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Dash HR, Kaitholia K, Kumawat RK, Singh AK, Shrivastava P, Chaubey G, Das S. Sequence variations, flanking region mutations, and allele frequency at 31 autosomal STRs in the central Indian population by next generation sequencing (NGS). Sci Rep 2021; 11:23238. [PMID: 34853383 PMCID: PMC8636586 DOI: 10.1038/s41598-021-02690-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 11/18/2021] [Indexed: 02/05/2023] Open
Abstract
Capillary electrophoresis-based analysis does not reflect the exact allele number variation at the STR loci due to the non-availability of the data on sequence variation in the repeat region and the SNPs in flanking regions. Herein, this study reports the length-based and sequence-based allelic data of 138 central Indian individuals at 31 autosomal STR loci by NGS. The sequence data at each allele was compared to the reference hg19 sequence. The length-based allelic results were found in concordance with the CE-based results. 20 out of 31 autosomal STR loci showed an increase in the number of alleles by the presence of sequence variation and/or SNPs in the flanking regions. The highest gain in the heterozygosity and allele numbers was observed in D5S2800, D1S1656, D16S539, D5S818, and vWA. rs25768 (A/G) at D5S818 was found to be the most frequent SNP in the studied population. Allele no. 15 of D3S1358, allele no. 19 of D2S1338, and allele no. 22 of D12S391 showed 5 isoalleles each with the same size and with different intervening sequences. Length-based determination of the alleles showed Penta E to be the most useful marker in the central Indian population among 31 STRs studied; however, sequence-based analysis advocated D2S1338 to be the most useful marker in terms of various forensic parameters. Population genetics analysis showed a shared genetic ancestry of the studied population with other Indian populations. This first-ever study to the best of our knowledge on sequence-based STR analysis in the central Indian population is expected to prove the use of NGS in forensic case-work and in forensic DNA laboratories.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Integrated High-Tech Complex, Forensic Science Laboratory, Bhopal, Madhya Pradesh, 462003, India.
| | - Kamlesh Kaitholia
- DNA Fingerprinting Unit, Integrated High-Tech Complex, Forensic Science Laboratory, Bhopal, Madhya Pradesh, 462003, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, 302016, India
| | - Anil Kumar Singh
- DNA Fingerprinting Unit, Integrated High-Tech Complex, Forensic Science Laboratory, Bhopal, Madhya Pradesh, 462003, India
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, Madhya Pradesh, 769001, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Surajit Das
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, 470001, India
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Sharma V, Young B, Armogida L, Khan A, Wurmbach E. Evaluation of ArmedXpert software tools, MixtureAce and Mixture Interpretation, to analyze MPS-STR data. Forensic Sci Int Genet 2021; 56:102603. [PMID: 34673336 DOI: 10.1016/j.fsigen.2021.102603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/28/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022]
Abstract
Massively parallel sequencing (MPS) technologies have revolutionized studies of genomic variations and transformed DNA analysis in multiple fields. Assays based on MPS must be capable of discriminating variations introduced by the method, i.e. artifacts from true polymorphisms. In PCR-MPS methods targeting microsatellite markers, artifacts can arise from PCR mis-incorporation, PCR strand slippage (stutter), and sequencing error. Reliable detection of artifacts in mixed DNA samples is a significant challenge that must be addressed in forensic DNA analysis. The ArmedXpert (NicheVision) software tools, MixtureAce™ and Mixture Interpretation, can analyze MPS data by categorizing sequence reads in alleles, stutter, and non-stutter artifacts and analyzing autosomal STR loci of mixed samples. In this study, we evaluated the ArmedXpert tools for the analysis of STR profiles of single-sourced and mixed samples generated by the ForenSeq™ DNA Signature Prep kit (Verogen). Data from eight experimental runs (240 samples) were analyzed: one benchmark run, two runs testing sensitivity with down to 50 pg DNA input, one run testing artificially degraded samples and DNA derived from bones, blood cards and teeth, as well as four runs with mixed DNA samples of varying ratios, sex, and different number of contributors (two to six). The MixtureAce stutter thresholds were initially set following the recommendations from Verogen, plus a non-stutter artifact threshold was set at 5% of allele read counts. A benchmark run, of 30 samples, plus two controls, containing 2310 total alleles, revealed over 5000 artifacts, above an analytical threshold of 10. A total of 4869 artifacts were correctly classified, while 435 were mis-classified as alleles due to exceedance of initial threshold settings. False positives must be resolved by an analyst, which can be time consuming. Stutter thresholds were adjusted based on the benchmark data and the samples were re-tested, resulting in only 57 false positive allele calls. The revised settings were then used in the analysis of the remaining seven experimental runs. Results show that MixtureAce can accurately classify artifacts and alleles when laboratory-specific threshold settings are used. The Mixture Interpretation tool was applied on two- and three-person mixtures. This tool utilized the analyzed data from MixtureAce to calculate, based on the number of alleles at a locus and their read counts, possible deconvolution outcomes with their respective ratios.
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Affiliation(s)
- Vishakha Sharma
- New York City Office of Chief Medical Examiner, Department of Forensic Biology, 421 East 26th Street, New York, NY 10016, USA
| | - Brian Young
- NicheVision Forensics, LLC., 526 South Main Street, Akron, OH 44311, USA
| | - Luigi Armogida
- NicheVision Forensics, LLC., 526 South Main Street, Akron, OH 44311, USA
| | - Amber Khan
- New York City Public Health Laboratory, Department of Health and Mental Hygiene, 455 East 26th Street, New York, NY 10016, USA
| | - Elisa Wurmbach
- New York City Office of Chief Medical Examiner, Department of Forensic Biology, 421 East 26th Street, New York, NY 10016, USA.
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Jian H, Wang L, Lv M, Tan Y, Zhang R, Qu S, Wang J, Zha L, Zhang L, Liang W. A Novel SNP-STR System Based on a Capillary Electrophoresis Platform. Front Genet 2021; 12:636821. [PMID: 33613649 PMCID: PMC7893108 DOI: 10.3389/fgene.2021.636821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/14/2021] [Indexed: 11/13/2022] Open
Abstract
Various compound markers encompassing two or more variants within a small region can be regarded as generalized microhaplotypes. Many of these markers have been investigated for various forensic purposes, such as individual identification, deconvolution of DNA mixtures, or forensic ancestry inference. SNP-STR is a compound biomarker composed of a single nucleotide polymorphism (SNP) and a closely linked short tandem repeat polymorphism (STR), and possess the advantages of both SNPs and STRs. In addition, in conjunction with a polymerase chain reaction (PCR) technique based on the amplification refractory mutation system (ARMS), SNP-STRs can be used for forensic unbalanced DNA mixture analysis based on capillary electrophoresis (CE), which is the most commonly used platform in worldwide forensic laboratories. Our previous research reported 11 SNP-STRs, but few of them are derived from the commonly used STR loci, for which existing STR databases can be used as a reference. For maximum compatibility with existing DNA databases, in this study, we screened 18 SNP-STR loci, of which 14 were derived from the expanded CODIS core loci set. Stable and sensitive SNP-STR multiplex PCR panels based on the CE platform were established. Assays on simulated two-person DNA mixtures showed that all allele-specific primers could detect minor DNA components in 1:500 mixtures. Population data based on 113 unrelated Chengdu Han individuals were investigated. A Bayesian framework was developed for the likelihood ratio (LR) evaluation of SNP-STR profiling results obtained from two-person mixtures. Furthermore, we report on the first use of SNP-STRs in casework to show the advantages and limitations for use in practice. Compared to 2.86 × 103 for autosomal STR kits, the combined LR reached 7.14 × 107 using the SNP-STR method in this casework example.
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Affiliation(s)
- Hui Jian
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yu Tan
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jijun Wang
- HI-TECH Industrial Sub-Branch of Chengdu Municipal Public Security Bureau, Chengdu, China
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
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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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Wei T, Liao F, Wang Y, Pan C, Xiao C, Huang D. A novel multiplex assay of SNP-STR markers for forensic purpose. PLoS One 2018; 13:e0200700. [PMID: 30020969 PMCID: PMC6051632 DOI: 10.1371/journal.pone.0200700] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 05/15/2018] [Indexed: 01/08/2023] Open
Abstract
Like DIP-STR markers (deletion/insertion polymorphism-short tandem repeat combinations), SNP-STR markers (single nucleotide polymorphism-STR combinations) are also valuable in forensic DNA mixture analysis. In this study, eight SNP-STRs were selected, and a stable and sensitive multiplex polymerase chain reaction (PCR) assay was developed for amplifying these SNP-STRs and the Amelogenin gender marker according to the principle of amplification refractory mutation system (ARMS). This novel multiplex set allows detection of the minor DNA contributor in a DNA mixture of any gender and cellular origin with high resolution (beyond a DNA ratio of 1:20). In addition, SNP-STR haplotype frequencies were estimated based on a survey of 350 unrelated individuals from Chinese Han population, and the combined power of discrimination (PD) and power of exclusion (PE) of the eight SNP-STRs were calculated as 0.99999999965 and 0.9996, which were obviously higher than that of the eight STR loci: 0.9999999954 and 0.9989 respectively. The results indicated that the SNP-STR compound markers have higher application value in forensic identification compared to standard autosomal STRs, especially in the analysis of imbalanced DNA mixtures.
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Affiliation(s)
- Tian Wei
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei province, China
| | - Fei Liao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei province, China
| | - Yaowu Wang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei province, China
| | - Chao Pan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei province, China
| | - Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei province, China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei province, China
- * E-mail:
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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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Xue J, Wu R, Pan Y, Wang S, Qu B, Qin Y, Shi Y, Zhang C, Li R, Zhang L, Zhou C, Sun H. Integrated massively parallel sequencing of 15 autosomal STRs and Amelogenin using a simplified library preparation approach. Electrophoresis 2018; 39:1466-1473. [DOI: 10.1002/elps.201700429] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/22/2018] [Accepted: 03/27/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Jian Xue
- Forensic Science Service of the Beijing Public Security Bureau; Beijing P. R. China
| | - Riga Wu
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center; Sun Yat-sen University; Guangzhou Guangdong P. R. China
| | - Yajiao Pan
- IPE Biotechnology Co., Ltd.; Beijing P. R. China
| | - Shunxia Wang
- Forensic Science Service of the Beijing Public Security Bureau; Beijing P. R. China
| | - Baowang Qu
- IPE Biotechnology Co., Ltd.; Beijing P. R. China
| | - Ying Qin
- Zhuhai Municipal Public Security Forensic Science Center; Zhuhai P. R. China
| | - Yuequn Shi
- Zhuhai Municipal Public Security Forensic Science Center; Zhuhai P. R. China
| | - Chuchu Zhang
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Ran Li
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Liyan Zhang
- Zhuhai Municipal Public Security Forensic Science Center; Zhuhai P. R. China
| | - Cheng Zhou
- IPE Biotechnology Co., Ltd.; Beijing P. R. China
| | - Hongyu Sun
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center; Sun Yat-sen University; Guangzhou Guangdong P. R. China
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Development of a SNP-STRs multiplex for forensic identification. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.236] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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