useful tool for forensic application.
- Published
- 2014
30. Application of Next-generation Sequencing Technology in Forensic Science
- Author
-
Jiangwei Yan, Yaran Yang, and Bingbing Xie
- Subjects
Monozygotic twin ,Degradation of DNA ,Genomics ,Review ,Biology ,Biochemistry ,Field (computer science) ,DNA sequencing ,DNA database ,Genetics ,Humans ,Species identification ,lcsh:QH301-705.5 ,Molecular Biology ,Forensics ,business.industry ,Forensic Sciences ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,Data science ,Biotechnology ,Forensic science ,Computational Mathematics ,lcsh:Biology (General) ,Next-generation sequencing ,business - Abstract
Next-generation sequencing (NGS) technology, with its high-throughput capacity and low cost, has developed rapidly in recent years and become an important analytical tool for many genomics researchers. New opportunities in the research domain of the forensic studies emerge by harnessing the power of NGS technology, which can be applied to simultaneously analyzing multiple loci of forensic interest in different genetic contexts, such as autosomes, mitochondrial and sex chromosomes. Furthermore, NGS technology can also have potential applications in many other aspects of research. These include DNA database construction, ancestry and phenotypic inference, monozygotic twin studies, body fluid and species identification, and forensic animal, plant and microbiological analyses. Here we review the application of NGS technology in the field of forensic science with the aim of providing a reference for future forensics studies and practice.
- Published
- 2014
- Full Text
- View/download PDF
31. 24 Y-chromosomal STR haplotypic structure for Chinese Kazak ethnic group and its genetic relationships with other groups
- Author
-
Jian-Gang Chen, Yao-Shun Liu, Jiangwei Yan, Hao-Tian Meng, Ting Mei, Bo-Feng Zhu, and Li-Ping Zhang
- Subjects
Male ,0301 basic medicine ,Genetics ,China ,Chromosomes, Human, Y ,Haplotype ,Ethnic group ,Genetic Variation ,Biology ,Pathology and Forensic Medicine ,03 medical and health sciences ,Genetics, Population ,030104 developmental biology ,0302 clinical medicine ,Haplotypes ,Genetic variation ,Ethnicity ,Str loci ,Humans ,Microsatellite ,Y-STR ,030216 legal & forensic medicine ,Multidimensional scaling ,Microsatellite Repeats - Abstract
The Kazak ethnic minority is a large ethnic group in the Xinjiang Uygur Autonomous Region of China and is valuable resource for the study of ethnogeny. In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 201 unrelated Kazak male individuals from Ili Kazak Autonomous Prefecture, Xinjiang, China. The gene diversity of the 24 Y-STR loci in the studied Kazak group ranged from 0.0050 to 0.9104. According to haplotypic analysis of the 24 Y-STR loci, 113 different haplotypes were obtained, 96 of which were unique. The haplotype diversity and discrimination capacity in Kazak group were 0.9578 and 0.5622 at 24 STR loci, respectively. The haplotype diversity and discrimination capacity at Y-filer 17 loci, extended 11 loci, and minimal 9 loci were reduced to 0.9274 and 0.4279, 0.8459 and 0.3284, and 0.8354 and 0.2985, respectively, which could indicate that the more loci were detected, the higher forensic efficacy was obtained. We evaluated the application value of the 24 loci in forensic sciences and analyzed interpopulation differentiations by making comparisons between the Kazak1 (represent our samples from Ili Kazak Autonomous Prefecture) group and other 14 groups. The results of pairwise genetic distances, multidimensional scaling plot, and neighbor-joining tree at the same set of 17 Y-filer loci indicated that the Kazak1 group had the closer genetic relationships with Kazak2 (represent samples from the whole territory of Xinjiang Uygur Autonomous Region), Mongolian, and Uygur ethnic groups. The present results may provide useful information for paternal lineages in forensic cases and can also increase our understanding of the genetic relationships between Kazak1 and other groups.
- Published
- 2016
32. Autosomal-STR based genetic structure of Chinese Xibe ethnic group and its relationships to various groups
- Author
-
Bofeng Zhu, Jiangwei Yan, Qian Dong, Jianfeng Shi, Yuxin Guo, Guang Yang, and Hao-Tian Meng
- Subjects
0301 basic medicine ,China ,Genotype ,Ethnic group ,Locus (genetics) ,Genetic relationship ,Biology ,Pathology and Forensic Medicine ,03 medical and health sciences ,Forensic dna ,0302 clinical medicine ,Gene Frequency ,Ethnicity ,Humans ,030216 legal & forensic medicine ,Allele ,Genetics ,Principal Component Analysis ,Polymorphism, Genetic ,Amelogenin ,DNA Fingerprinting ,humanities ,Genetics, Population ,030104 developmental biology ,Genetic structure ,Str loci ,Microsatellite ,Microsatellite Repeats - Abstract
The short tandem repeat (STR) is one of the most widely used genetic makers in forensic DNA labs worldwide. In the present study, we investigated the genetic structure of 19 autosomal STRs and 1 sex-determining locus (amelogenin) in the Xibe ethnic group in China, as well as its relationships to other groups. One hundred and ninety-five alleles were detected in 222 unrelated healthy Xibe individuals. The values of combined power of discrimination and probability of exclusion of all 19 STR loci were 0.99999999999999999999996912 and 0.999999997538, respectively. Principal component analysis revealed relationships between the Xibe group and other groups, which showed a relatively close genetic relationship between the Xibe and Korean groups.
- Published
- 2016
33. Inconsistent genotyping call at DYS389 locus and implications for interpretation
- Author
-
Jingjing Zhang, Chen Li, Xi Zhang, Zailiang Yu, Yaran Yang, Yan Wang, Zhiyong Liu, Dongtao Jia, Yang Meng, Jiangwei Yan, and Man Chen
- Subjects
Genetic Markers ,Male ,China ,Genotype ,Locus (genetics) ,Biology ,Polymerase Chain Reaction ,Polymorphism, Single Nucleotide ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,Asian People ,Humans ,Multiplex ,Y-STR ,030216 legal & forensic medicine ,030212 general & internal medicine ,Genotyping ,Genetics ,Chromosomes, Human, Y ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,DNA Fingerprinting ,DNA profiling ,Genetic marker ,Mutation ,Microsatellite ,Female ,Microsatellite Repeats - Abstract
The male-specific Y chromosome short tandem repeat (STR) locus is used widely in forensic case, which are useful molecular tool to providing the biological evidence for male/female mixture and paternal lineage cases. The Y-STR analysis has been greatly facilitated by advent of commercial multiplex kit. However, even with well-designed robust multiplex kit, abnormal genotyping profile may be observed when encountering with mutations, such as deletion/duplication within the target region or mutation at the primer binding site. In this study, a single-allele shift by five nucleotides for the DYS389I marker between the AmpFlSTR® Yfiler® and Yfiler® Plus PCR amplification kits while the same allele count for DYS389II was observed in eight unrelated Chinese male individuals. After further investigations by re-amplified with three additional multiplex kits, sanger, and next-generation sequencing, the discordance was finally proven caused by existing rare mutation in those sample, which contained two adjacent SNPs only one base apart in the sequence. This paper describes the molecular basis of the discordance at DYS389I genotyping between different commercial multiplex kits and could provide available information for enhancing of interpretation of abnormal Y-STR genotyping in forensic practice.
- Published
- 2017
34. Massively parallel sequencing of microRNA in bloodstains and evaluation of environmental influences on miRNA candidates using realtime polymerase chain reaction
- Author
-
Huijuan Wu, Qifan Sun, Chen Fang, Junbo Li, Jiangwei Yan, Liu Xu, Liu Wenli, Tian Yanjie, Jing Zhao, Qian Jialin, and Anquan Ji
- Subjects
0301 basic medicine ,Adult ,Male ,Adolescent ,RNA Stability ,Computational biology ,Biology ,Real-Time Polymerase Chain Reaction ,Pathology and Forensic Medicine ,law.invention ,Specimen Handling ,03 medical and health sciences ,Young Adult ,0302 clinical medicine ,law ,Mirna expression ,microRNA ,Genetics ,Humans ,Biological evidence ,030216 legal & forensic medicine ,Polymerase chain reaction ,Massive parallel sequencing ,Microarray analysis techniques ,Sequence Analysis, RNA ,Gene Expression Profiling ,High-Throughput Nucleotide Sequencing ,Middle Aged ,Tissue specificity ,MicroRNAs ,030104 developmental biology ,Blood Stains ,Female - Abstract
MicroRNAs (miRNA) are small (22–24 nucleotides) non-coding RNAs with potential application in forensic science because of their anti-degradation property and tissue specificity. Recent studies on the use of miRNA in forensic applications have mainly focused on body fluid identification using realtime polymerase chain reaction or microarray analysis. However, the exploration of miRNA in bloodstains, which are the most valuable source of biological evidence during case investigations, is currently lacking, particularly for aged and environmentally compromised forensic samples. Recent developments in massively parallel sequencing (MPS) technology provide the opportunity to establish a whole-genome miRNA profile with high throughput and efficiency. However, MPS analysis of genome-wide miRNA profiles from bloodstains has not been reported to date. In this study, the whole-genome miRNA profiles of bloodstains were examined using MPS, revealing 633 known miRNAs and 266 novel miRNAs. To further explore the stability of miRNAs in bloodstains under various circumstances, the expression levels of six miRNAs (miR-16-5p, miR-20a-5p, miR-486-5p, miR-148a-3p, miR-151a-3p, and miR-451a) that were abundant in blood/bloodstains were examined. The results showed that freezing/thawing and a high concentration of oxidant solution affects the absolute expression of miRNA significantly, while storage for up to 5 months and a temperature of 37 °C did not have any observed effects. This study not only provides a novel method to explore miRNA profiles in bloodstains using MPS, but also points to the circumstantial influences on miRNA expression, which are an important consideration for practical application. Collectively, our work may shed light on MPS-based approaches with miRNA analysis of bloodstains in forensics.
- Published
- 2017
35. Diversity study of 12 X-chromosomal STR loci in Hui ethnic from China
- Author
-
Jun-Tao Han, Ru-Hua Zhou, Jiangwei Yan, Jian-Xin Guo, Hongdan Wang, Yu-Dang Zhang, Xing Wei, Bofeng Zhu, Yu-Hong Zhang, Tian-Ju Wang, Hao-Tian Meng, Wen-Juan Liu, Jing-feng Huang, and Wei-An Du
- Subjects
Genetics ,Linkage (software) ,education.field_of_study ,media_common.quotation_subject ,Clinical Biochemistry ,Population ,Ethnic group ,Population genetics ,Biology ,Biochemistry ,humanities ,Analytical Chemistry ,symbols.namesake ,Bonferroni correction ,Str loci ,symbols ,Allele ,education ,Diversity (politics) ,media_common - Abstract
X-chromosomal STRs (X-STRs) have been used as complements of autosomal STR application in recent years. In this work, we present population genetic data of 12 X-STRs including DXS101, DXS10159, DXS10162, DXS10164, DXS6789, DXS7133, DXS7423, DXS7424, DXS8378, DXS981, GATA165B12, and GATA31E08 loci in a sample of 231 unrelated healthy individuals from the Hui ethnic group in Ningxia Hui Autonomous Region, China. Allelic frequencies of the 12 X-STR loci and haplotypic frequencies of the reported linkage groups (DXS7424-DXS101 and DXS10159-DXS10164-DXS10162) were investigated in the group, respectively. No STR loci showed significant deviations from the Hardy-Weinberg equilibriums and no linkage disequilibriums of pairwise loci were found after Bonferroni correction, respectively. A combined power of discrimination in female individuals was 0.999999999985 and that in male individuals was 0.99999967, respectively. The combined mean exclusion chance in deficiency cases, normal trios and duo cases were 0.999934, 0.995754, and 0.999796, respectively. Significant differences were observed from 0 to 8 loci, when making comparisons between the data of Hui ethnic group and previously reported data from other 16 populations. The results indicated the new panel of 12 X-STR loci might be useful for forensic science application.
- Published
- 2014
36. Structural polymorphism analysis of Chinese Mongolian ethnic group revealed by a new STR panel: Genetic relationship to other groups
- Author
-
Wen-Juan Liu, Richard E. White, Li-Jun Zhao, Chun-Mei Shen, Hao-Tian Meng, Jiangwei Yan, Hua Wu, Hongdan Wang, Guo-lian Yuan, Xing Wei, Ying Gao, Yu-Dang Zhang, and Jun-Tao Han
- Subjects
Genetics ,China ,Principal Component Analysis ,Linkage disequilibrium ,Polymorphism, Genetic ,Clinical Biochemistry ,Ethnic group ,Population genetics ,Genetic relationship ,Locus (genetics) ,Biology ,Biochemistry ,Analysis of molecular variance ,Linkage Disequilibrium ,Analytical Chemistry ,Asian People ,Gene Frequency ,Genetic distance ,Ethnicity ,Cluster Analysis ,Humans ,Allele ,Phylogeny ,Microsatellite Repeats - Abstract
Mongolian is the eighth largest ethnic minority on Chinese population data according to the 2010 census. In the present study, we presented the first report about the allelic frequencies and forensic statistical parameters at the 21 new STRs and analyzed linkage disequilibrium of pairwise loci in the Mongolian ethnic minority, China. Hardy-Weinberg equilibrium tests demonstrated no significant deviations except for the D1S1627 locus. The cumulative power of discrimination and power of exclusion of all the loci are 0.9999999999999999992576 and 0.9999997528, respectively. The results of analysis of molecular variance showed that significant differences between the Mongolian and the other eight populations were found at 1-9 STR loci. In population genetics, the results of principal component analysis, structure analysis, and phylogenetic reconstruction analysis indicated shorter genetic distance between the Mongolian group and the Ningxia Han. All the results suggest that the 21 new STR loci will contribute to Chinese population genetics and forensic caseworks in the Mongolian group.
- Published
- 2014
37. Characterization of miRNomes in Acute and Chronic Myeloid Leukemia Cell Lines
- Author
-
Yaran Yang, Qian Xiong, Jiangwei Yan, Xiangdong Fang, Yanming Li, Yadong Yang, Jie Li, Kan Cai, Hai Wang, Songnian Hu, Shaobin Wang, and Xiuyan Ruan
- Subjects
Myeloid ,Cellular differentiation ,Cell ,Myeloid differentiation ,Biology ,Biochemistry ,Massively parallel signature sequencing ,Cell Line, Tumor ,Leukemia, Myelogenous, Chronic, BCR-ABL Positive ,hemic and lymphatic diseases ,microRNA ,Genetics ,medicine ,Humans ,Molecular Biology ,Original Research ,Acute myeloid leukemia ,Gene Expression Profiling ,Chronic myeloid leukemia ,Myeloid leukemia ,Cell Differentiation ,Gene Expression Regulation, Neoplastic ,Gene expression profiling ,Leukemia, Myeloid, Acute ,MicroRNAs ,Computational Mathematics ,medicine.anatomical_structure ,Immunology ,Cancer research ,miRNA profiling ,K562 cells - Abstract
Myeloid leukemias are highly diverse diseases and have been shown to be associated with microRNA (miRNA) expression aberrations. The present study involved an in-depth miRNome analysis of two human acute myeloid leukemia (AML) cell lines, HL-60 and THP-1, and one human chronic myeloid leukemia (CML) cell line, K562, via massively parallel signature sequencing. mRNA expression profiles of these cell lines that were established previously in our lab facilitated an integrative analysis of miRNA and mRNA expression patterns. miRNA expression profiling followed by differential expression analysis and target prediction suggested numerous miRNA signatures in AML and CML cell lines. Some miRNAs may act as either tumor suppressors or oncomiRs in AML and CML by targeting key genes in AML and CML pathways. Expression patterns of cell type-specific miRNAs could partially reflect the characteristics of K562, HL-60 and THP-1 cell lines, such as actin filament-based processes, responsiveness to stimulus and phagocytic activity. miRNAs may also regulate myeloid differentiation, since they usually suppress differentiation regulators. Our study provides a resource to further investigate the employment of miRNAs in human leukemia subtyping, leukemogenesis and myeloid development. In addition, the distinctive miRNA signatures may be potential candidates for the clinical diagnosis, prognosis and treatment of myeloid leukemias.
- Published
- 2014
38. A 30-InDel Assay for Genetic Variation and Population Structure Analysis of Chinese Tujia Group
- Author
-
Bofeng Zhu, Tian-hua Yao, Fadao Tai, Zhi-Dan Li, Jiangwei Yan, Bo Wang, Xiao-Hua Bie, Yu-Dang Zhang, and Chun-Mei Shen
- Subjects
0301 basic medicine ,China ,Linkage disequilibrium ,Genotyping Techniques ,Population ,Locus (genetics) ,Biology ,Analysis of molecular variance ,Article ,Linkage Disequilibrium ,White People ,03 medical and health sciences ,0302 clinical medicine ,Asian People ,Gene Frequency ,INDEL Mutation ,Genetic variation ,Humans ,030216 legal & forensic medicine ,Indel ,education ,Allele frequency ,Phylogeny ,Genetics ,education.field_of_study ,Polymorphism, Genetic ,Multidisciplinary ,030104 developmental biology ,Genetic structure ,Microsatellite Repeats - Abstract
In the present study, thirty autosomal insertion and deletion polymorphic loci were simultaneously amplified and genotyped in a multiplex system, and their allelic frequencies as well as several forensic parameters were obtained in a sample of 236 unrelated healthy Tujia individuals. All the loci were in Hardy-Weinberg equilibrium after applying a Bonferroni correction and all pair-wise loci showed no significant linkage disequilibrium. These loci were observed to be relatively informative and discriminating, quite efficient for forensic applications. Allelic frequencies of 30 loci were compared between the Tujia group and other reference populations, and the results of analysis of molecular variance indicated the Tujia group showed the least significant differences with the Shanghai Han at one locus, and the most with Central Spanish population at 22 loci. We analyzed the population genetic structure by the principal component analysis, the clustering of STRUCTURE program and a Neighbor-Joining tree, and then evaluated the genetic relationships among Tujia and other 15 populations.
- Published
- 2016
39. Genetic profile characterization and population study of 21 autosomal STR in Chinese Kazak ethnic minority group
- Author
-
Bofeng Zhu, Guang Yang, Xiao-Ye Wang, Hongdan Wang, Jiangwei Yan, Chun-Mei Shen, Hong-Wei Pu, Hao-Tian Meng, Yan-Li Wang, Wen-Juan Liu, Jing-Yi Yuan, Hang Jing, and Yu-Dang Zhang
- Subjects
Genetics ,education.field_of_study ,Clinical Biochemistry ,Population ,Population genetics ,Locus (genetics) ,Genetic relationship ,Biology ,Biochemistry ,Analysis of molecular variance ,Analytical Chemistry ,Population study ,Microsatellite ,Allele ,education - Abstract
Short tandem repeat loci have been recognized as useful tools in the routine forensic application and in recent decades, more and more new short tandem repeat (STR) loci have been constantly discovered, studied, and applied in forensic caseworks. In this study, we investigated the genetic polymorphisms of 21 STR loci in the Kazak ethnic minority as well as the genetic relationships between the Kazak ethnic minority and other populations. Allelic frequencies of 21 STR loci were obtained from 114 unrelated healthy Kazak individuals in the Ili Kazak Autonomous Prefecture, Xinjiang Uigur Autonomous Region of China. We observed a total of 159 alleles in the group with the allelic diversity values ranging from 0.0044 to 0.5088. The highest polymorphism was found at D19S433 locus and the lowest was found at D1S1627. Statistical analysis of the generated data indicated no deviation from Hardy-Weinberg equilibriums at all 21 STR loci. In order to estimate the population differentiation, allelic frequencies of all STR loci of the Kazak were compared with those of other neighboring populations using analysis of molecular variance method. Statistically significant differences were found between the studied population and other populations at 2-7 STR loci. A neighbor-joining tree was constructed based on allelic frequencies of the 21 STR loci and phylogenetic analysis indicates that the Kazak has a close genetic relationship with the Uigur ethnic group. The present results may provide useful information for forensic sciences and population genetics studies, and can also increase our understanding of the genetic background of this group. The present findings showed that all the 21 STR loci are highly genetically polymorphic in the Kazak group, which provided valuable population genetic data for the genetic information study, forensic human individual identification, and paternity tests.
- Published
- 2013
40. Transcriptome dynamics during human erythroid differentiation and development
- Author
-
Heyuan Qi, Edward K. Wakeland, Yadong Yang, Zhaojun Zhang, Jiangwei Yan, Songnian Hu, Xiangdong Fang, Yajuan Li, Peng Cui, Qiang Lin, Chang Shu, Hongzhu Qu, Hai Wang, Kai Hsin Chang, Yaran Yang, Qian Xiong, Xiuyan Ruan, and Quan Zhen Li
- Subjects
Erythroblasts ,Cellular differentiation ,Gene regulatory network ,Development ,Biology ,Article ,Cell Line ,Transcriptome ,Erythroid Cells ,Cell differentiation ,Genetics ,Humans ,Erythropoiesis ,Gene Regulatory Networks ,Embryonic Stem Cells ,Cell Proliferation ,Genome, Human ,Cell growth ,Gene Expression Profiling ,Gene Expression Regulation, Developmental ,High-Throughput Nucleotide Sequencing ,Embryonic stem cell ,Molecular biology ,High-throughput RNA sequencing ,Gene expression profiling ,Cell culture - Abstract
To explore the mechanisms controlling erythroid differentiation and development, we analyzed the genome-wide transcription dynamics occurring during the differentiation of human embryonic stem cells (HESCs) into the erythroid lineage and development of embryonic to adult erythropoiesis using high throughput sequencing technology. HESCs and erythroid cells at three developmental stages: ESER (embryonic), FLER (fetal), and PBER (adult) were analyzed. Our findings revealed that the number of expressed genes decreased during differentiation, whereas the total expression intensity increased. At each of the three transitions (HESCs–ESERs, ESERs–FLERs, and FLERs–PBERs), many differentially expressed genes were observed, which were involved in maintaining pluripotency, early erythroid specification, rapid cell growth, and cell–cell adhesion and interaction. We also discovered dynamic networks and their central nodes in each transition. Our study provides a fundamental basis for further investigation of erythroid differentiation and development, and has implications in using ESERs for transfusion product in clinical settings.
- Published
- 2013
41. Population genetics and forensic efficiency of twenty-one novel microsatellite loci of Chinese Yi ethnic group
- Author
-
Hao-Tian Meng, Hang Jing, Jiangwei Yan, Bofeng Zhu, Wen-Juan Liu, Rui Liu, Hongdan Wang, Chun-Mei Shen, Feng Pan, Peng Xu, Yu-Dang Zhang, Yan-Li Wang, and Jian-Xin Guo
- Subjects
Forensic science ,Loss of heterozygosity ,Genetics ,Genetic distance ,Clinical Biochemistry ,Genetic structure ,Population genetics ,Microsatellite ,Allele ,Biology ,Biochemistry ,Analysis of molecular variance ,Analytical Chemistry - Abstract
In this study, we investigated polymorphic distributions of allelic frequencies and forensic genetic parameters of 21 novel autosomal microsatellite loci from 110 unrelated healthy individuals of Chinese Yi ethnic group. Expected heterozygosity, power of discrimination, and polymorphic information content ranged from 0.617 to 0.812, 0.777 to 0.936 and 0.560 to 0.790. The microsatellite loci showed high forensic efficiency. The total discrimination power and cumulate probability of exclusion were 0.99999999999999999986902 and 0.999998818, respectively. Locus-by-locus allelic frequencies were compared using analysis of molecular variance (AMOVA) method, and the statistically significant differences were observed between Yi group and Russian, Tujia, Kazak, Bai, Ningxia Han, Salar, Tibetan, and Uigur groups at 5, 6, 7, 7, 7, 8, 12, and 13 loci, respectively. The results of genetic distance comparisons, genetic structure analyses, and principal component analysis all indicated that the Yi group showed relatively short genetic relationships with Russian, Salar, and Bai group. The experimental results showed that the 21 loci in the multiplex system provided highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, also basic population data for population genetics and anthropological research.
- Published
- 2013
42. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China
- Author
-
Wen-Juan Liu, Bofeng Zhu, Chun-Mei Shen, Jiangwei Yan, Guang Yang, Yu-Dang Zhang, Hai-xia Qin, and Hongdan Wang
- Subjects
Adult ,Forensic Genetics ,Genetic Markers ,Male ,China ,Combined DNA Index System ,Adolescent ,Population ,Locus (genetics) ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Russia ,Young Adult ,Gene Frequency ,Databases, Genetic ,Multiplex polymerase chain reaction ,Humans ,General Pharmacology, Toxicology and Pharmaceutics ,education ,Allele frequency ,Minority Groups ,Aged ,Genetics ,education.field_of_study ,Genetic diversity ,Amelogenin ,General Veterinary ,General Medicine ,Middle Aged ,DNA Fingerprinting ,Biomedicine ,Genetics, Population ,DNA profiling ,Microsatellite ,Female ,geographic locations ,Microsatellite Repeats - Abstract
We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population's genetic background, for individual identification, and for paternity testing in forensic practice.
- Published
- 2013
43. Genetic data provided by 21 autosomal STR loci from Chinese Tujia ethnic group
- Author
-
Jie Yuan, Bofeng Zhu, Guang Yang, Wen-Juan Liu, Guo-lian Yuan, Jiangwei Yan, Tong Xie, Chun-Mei Shen, Zuochun Liu, Hangyan Ran, Hai-xia Qin, and Hongdan Wang
- Subjects
Forensic Genetics ,China ,Linkage disequilibrium ,STR multiplex system ,Population ,Paternity ,Biology ,Linkage Disequilibrium ,Gene Frequency ,Multiplex polymerase chain reaction ,Genetics ,medicine ,Genetic Testing ,education ,Molecular Biology ,Allele frequency ,Genetic testing ,education.field_of_study ,medicine.diagnostic_test ,Sequence Analysis, DNA ,General Medicine ,Genetic Loci ,Genetic marker ,Microsatellite ,Microsatellite Repeats - Abstract
The aim of this study was to investigate allelic frequency distribution and forensic genetic parameters of autosomal short tandem repeats (STR) loci of the population samples from 107 Tujia individuals from Chinese Hubei Province. Twenty-one autosomal STR genetic markers (D9S1122, D6S474, D6S1017, D5S2500, D4S2408, D3S4529, D2S441, D2S1776, D22S1045, D20S482, D1S1677, D1S1627, D1GATA113, D19S433, D18S853, D17S1301, D11S4463, D12ATA63, D10S1248, D10S1435 and D14S1434) were simultaneously amplified in a new multiplex polymerase chain reaction system. 155 alleles for all the STR loci from the Tujia population were observed and the corresponding allelic frequencies ranged from 0.005 to 0.589. Expected heterozygosity, polymorphic information content, power of discrimination and power of exclusion of the 21 STR loci in the Tujia population were from 0.579 to 0.824, from 0.525 to 0.802, from 0.773 to 0.945 and from 0.257 to 0.641, respectively. Our results indicate that the autosomal STRs multiplex system provides highly informative STR data and could be useful in forensic individual identification and parentage testing in this region.
- Published
- 2012
44. Genetic polymorphism and evolutionary differentiation of Eastern Chinese Han: a comprehensive and comparative analysis on KIRs
- Author
-
Jiangwei Yan, Feng Chen, Bofeng Zhu, Qiang Ji, Jinchuan Yan, Zheng Li, Caiyong Yin, Huijie Huang, Li Hu, Xiaochao Kong, Zhongqun Wang, and Yanfang Yu
- Subjects
0301 basic medicine ,Linkage disequilibrium ,China ,Heterozygote ,Genotype ,Genetic Linkage ,Population genetics ,Biology ,Linkage Disequilibrium ,Article ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Asian People ,Gene Frequency ,Receptors, KIR ,Genetic linkage ,Humans ,Allele ,Allele frequency ,Genotyping ,Alleles ,Phylogeny ,Genetics ,Multidisciplinary ,Polymorphism, Genetic ,030104 developmental biology ,Genetics, Population ,Multigene Family ,Population study ,030215 immunology - Abstract
Killer cell immunoglobulin-like receptor genes, namely KIRs, cluster together within the 160 kb genomic DNA region. In this study, we used PCR-SSP approach and successfully identified the genotype of 17 KIR genes in 123 independent healthy donors residing in the Jiangsu province, China. All individuals were positive at the 7 genes. The observed carrier gene frequencies (OFs) of remaining 10 KIRs ranged from 14.63% (KIR2DS3) to 95.93% (KIR3DL1). We found 27 distinct genotypes excluding KIR1D. The most frequent occurred in 63 individuals (51.22%). The linkage disequilibrium analysis signified 29 positive and 6 negative relations in 45 pairwise comparisons. To study population differentiation, we drew a Heatmap based on the data of KIRs from 59 populations and conducted Hierarchical Clustering by Euclidean distances. We next validated our results by estimating pairwise DA distances and illustrating a Neighbor-Joining tree, as well as a MDS plot covering 3 additional Chinese Han groups. The phylogenetic reconstruction and cluster analysis strongly indicated a genetically close relationship between Eastern and Jilin Hans. In conclusion, the present study provided a meritorious resource of KIR genotyping for population genetics, and could be helpful to uncover the genetic mechanism of KIRs in immune disease in the future.
- Published
- 2016
45. Whole genome nucleosome sequencing identifies novel types of forensic markers in degraded DNA samples
- Author
-
Shujin Li, Jiangwei Yan, Xiangdong Fang, Bin Cong, Yaran Yang, Chunnan Dong, Xiaojing Zhang, and Yadong Yang
- Subjects
0301 basic medicine ,Genotyping Techniques ,Biology ,Polymorphism, Single Nucleotide ,Genome ,Article ,DNase-Seq ,03 medical and health sciences ,0302 clinical medicine ,INDEL Mutation ,Humans ,030216 legal & forensic medicine ,Genotyping ,Whole genome sequencing ,Genetics ,Multidisciplinary ,Genome, Human ,High-Throughput Nucleotide Sequencing ,DNA ,Forensic Medicine ,Linker DNA ,Nucleosomes ,030104 developmental biology ,DNA profiling ,Human genome ,Biomarkers ,Microsatellite Repeats - Abstract
In the case of mass disasters, missing persons and forensic caseworks, highly degraded biological samples are often encountered. It can be a challenge to analyze and interpret the DNA profiles from these samples. Here we provide a new strategy to solve the problem by taking advantage of the intrinsic structural properties of DNA. We have assessed the in vivo positions of more than 35 million putative nucleosome cores in human leukocytes using high-throughput whole genome sequencing, and identified 2,462 single nucleotide variations (SNVs), 128 insertion-deletion polymorphisms (indels). After comparing the sequence reads with 44 STR loci commonly used in forensics, five STRs (TH01, TPOX, D18S51, DYS391, and D10S1248)were matched. We compared these “nucleosome protected STRs” (NPSTRs) with five other non-NPSTRs using mini-STR primer design, real-time PCR, and capillary gel electrophoresis on artificially degraded DNA. Moreover, genotyping performance of the five NPSTRs and five non-NPSTRs was also tested with real casework samples. All results show that loci located in nucleosomes are more likely to be successfully genotyped in degraded samples. In conclusion, after further strict validation, these markers could be incorporated into future forensic and paleontology identification kits, resulting in higher discriminatory power for certain degraded sample types.
- Published
- 2016
46. Genetic polymorphism analyses of a novel panel of 19 X-STR loci in the Chinese Uygur ethnic minority
- Author
-
Qian Dong, Tian-hua Yao, Bofeng Zhu, Yuxin Guo, Li-Ping Zhang, Jiangwei Yan, Jian-Gang Chen, Jing Chen, Yao-Shun Liu, Yan Wang, Yu-Dang Zhang, Ting Mei, Hao-Tian Meng, and Guang Yang
- Subjects
0301 basic medicine ,Male ,Linkage disequilibrium ,China ,Genotype ,Population ,Biology ,Polymerase Chain Reaction ,General Biochemistry, Genetics and Molecular Biology ,Linkage Disequilibrium ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Sex Factors ,Asian People ,Gene Frequency ,Humans ,030216 legal & forensic medicine ,General Pharmacology, Toxicology and Pharmaceutics ,Allele ,education ,Allele frequency ,Alleles ,Minority Groups ,Probability ,Genetics ,education.field_of_study ,Chromosomes, Human, X ,Polymorphism, Genetic ,General Veterinary ,Haplotype ,General Medicine ,Articles ,030104 developmental biology ,Bonferroni correction ,Genetics, Population ,Haplotypes ,symbols ,Microsatellite ,Female ,Algorithms ,Microsatellite Repeats - Abstract
The population genetic data and forensic parameters of 19 X-chromosome short tandem repeat (X-STR) loci in Chinese Uygur ethnic minority are presented. These loci were detected in a sample of 233 (94 males and 139 females) unrelated healthy individuals. We observed 238 alleles at the 19 X-STR loci, with the corresponding gene frequencies spanning the range from 0.0021 to 0.5644. After Bonferroni correction (P>0.0026), there were no significant deviations from Hardy-Weinberg equilibrium. The cumulative power of discrimination in females and males, and the probability of exclusion of the 19 X-STR loci were 0.999 999 999 999 999 999 998 091, 0.999 999 999 999 966, and 0.999 999 986 35, respectively. The cumulative mean exclusion chance was 0.999 999 992 849 in deficiency cases, 0.999 999 999 999 628 in normal trios, and 0.999 999 998 722 in duo cases. The high value of the forensic parameters mentioned above revealed that the novel panel of 19 loci had important values for forensic applications in the Uygur group.
- Published
- 2016
47. Forensic effectiveness and population differentiations study of AGCU 21+1 fluorescence multiplex in Chinese Henan Han population
- Author
-
Yuxin Guo, Ruilin Ma, Fadao Tai, Qian Dong, Xinxin Wang, Zhan-Qi Feng, Hao-Tian Meng, Chun-Mei Shen, Jiangwei Yan, Hongdan Wang, and Bofeng Zhu
- Subjects
0301 basic medicine ,China ,Population ,Biology ,Polymerase Chain Reaction ,Fluorescence ,Pathology and Forensic Medicine ,03 medical and health sciences ,0302 clinical medicine ,Asian People ,Gene Frequency ,Polymorphism (computer science) ,Genetics ,Ethnicity ,Humans ,Multiplex ,030216 legal & forensic medicine ,Han population ,education ,Allele frequency ,education.field_of_study ,Polymorphism, Genetic ,DNA Fingerprinting ,Forensic science ,030104 developmental biology ,Genetics, Population ,DNA profiling ,Indicators and Reagents ,Microsatellite Repeats - Published
- 2016
48. Study of genetic diversity of killer cell immunoglobulin-like receptor loci in the Tujia ethnic minority
- Author
-
Bofeng Zhu, Li Zhang, Zhan-Qi Feng, Yu-Dang Zhang, Hongdan Wang, Yuxin Guo, Qiannan Guo, Chun-Mei Shen, Jiangwei Yan, and Peng-Fei Dai
- Subjects
0301 basic medicine ,Linkage disequilibrium ,China ,Genotype ,Pseudogene ,Immunology ,Killer-cell immunoglobulin-like receptor ,chemical and pharmacologic phenomena ,Biology ,Linkage Disequilibrium ,03 medical and health sciences ,0302 clinical medicine ,Asian People ,Gene Frequency ,Receptors, KIR ,otorhinolaryngologic diseases ,Ethnicity ,Immunology and Allergy ,Humans ,Allele frequency ,Genetics ,Genetic diversity ,Polymorphism, Genetic ,General Medicine ,Killer Cells, Natural ,030104 developmental biology ,Genetics, Population ,Gene pool ,KIR3DL1 ,Pseudogenes ,030215 immunology - Abstract
The aim of this study was to analyze the genetic profiles of 14 killer cell immunoglobulin-like receptor (KIR) genes and 2 pseudogenes of 124 individuals from Tujia ethnic minority residing in Enshi Tujia and Miao autonomous prefecture of Hubei province of China and investigate the genetic relationships between the Tujia ethnic minority and other reported groups for the first time. Sequence specific primer amplification (PCR-SSP) methods were used to genotype the 14 KIR genes and 2 pseudogenes. The observed carrier frequencies (OF) and the gene frequencies (GF) of the KIR genes were measured. Neighbor-joining (N-J) tree and the principal component analysis (PCA) plot were constructed. All individuals were typed positive for the three framework loci KIR3DL3, 2DL4 and 3DL2, as well as for pseudogene KIR3DP1. The gene frequencies of the other KIR genes ranged from 9% in KIR2DS2 to 98% in KIR2DP1 and KIR3DL1. The present study of the KIR genes may be a powerful tool for enriching the Chinese ethnical gene information resources of the KIR gene pool, as well as for the anthropological research.
- Published
- 2016
49. Genetic variability and forensic efficiency of 39 microsatellite loci in the Li ethnic group from Hainan Island in the South China Sea
- Author
-
Xiu Liu, Yuexin Lv, Bingbing Xie, Xiangdong Fang, Jiangwei Yan, Yaran Yang, Chuguang Chen, Chen Jing, Huijuan Wu, Yang Meng, and Chao Liu
- Subjects
0301 basic medicine ,Aging ,China ,Genotype ,Physiology ,Epidemiology ,Population ,Ethnic group ,Biology ,03 medical and health sciences ,0302 clinical medicine ,Gene Frequency ,Genetics ,Ethnicity ,Humans ,030216 legal & forensic medicine ,Genetic variability ,Allele ,education ,Allele frequency ,Islands ,education.field_of_study ,Polymorphism, Genetic ,Public Health, Environmental and Occupational Health ,Genotype frequency ,Forensic science ,030104 developmental biology ,Microsatellite ,Microsatellite Repeats - Abstract
Background: Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential pre-requisite in forensic application. Aim: The present study obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from a Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations. Subjects and methods: Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified in two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of the Chinese Li ethnic group. The allele frequency distribution and several parameters commonly used in forensic science were statistically analysed. Results: A total of 378 alleles were observed with corresponding allelic frequencies ranging from 0.0026–0.5899. The power of discrimination and power of exclusion ranged from 0.7569–0.9672 and 0.2513–0.7355, respectively. The power of exclusion (PE) ranged from 0.2580–0.7943 for trio paternity cases and 0.1693–0.5940 for duo paternity cases. The polymorphism information content (PIC) ranged from 0.5001–0.8611. The cumulative match probability across these 39 loci was 2.4242 × 10−38. Conclusion: The results indicate that 39 STR loci are polymorphic among the Li ethnic group in Hainan Island in the South China Sea. This set of polymorphic STR loci provide highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, as well as basic population data for population genetics and anthropological research.
- Published
- 2016
- Full Text
- View/download PDF
50. A novel strategy for forensic age prediction by DNA methylation and support vector regression model
- Author
-
Yaran Yang, Bingbing Xie, Jiangwei Yan, Hongzhu Qu, Guangyu Wang, Yi Shi, Lan Hu, Lei Feng, Cheng Xu, Xiangdong Fang, and Zhao Zhao
- Subjects
Adult ,Forensic Genetics ,Genetic Markers ,Male ,False discovery rate ,China ,Multivariate statistics ,Support Vector Machine ,Population ,Biology ,Polymerase Chain Reaction ,Article ,Bayesian multivariate linear regression ,Statistics ,Linear regression ,Humans ,education ,Aged ,Aged, 80 and over ,Genetics ,education.field_of_study ,Multidisciplinary ,Regression analysis ,DNA Methylation ,Middle Aged ,Support vector machine ,Regression Analysis ,CpG Islands ,Female ,Nonlinear regression - Abstract
High deviations resulting from prediction model, gender and population difference have limited age estimation application of DNA methylation markers. Here we identified 2,957 novel age-associated DNA methylation sites (P 2 > 0.5) in blood of eight pairs of Chinese Han female monozygotic twins. Among them, nine novel sites (false discovery rate
- Published
- 2015
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.