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Jiang L, Liu J, Li S, Wen Y, Zheng X, Qin L, Hou Y, Wang Z. CmVCall: An automated and adjustable nanopore analysis pipeline for heteroplasmy detection of the control region in human mitochondrial genome. Forensic Sci Int Genet 2023; 67:102930. [PMID: 37595417 DOI: 10.1016/j.fsigen.2023.102930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023]
Abstract
Genetic associations between human mitochondrial DNA (mtDNA) heteroplasmy and mitochondrial diseases, aging, and cancer have been elaborated, contributing a lot to the further understanding of mtDNA polymorphic spectrum in anthropology, population, and forensic genetics. In the past decade, heteroplasmy detection using Sanger sequencing and next generation sequencing (NGS) was hampered by the former's inefficiency and the latter's inherent bias due to amplification and mapping of short reads, respectively. Nanopore sequencing stands out for its ability to yield long contiguous segments of DNA, providing a new insight into heterogeneity authentication. In addition to MinION from Oxford Nanopore Technologies, an alternative nanopore sequencer QNome (Qitan Technology) has also been applied to various biological research and the forensic applicability of this platform has been proved recently. In this study, we evaluated the performance of four commonly used variant callers in the heterogeneity authentication of the control region of human mtDNA based on simulations of different ratios generated by mixing QNome nanopore sequencing reads of two synthetic sequences. Then, an open-source and python-based nanopore analytics pipeline, CmVCall was developed and incorporated multiple programs including reads filtering, removal of nuclear mitochondrial sequences (NUMTs), alignment, optional 'Correction' mode, and heterogeneity identification. CmVCall can achieve high precision, accuracy, and recall of 100%, 99.9%, and 92.3% with a 5% heteroplasmy level in 'Correction' mode. Moreover, blood, saliva, and hair shaft samples from monozygotic (MZ) twins were used for heterogeneity evaluation and comparison with the NGS data. Results of MZ twin samples showed that CmVCall could identify more point heteroplasmy sites, revealing significant levels of inter- and intra-individual mtDNA polymorphism. In conclusion, we believe that this analysis pipeline will lay a solid foundation for the development of a comprehensive nanopore analysis pipeline targeting the whole mitochondrial genome.
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Affiliation(s)
- Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xinyue Zheng
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Liu Qin
- Qitan Technology Ltd., Chengdu, Chengdu 610044, China.
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.
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Huang S, Jin X, Zhang H, Jin H, Ren Z, Wang Q, Liu Y, Ji J, Yang M, Zhang H, Zheng X, Song D, Zheng B, Huang J. Developmental Validation of the Novel Five-Dye-Labeled Multiplex Autosomal STR Panel and Its Forensic Efficiency Evaluation. Front Genet 2022; 13:897650. [PMID: 35711918 PMCID: PMC9194853 DOI: 10.3389/fgene.2022.897650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Short tandem repeats (STRs) are the most frequently used genetic markers in forensic genetics due to their high genetic diversities and abundant distributions in the human genome. Currently, the combined DNA index system is commonly incorporated into various commercial kits for forensic research. Some novel STRs that are different from the combined DNA index system were not only used to assess complex paternity cases but also could provide more genetic information and higher forensic efficiency in combination with those commonly used STRs. In this study, we validated forensic performance of a novel multiplex amplification STR panel to evaluate its sensitivity, species specificity, forensic application values, and so on. Obtained results revealed that the kit showed high sensitivity, and the complete allelic profile could be observed at 0.125 ng DNA sample. In addition, the kit possessed high species specificity, good tolerance to common inhibitors, and accurate genotyping ability. More importantly, STRs out of the kit displayed high discrimination power and probability of exclusion. To sum up, the novel kit presented in this study can be viewed as a promising tool for forensic human identification and complex paternity analysis.
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Affiliation(s)
- Shimei Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Haiying Jin
- Ningbo Health Gene Technologies Co.,Ltd, Ningbo, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Xingkai Zheng
- Ningbo Health Gene Technologies Co.,Ltd, Ningbo, China
| | - Danlu Song
- Ningbo Health Gene Technologies Co.,Ltd, Ningbo, China
| | - Bingjie Zheng
- Ningbo Health Gene Technologies Co.,Ltd, Ningbo, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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Li S, Lin J, Hao H, Jin H, Song D, Zhu B. Validation of a 6-Dye Short Tandem Repeat System: A Dry Kit With Lyophilized Amplification Reagent. Front Genet 2021; 12:705819. [PMID: 34552616 PMCID: PMC8451954 DOI: 10.3389/fgene.2021.705819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/13/2021] [Indexed: 11/18/2022] Open
Abstract
The SureID®S6 system used a lyophilized pellet as the amplification reagent to enable multiplexing of sex-determining marker Amelogenin, 21 autosomal short tandem repeats (STRs), and one Y-STR. To assess the performance, reliability, and limitation of the dry amplification system, the validation studies including PCR condition, reproducibility, sizing and precision, analytical threshold calculation, sensitivity and stochastic threshold calculation, species specificity, stability, mixture, case sample, and population and concordance were conducted according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) Validation Guidelines. Experimental data suggested that the optimal range of total input DNA was from 125 to 500 pg; the appropriate analytical threshold was 80 relative fluorescence units (RFUs) while the stochastic threshold was 260 RFUs; for the stability studies, SureID®S6 system could resist against less than 500 μmol/L of hematin, 100 ng/μl of humic acid, 4 mM of indigotin, 800 mM of tannic acid, and 800 mM of calcium ion. Population and concordance studies using 500 unrelated individuals showed that the combined probability of discrimination (CPD) and cumulative probability of exclusion (CPE) values were 0.999999999999 and 0.999999998416, respectively. The genotypes for the same sample were concordant with the previously validated HUAXIA™ Platinum kit. The validation results demonstrated that the SureID®S6 system could be used for forensic applifications.
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Affiliation(s)
- Shuanglin Li
- Department of Forensic Genetics, Multi-Omics Innovative Research Center of Forensic Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Jinfeng Lin
- School of Medicine, Ningbo University, Ningbo, China
| | - Honglei Hao
- Zhejiang Key Laboratory of Forensic Science and Technology, Hangzhou, China
| | - Haiying Jin
- Ningbo Health Gene Technologies Co., Ltd, Ningbo, China
| | - Danlu Song
- Ningbo Health Gene Technologies Co., Ltd, Ningbo, China
| | - Bofeng Zhu
- Department of Forensic Genetics, Multi-Omics Innovative Research Center of Forensic Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
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Qu Y, Tao R, Yu H, Yang Q, Wang Z, Tan R, Zhang X, Xia R, Xiong L, Xi S, Wu J, Gao Y, Zhang S, Li C. Development and validation of a forensic six-dye multiplex assay with 29 STR loci. Electrophoresis 2021; 42:1419-1430. [PMID: 33864289 DOI: 10.1002/elps.202100019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/05/2021] [Accepted: 04/10/2021] [Indexed: 11/10/2022]
Abstract
This paper describes the development and validation of a novel 31-locus, six-dye STR multiplex system, which is designed to meet the needs of the rapidly growing Chinese forensic database. This new assay combines 20 extended-CODIS core loci (D3S1358, D5S818, TPOX, CSF1PO, TH01, vWA, D7S820, D21S11, D8S1179, D18S51, D16S539, D13S317, FGA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045), nine highly polymorphic loci in Chinese Han population (D3S3045, D6S1043, D6S477, D8S1132, D10S1435, D15S659, D19S253, Penta D, and Penta E), and two gender determining markers, amelogenin and Y-Indel, which could amplify DNA from extracts, as well as direct amplification from substrates. To demonstrate the suitability for forensic applications, this system was validated by precision and accuracy evaluation, concordance tests, case sample tests, sensitivity, species specificity, stability, stutter calculation, and DNA mixtures, according to the guidelines described by the Scientific Working Group on DNA Analysis Methods (SWGDAM) and regulations published by the China Ministry of Public Security. The validation results indicate the robustness and reliability of this new system, and it could be a potentially helpful tool for human identification and paternity testing in the Chinese population, as well as facilitating global forensic DNA data sharing.
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Affiliation(s)
- Yiling Qu
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - RuiYang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Huan Yu
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Qi Yang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Ziwei Wang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Rui Tan
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Xiaochun Zhang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, P. R. China
| | - Lei Xiong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China.,School of Basic Medicine, Inner Mongolia Medical University, Hohhot, P. R. China
| | - Shihan Xi
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China.,Clinical Medical School of Inner Mongolia University for the Nationalities, Tongliao, P. R. China
| | - Jun Wu
- PeopleSpot Inc., Beijing, P. R. China
| | - Yuzhen Gao
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Chengtao Li
- Department of Forensic Science, Medical School of Soochow University, Suzhou, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
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Green R, Elliott JL, Norona W, Go F, Nguyen VT, Ge J, Short ML, Mulero JJ, Zhong C. Developmental validation of VeriFiler™ Plus PCR Amplification Kit: A 6-dye multiplex assay designed for casework samples. Forensic Sci Int Genet 2021; 53:102494. [PMID: 33740707 DOI: 10.1016/j.fsigen.2021.102494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
The VeriFiler™ Plus PCR Amplification Kit is a 6-dye multiplex assay that simultaneously amplifies a set of 23 autosomal markers (D3S1358, vWA, D16S539, CSF1PO, D6S1043, D8S1179, D21S11, D18S51, D5S818, D2S441, D19S433, FGA, D10S1248, D22S1045, D1S1656, D13S317, D7S820, Penta E, Penta D, TH01, D12S391, D2S1338, and TPOX), a quality indicator system, and two sex-identification markers. Combined, the markers satisfy the requirements of the Chinese National autosomal DNA database as well as expanded CODIS (Combined DNA Index System). The VeriFiler Plus kit was developed with an improved Master Mix which incorporates the brighter TED™ dye, and accommodates a higher sample loading volume thus allowing for increased sensitivity and enabling maximum information recovery from challenging casework samples including touch, degraded, and inhibited samples. Here, we report the results of the developmental validation study which followed the SWGDAM (Scientific Working Group on DNA Analysis Methods) guidelines and includes data for PCR-based studies, sensitivity, species specificity, stability, precision, reproducibility and repeatability, concordance, stutter, DNA mixtures, and performance on mock casework samples. The results validate the multiplex design as well as demonstrate the kit's robustness, reliability, and suitability as an assay for human identification with casework DNA samples.
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Affiliation(s)
- Robert Green
- Thermo Fisher Scientific Inc., 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Jennifer L Elliott
- Thermo Fisher Scientific Inc., 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Wilma Norona
- Thermo Fisher Scientific Inc., 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Francine Go
- Thermo Fisher Scientific Inc., 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Vivian T Nguyen
- Thermo Fisher Scientific Inc., 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Jianye Ge
- Thermo Fisher Scientific Inc., 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Marc L Short
- Thermo Fisher Scientific Inc., 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Julio J Mulero
- Thermo Fisher Scientific Inc., 180 Oyster Point Blvd., South San Francisco, CA 94080, USA
| | - Chang Zhong
- Thermo Fisher Scientific Inc., 180 Oyster Point Blvd., South San Francisco, CA 94080, USA.
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