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Qiang R, Wang L, He J, Xu WJ, Li W, Cai N, Wang XB, Zhang R, Zhang LP, Ma XP, Wei C, Song C, Yu W, Wang X, Li X. Development of a mutation hotspot detection kit for the phenylalanine hydroxylase gene by ARMS-PCR combined with fluorescent probe technology. Biosci Rep 2021; 41:BSR20201660. [PMID: 33564846 PMCID: PMC7897920 DOI: 10.1042/bsr20201660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/24/2021] [Accepted: 02/09/2021] [Indexed: 11/17/2022] Open
Abstract
To develop a screening kit for detecting mutation hotspots of the phenylalanine hydroxylase (PAH) gene. Thirteen exons of the PAH gene were sequenced in 84 cases with phenylketonuria (PKU) diagnosed during neonatal genetic and metabolic disease screening in Shaanxi province, and their mutations were analyzed. We designed and developed a screening kit to detect nine mutation sites covering more than 50% of the PAH mutations found in Shaanxi province (c.728G>A, c.1197A>T, c.331C>T, c.1068C>A, c.611A>G, c.1238G>C, c.721C>T, c.442-1G>A, and c.158G>A) by using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) combined with fluorescent probe technology. Peripheral blood and dried blood samples from PKU families were used for clinical verification of the newly developed kit. PAH gene mutations were detected in 84 children diagnosed with PKU. A total of 159 mutant alleles were identified, consisting of 100 missense mutations, 28 shear mutations, 24 nonsense mutations, and 7 deletion mutations. Exon 7 had the highest mutation frequency (32.08%). Among them, the mutation frequency of p.R243Q was the highest, accounting for 20.13% of all mutations, followed by p.R111X, IVS4-1G>A, EX6-96A>G, and p.R413P; these five loci accounted for 47.17% (75/159) of all mutations. In addition, we identified three previously unreported PAH gene mutations (p.C334X, p.G46D, and p.G256D). Fifteen mutation sites were identified in the 47 PAH carriers identified by next-generation sequencing (NGS), which were verified by the newly developed kit, with an agreement rate of 100%. This newly developed kit based on ARMS-PCR combined with fluorescent probe technology can be used to detect common PAH gene mutations.
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Affiliation(s)
- Rong Qiang
- Center for Translational Medicine, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, P.R. China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, P.R. China
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - Lin Wang
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - JinHua He
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, Guangdong 511400, P.R. China
| | - Wei Jie Xu
- Molecular Diagnosis Department, Guangzhou Lanji Biotechnology Co., Ltd., Guangzhou, Guangdong 510665, P.R. China
| | - Wei Li
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - Na Cai
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - Xiao Bin Wang
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - RuiXue Zhang
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - Li Ping Zhang
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - Xiao Ping Ma
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - Chen Wei
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - ChengRong Song
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - WenWen Yu
- Medical Heredity Research Center, Northwest Women’s and Children’s Hospital, Shaanxi, Xi’an 710003, P.R. China
| | - Xiang Wang
- Center for Translational Medicine, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, P.R. China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, P.R. China
| | - Xu Li
- Center for Translational Medicine, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, P.R. China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, P.R. China
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Zhang Y, Wang S, He H, Wang X, Zhu D, Wen X, Zhang S. Evaluation of three microhaplotypes in individual identification and ancestry inference. Forensic Sci Int 2021; 320:110681. [PMID: 33549990 DOI: 10.1016/j.forsciint.2021.110681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022]
Abstract
Microhaplotype as an emerging genetic marker has attracted more attention in forensic field. The purpose of this study was to evaluate the potential of microhaplotypes in individual identification and ancestry inference in Chinese Hainan Li and 26 1000 G populations. Three microhaplotypes were genotyped from 100 Li individuals using Agena MassARRAY. Moreover, 2504 individuals from 26 populations (1000 Genomes Project database) were enrolled. The genotypes frequencies of microhaplotypes in each population were calculated by the Plink software. We used Structure, Arlequin, and MEGA6 software to analyze the genetic structure, differentiation and genetic background difference, respectively. The forensic parameters of these microhaplotypes were calculated using Modified Powerstats software. The distribution of genotypes frequencies of three microhaplotypes elaborated the high diversities among the Li and 26 1000 G populations. Li population had a close genetic relationship with EAS populations using structure analysis. No differentiation was observed between Li and CHS population by Fst analysis. The NJ tree showed that the genetic background of Li and CHS is most similar. The average heterozygosity (HE), probability of match (PM), power of discrimination (PD), probability of exclusion (PE) and polymorphism information content (PIC) values for the three microhaplotypes in 27 populations were 0.535, 0.497, 0.465, 0.325, and 0.481, respectively. In conclusion, our results revealed three microhaplotypes as individual identification and ancestry inference genetic markers among Li population and 26 1000 G populations. Future studies are needed to confirm our results with larger samples and select much higher forensic efficacy microhaplotypes.
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Affiliation(s)
- Yingai Zhang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China; School of Life and Pharmaceutical Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Shunlan Wang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Haowei He
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Xianwen Wang
- Criminal Technical Detachment, Haikou City Public Security Bureau, Haikou, Hainan, 570208, China
| | - Dan Zhu
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Xiaohong Wen
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China
| | - Shufang Zhang
- Central Laboratory, Affiliated Haikou Hospital of Xiangya Medical College, Central South University, Haikou, Hainan, 570208, China.
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Zhang R, Tan Y, Jian H, Qu S, Liu Y, Zhu J, Wang L, Lv M, Liao M, Zhang L, Yang F, Liang W. A new approach to detect a set of SNP-SNP markers: Combining ARMS-PCR with SNaPshot technology. Electrophoresis 2020; 41:1189-1197. [PMID: 32333411 DOI: 10.1002/elps.202000009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/10/2020] [Accepted: 04/17/2020] [Indexed: 12/28/2022]
Abstract
Microhaplotypes are a new promising type of forensic genetic marker. Without the interference of stutter and high mutation rates as for STRs, and with short amplification lengths and a higher degree of polymorphism than single SNP, microhaplotypes composed of two SNPs, SNP-SNP, have a strong application potential. Currently, the most common method to detect microhaplotypes is massive parallel sequencing. However, the cost and extensive use of instruments limit its wide application in forensic laboratories. In this study, we screened 23 new SNP-SNP loci and established a new detection method by combining a multiplex amplification refractory mutation system-based PCR (ARMS-PCR) and SNaPshot technology based on CE. First, we introduced an additional deliberate mismatch at the antepenultimate base from the 3' end of primers when designing ARMS-PCR for SNP 1 (the first SNP of the SNP-SNP). Then, single base extension primers for SNaPshot assay were designed next to the position of SNP 2 (the second SNP). Finally, 15 loci were successfully built into four panels and these loci showed a relatively high level of polymorphism in the Southwest Chinese Han population. All the loci had an average probability of informative genotypes (I value) of 0.319 and a combined discrimination power of 0.999999999. Therefore, this new detection system will provide a valuable supplement to current methods.
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Affiliation(s)
- Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Hui Jian
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yuqing Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jing Zhu
- Department of Forensic Science and Technology, Sichuan Police College, Luzhou, Sichuan, P. R. China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Chengdu, Sichuan, P. R. China
| | - Meili Lv
- Department of Immunology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Fan Yang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Chengdu, Sichuan, P. R. China.,Department of Ultrasonography, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
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Pang JB, Rao M, Chen QF, Ji AQ, Zhang C, Kang KL, Wu H, Ye J, Nie SJ, Wang L. A 124-plex Microhaplotype Panel Based on Next-generation Sequencing Developed for Forensic Applications. Sci Rep 2020; 10:1945. [PMID: 32029845 PMCID: PMC7004988 DOI: 10.1038/s41598-020-58980-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/23/2020] [Indexed: 11/09/2022] Open
Abstract
Microhaplotypes are an emerging type of forensic genetic marker that are expected to support multiple forensic applications. Here, we developed a 124-plex panel for microhaplotype genotyping based on next-generation sequencing (NGS). The panel yielded intralocus and interlocus balanced sequencing data with a high percentage of effective reads. A full genotype was determined with as little as 0.1 ng of input DNA. Parallel mixture experiments and in-depth comparative analyses were performed with capillary-electrophoresis-based short tandem repeat (STR) and NGS-based microhaplotype genotyping, and demonstrated that microhaplotypes are far superior to STRs for mixture deconvolution. DNA from Han Chinese individuals (n = 256) was sequenced with the 124-plex panel. In total, 514 alleles were observed, and the forensic genetic parameters were calculated. A comparison of the forensic parameters for the 20 microhaplotypes with the top Ae values in the 124-plex panel and 20 commonly used forensic STRs showed that these microhaplotypes were as effective as STRs in identifying individuals. A linkage disequilibrium analysis showed that 106 of the 124 microhaplotypes were independently hereditary, and the combined match probability for these 106 microhaplotypes was 5.23 × 10-66. We conclude that this 124-plex microhaplotype panel is a powerful tool for forensic applications.
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Affiliation(s)
- Jing-Bo Pang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, PR China
| | - Min Rao
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, PR China
| | - Qing-Feng Chen
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
| | - An-Quan Ji
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, PR China
| | - Chi Zhang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
| | - Ke-Lai Kang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
| | - Hao Wu
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China.
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China.
| | - Sheng-Jie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, PR China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China.
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, PR China.
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, PR China.
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5
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Zhang C, Cao YD, Song JJ, Rao M, Nie SJ, Zhang GF, Kang KL, Ji AQ, Ye J, Wang L. MHTyper: a microhaplotype allele-calling pipeline for use with next generation sequencing data. AUST J FORENSIC SCI 2019. [DOI: 10.1080/00450618.2019.1699956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Chi Zhang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | | | - Jiao-Jiao Song
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | - Min Rao
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan, PR China
- Forensic Science Institute of Zhongshan Municipal Public Security Bureau, Zhongshan, Guangdong, PR China
| | - Sheng-Jie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, Yunnan, PR China
| | - Guang-Feng Zhang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | - Ke-Lai Kang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | - An-Quan Ji
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, PR China
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6
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Oldoni F, Podini D. Forensic molecular biomarkers for mixture analysis. Forensic Sci Int Genet 2019; 41:107-119. [DOI: 10.1016/j.fsigen.2019.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
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Turchi C, Melchionda F, Pesaresi M, Tagliabracci A. Evaluation of a microhaplotypes panel for forensic genetics using massive parallel sequencing technology. Forensic Sci Int Genet 2019; 41:120-127. [DOI: 10.1016/j.fsigen.2019.04.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/30/2019] [Accepted: 04/30/2019] [Indexed: 11/29/2022]
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Liu J, Li W, Wang J, Chen D, Liu Z, Shi J, Cheng F, Li Z, Ren J, Zhang G, Yun K. A new set of DIP-SNP markers for detection of unbalanced and degraded DNA mixtures. Electrophoresis 2019; 40:1795-1804. [PMID: 31120138 DOI: 10.1002/elps.201900017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 04/15/2019] [Accepted: 05/18/2019] [Indexed: 11/11/2022]
Abstract
Unbalanced and degraded mixtures (UDM) are frequently encountered during forensic DNA analysis. For example, forensic DNA units regularly encounter DNA mixture signal where the DNA signal from the alleged offender is masked or swamped by high quantities of DNA from the victim. Our previous data presented a new kind of DNA markers that composed of a deletion/insertion polymorphism (DIP) and a SNP and we termed this new kind of microhaplotypes DIP-SNP (combination of DIP and SNP). Since such markers could be designed short enough for degraded DNA amplification, we hypothesized that DIP-SNP markers are applicable for typing of UDM. In this study, we developed a new set of DIP-SNPs with short amplicons which were complement to our prior developed system. The multiplex PCR and SNaPshot assay were established for 20 DIP-SNPs in a Chinese Han population. The DIP-SNPs were capable of detecting the minor contributor's allele in home-made DNA mixture with sensitivities from 1:100 to 1:1000 with a total of 1 -10 ng input DNA. Moreover, this system successfully typed the degraded DNA whether it came from the single source or mixture samples. In Chinese population, the system showed an average informative value of 0.293 and combined informative value of 0.998363862. Our results demonstrated that DIP-SNPs may serve as a valuable tool in detection of UDM in forensic medicine.
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Affiliation(s)
- Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Wenyan Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Deqing Chen
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jie Shi
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jianbo Ren
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
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Zhu J, Lv M, Zhou N, Chen D, Jiang Y, Wang L, He W, Peng D, Li Z, Qu S, Wang Y, Wang H, Luo H, An G, Liang W, Zhang L. Genotyping polymorphic microhaplotype markers through the Illumina® MiSeq platform for forensics. Forensic Sci Int Genet 2019; 39:1-7. [DOI: 10.1016/j.fsigen.2018.11.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 10/07/2018] [Accepted: 11/06/2018] [Indexed: 01/09/2023]
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10
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Zhu J, Chen P, Qu S, Wang Y, Jian H, Cao S, Liu Y, Zhang R, Lv M, Liang W, Zhang L. Evaluation of the microhaplotype markers in kinship analysis. Electrophoresis 2019; 40:1091-1095. [DOI: 10.1002/elps.201800351] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 11/02/2018] [Accepted: 12/12/2018] [Indexed: 01/28/2023]
Affiliation(s)
- Jing Zhu
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Peng Chen
- Department of Forensic MedicineNanjing Medical University Nanjing P. R. China
| | - Shengqiu Qu
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Yinji Wang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Hui Jian
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Shuqiang Cao
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Yuqing Liu
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Ranran Zhang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Meili Lv
- Department of ImmunologyWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Weibo Liang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Lin Zhang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
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Zhang B, Li Z, Li K, Chen P, Chen F. Forensic parameters and mutation analysis of 23 short tandem repeat (PowerPlex® Fusion System) loci in Fujian Han Chinese population. Leg Med (Tokyo) 2019; 37:33-36. [PMID: 30612022 DOI: 10.1016/j.legalmed.2019.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/30/2018] [Accepted: 01/01/2019] [Indexed: 01/10/2023]
Abstract
Kinship testing based on genetic markers has valuable practical applications. Short tandem repeat polymorphisms (STRPs) can have large number of alleles, and become the dominant marker for kinship identification. However, the high mutation rates affect the identification accuracy. Thus, accurate investigation of the mutation rate of STR loci in different populations is crucial for the reliability of phylogenetic relationships. In present study, forensic parameters and mutation rates (include 95% CI) of 23 short tandem repeats (STR) loci (D3S1358, D1S1656, D2S441, D10S1248, D13S317, D16S539, D18S51, D2S1338, CSF1PO, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, FGA, D22S1045, PentaE, PentaD and DYS391) were investigated through PowerPlex® Fusion System in Fujian Han population. The high level of CDP (0.999999999999999999999999992) and CPE (0.999999993) indicated the panel was high efficiency in forensic DNA identification and paternity testing. In mutation analysis, 43 mutation cases were found through 54,124 parent-child meiotic transfers. The observed mutation rates ranged from 0 (D3S1358, D1S1656, D13S317, TH01, D19S433 and D22S1045) to 0.0025 (PentaE and FGA). The overall mutation rate across all loci was 0.0008 and the average mutation rate for the 23 loci was estimated to be 0.00078 per meiosis. The vast majority of mutations were single-step (88.4%) mutation and also include double-step (9.3%) and triple-step (2.3%) mutations. Paternal mutation rate was more common than maternal mutation rate with a ratio of 7.2:1. In addition, mutation rates indicated positive correlation (r = 0.633, p = 0.009) with the expected heterozygosity (He).
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Affiliation(s)
- Beilei Zhang
- Fujian Zhengtai Judicial Expertise Center, Xiamen, Fujian 361000, PR China
| | - Zheng Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Kai Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China
| | - Peng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China.
| | - Feng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, PR China.
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12
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Forensic efficiency and genetic divergence of 30 autosomal InDels in Chinese Han population from Jiangsu province. Forensic Sci Int Genet 2018; 37:e17-e19. [DOI: 10.1016/j.fsigen.2018.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/09/2018] [Accepted: 08/12/2018] [Indexed: 12/19/2022]
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13
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Chen P, Yin C, Li Z, Pu Y, Yu Y, Zhao P, Chen D, Liang W, Zhang L, Chen F. Evaluation of the Microhaplotypes panel for DNA mixture analyses. Forensic Sci Int Genet 2018; 35:149-155. [PMID: 29778046 DOI: 10.1016/j.fsigen.2018.05.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 04/12/2018] [Accepted: 05/11/2018] [Indexed: 11/17/2022]
Abstract
The identification of a suspect in a DNA mixture typed with the standard short tandem repeat polymorphism (STR) kits has faced challenges. Several improved methods or technologies have been introduced to address this issue. However, some complex situations in the process remain elusive. In the present study, we presented a panel of 26 tiny microhaplotypes, each generating a relatively high (>3.0) effective number of alleles (Ae) and possessing low (<50 bp) sequence lengths. The average Ae and heterozygosity values among the 9 populations of 26 microhaps were in ranges from 2.60 to 4.54 and 0.59 to 0.96, respectively. Power of discrimination and power of exclusion values were ranged from 0.49 to 0.87 and 0.29 to 0.94, respectively. Significant positive correlations have been found between Ae values and heterozygosity (r = 0.43, p = 0.02) or power of discrimination values (r = 0.55, p = 0.003), respectively. The cumulative probability of detecting a mixture of two unrelated individuals could reach 0.9999998 when using a panel of 26 microhaps with Ae = 3. We further tested the panel by using massively parallel sequencing, and 14 out of 26 microhaps were successfully genotyped in a single multiplex system. 60 unrelated Chinese Han individuals and 2 artificially prepared samples mixed by two unrelated contributors (in duplicate, ie. 4 mixtures) were sequenced. Approximately 32.14% of the 14 loci presented three or four alleles in the two mixtures. The likelihood ratio values to cognizance the mixtures' contributor were in a range from 1.95 × 106 to 1.10 × 107. The results demonstrated that the present panel could offer a valuable complementary tool in forensic applications.
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Affiliation(s)
- Peng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China.
| | - Caiyong Yin
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Zheng Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Yan Pu
- Department of Forensic Biology, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Youjia Yu
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Peng Zhao
- Institute of Forensic Science, Wuxi Public Security Bureau, Wuxi, 214002, Jiangsu, China
| | - Dexin Chen
- Department of Engineering, Columbia University, New York, 10027, USA
| | - Weibo Liang
- Department of Forensic Biology, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Lin Zhang
- Department of Forensic Biology, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Feng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China.
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14
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Zhu J, Chen P, Qu S, Wang H, Chen D, Liang W, Zhang L. Genotyping microhaplotype markers through massively parallel sequencing. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Estimate the heterozygote balance of microhaplotype marker with massively parallel sequencing. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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