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Tao R, Dong X, Zhen X, Xia R, Qu Y, Liu S, Zhang S, Li C. Population genetic analyses of Eastern Chinese Han nationality using ForenSeq™ DNA Signature Prep Kit. Mol Genet Genomics 2024; 299:9. [PMID: 38374461 DOI: 10.1007/s00438-024-02121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024]
Abstract
Currently, the most commonly used method for human identification and kinship analysis in forensic genetics is the detection of length polymorphism in short tandem repeats (STRs) using polymerase chain reaction (PCR) and capillary electrophoresis (CE). However, numerous studies have shown that considerable sequence variations exist in the repeat and flanking regions of the STR loci, which cannot be identified by CE detection. Comparatively, massively parallel sequencing (MPS) technology can capture these sequence differences, thereby enhancing the identification capability of certain STRs. In this study, we used the ForenSeq™ DNA Signature Prep Kit to sequence 58 STRs and 94 individual identification SNPs (iiSNPs) in a sample of 220 unrelated individuals from the Eastern Chinese Han population. Our aim is to obtain MPS-based STR and SNP data, providing further evidence for the study of population genetics and forensic applications. The results showed that the MPS method, utilizing sequence information, identified a total of 486 alleles on autosomal STRs (A-STRs), 97 alleles on X-chromosome STRs (X-STRs), and 218 alleles on Y-chromosome STRs (Y-STRs). Compared with length polymorphism, we observed an increase of 260 alleles (157, 31, and 72 alleles on A-STRs, X-STRs, and Y-STRs, respectively) across 36 STRs. The most substantial increments were observed in DYF387S1 and DYS389II, with increases of 287.5% and 250%, respectively. The most increment in the number of alleles was found at DYF387S1 and DYS389II (287.5% and 250%, respectively). The length-based (LB) and sequence-based (SB) combined random match probability (RMP) of 27 A-STRs were 6.05E-31 and 1.53E-34, respectively. Furthermore, other forensic parameters such as total discrimination power (TDP), cumulative probability of exclusion of trios (CPEtrio), and duos (CPEduo) were significantly improved when using the SB data, and informative data were obtained for the 94 iiSNPs. Collectively, these findings highlight the advantages of MPS technology in forensic genetics, and the Eastern Chinese Han genetic data generated in this study could be used as a valuable reference for future research in this field.
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Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
| | - Xinyu Dong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Minhang Branch of Shanghai Public Security Bureau, Shanghai, 201108, China
| | - Xiaoyuan Zhen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shiquan Liu
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, 100088, China.
| | - Suhua Zhang
- Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Key Laboratory of Forensic Science, Shanghai, 200063, China.
- Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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Feng Y, Zhao Y, Lu X, Li H, Zhao K, Shi M, Wen S. Forensic analysis and sequence variation of 133 STRs in the Hakka population. Front Genet 2024; 15:1347868. [PMID: 38317659 PMCID: PMC10839782 DOI: 10.3389/fgene.2024.1347868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction: Short Tandem Repeats (STRs) are highly valuable genetic markers in forensic science. However, the conventional PCR-CE technique has limitations, and the emergence of massively parallel sequencing (MPS) technology presents new opportunities for STR analysis. Yet, there is limited research on Chinese population diversity using MPS. Methods: In this study, we obtained genotype data for 52 A-STRs and 81 Y-STRs from the Hakka population in Meizhou, Guangdong, China, using the Forensic Analysis System Multiplecues SetB Kit on the MGISEQ-2000 platform. Results: Our findings demonstrate that these 133 STRs are highly efficient for forensic applications within the Meizhou Hakka population. Statistical analysis revealed Hobs values ranging from 0.61306 to 0.91083 and Hexp values ranging from 0.59156 to 0.91497 for A-STRs based on length polymorphism. For sequence polymorphism, Hobs values ranged from 0.61306 to 0.94586, and Hexp values fluctuated between 0.59156 and 0.94487. The CPE values were 1-5.0779620E-21 and 1-3.257436E-24 for length and sequence polymorphism, respectively, while the CPD values were 1-1.727007E-59 and 1-5.517015E-66, respectively. Among the 80 Y-STR loci, the HD values for length and sequence polymorphism were 0.99764282 and 0.99894195, respectively. The HMP values stood at 0.00418102 and 0.00288427, respectively, and the DC values were 0.75502742 and 0.83363803, respectively. For the 52 A-STR loci, we identified 554 and 989 distinct alleles based on length and sequence polymorphisms, respectively. For the 81 Y-STR loci, 464 and 652 unique alleles were detected at the length and sequence level, respectively. Population genetic analysis revealed that the Meizhou Hakka population has a close kinship relationship with the Asian populations THI and KOR based on length polymorphism data of A-STRs. Conversely, based on length polymorphism data of Y-STRs, the Meizhou Hakka population has the closest kinship relationship with the Henan Han population. Discussion: Overall, the variation information of repeat region sequences significantly enhances the forensic identification efficacy of STR genetic markers, providing an essential database for forensic individual and paternity testing in this region. Additionally, the data generated by our study will serve as a vital resource for research into the genetic structure and historical origins of the Meizhou Hakka population.
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Affiliation(s)
- Yuhang Feng
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing, China
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou, China
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou, China
| | - Kai Zhao
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou, China
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing, China
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Institute of Archaeological Science, Fudan University, Shanghai, China
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai, China
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Guo F, Liu Z, Long G, Zhang B, Dong X, Liu D, Yu S. High-resolution genotyping of 58 STRs in 635 Northern Han Chinese with MiSeq FGx ® Forensic Genomics System. Forensic Sci Int Genet 2023; 65:102879. [PMID: 37150076 DOI: 10.1016/j.fsigen.2023.102879] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/16/2023] [Accepted: 04/22/2023] [Indexed: 05/09/2023]
Abstract
Sequence polymorphisms were characterized at 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), and 24 Y chromosomal STRs (Y-STRs) in 635 Northern Han Chinese with the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Since repeat region (RR) and flanking region (FR) variation can be detected by massively parallel sequencing (MPS), the increase in the number of unique alleles and the average of gene diversity was 78.18% and 3.51% between sequence and length, respectively. A total of 74 novel RR variants were identified at 33 STRs compared with STRSeq and previous studies, and 13 FR variants (rs1770275883, rs2053373277, rs2082557941, rs1925525766, rs1926380862, rs1569322793, rs2051848492, rs2051848696, rs2016239814, rs2053269960, rs2044518192, rs2044536444, and rs2089968964) were first submitted to dbSNP. Also, 99.94% of alleles were concordant between the ForenSeq DNA Signature Prep Kit and commercial CE kits. Discordance resulted from the low performance at D22S1045 and occasionally at DYS392, flanking region deletions at D7S820 and DXS10074, and the strict alignment algorithm at DXS7132. Null alleles at DYS505 and DYS448 and multialleles at DYS387S1a/b, DYS385a/b, DYS448, DYS505, DXS7132, and HPRTB were validated with other MPS and CE kits. Thus, a high-resolution sequence-based (SB) and length-based (LB) allele frequencies dataset from Northern Han Chinese has been established already. As expected, forensic parameters increased significantly on combined power of discrimination (PD) and combined power of exclusion (PE) at A-STRs, mildly on combined PD and combined mean exclusion chance (MEC) at X-STRs, and barely on discrimination capacity (DC) at Y-STRs. Additionally, MiSeq FGx quality metrics and MPS performance were evaluated in this study, which presented the high-quality of the dataset at 20 consecutive runs, such as ≥ 60% bases with a quality score of 20 or higher (%≥ Q20), > 60% of effective reads, > 2000 × of depth of coverage (DoC), ≥ 60% of allele coverage ratio (ACR) or heterozygote balance, ≥ 70% of inter-locus balance, and ≤ 0.4 of the absolute value of observed minus expected heterozygosity (|Hexp - Hobs|). In conclusion, MiSeq FGx can help us generate a high-resolution and high-quality dataset for human identification and population genetic studies.
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Affiliation(s)
- Fei Guo
- School of Forensic Science and Technology, Criminal Investigation Police University of China, Shenyang, Liaoning 110854, PR China.
| | - Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Guannan Long
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Biao Zhang
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Xinyu Dong
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, PR China
| | - Dahua Liu
- Department of Forensic Medicine, Jinzhou Medical University, Jinzhou, Liaoning 121001, PR China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China.
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Dawnay N, Sheppard K. From crime scene to courtroom: A review of the current bioanalytical evidence workflows used in rape and sexual assault investigations in the United Kingdom. Sci Justice 2023; 63:206-228. [PMID: 36870701 DOI: 10.1016/j.scijus.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Sexual assault casework requires the collaboration of multiple agency staff to formalise an investigative pipeline running from crime scene to court. While the same could be said of many other forensic investigations, few require the additional support of health care staff and the combined forensic involvement of body-fluid examiners, DNA experts and analytical chemists. The sheer amount of collaborative effort between agencies is laid out through a detailed examination of the investigative workflow from crime scene to courtroom with each step in the pipelines detailed and discussed. Beginning with a review of sexual assault legislation in the United Kingdom this article details how sexual assault investigations are initiated by police and supported by sexual assault referral centre (SARC) staff who are often the first responders providing primary healthcare and patient support to victims while simultaneously collecting and assessing forensic evidence. Detailing the myriad of evidential material that can be documented and collected at the SARC, the review identifies and categorises key forensic tests to first detect and identify body-fluids recovered from evidence through to the secondary analysis of DNA to help identify the suspect. This review also focusses on the collection and analysis of biological material used to support the allegation that the sexual activity was non-consensual and provides a breakdown of common marks and trauma as well as a review of common analytical methods used to infer Drug Facilitated Sexual Assault (DFSA). The culmination of the investigative pipeline is discussed by reviewing the Rape and Serious Sexual Assault (RASSO) workflow used by the Crown Prosecution Service before providing our thoughts on the future of forensic analysis and possible changes to the described workflows.
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Affiliation(s)
- Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom.
| | - Kayleigh Sheppard
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom
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5
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Gutierrez R, Roman M, Houston R, Kalafut T. Detection and Analysis of DNA Mixtures with the MiSeq FGx®. Sci Justice 2022; 62:547-555. [DOI: 10.1016/j.scijus.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
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6
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Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment. J Hum Genet 2022; 67:487-493. [DOI: 10.1038/s10038-022-01033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/08/2022]
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Senst A, Caliebe A, Scheurer E, Schulz I. Validation and beyond: Next generation sequencing of forensic casework samples including challenging tissue samples from altered human corpses using the MiSeq FGx system. J Forensic Sci 2022; 67:1382-1398. [PMID: 35318655 PMCID: PMC9313618 DOI: 10.1111/1556-4029.15028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/15/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023]
Abstract
The proceeding developments in next generation sequencing (NGS) technologies enable increasing discrimination power for short tandem repeat (STR) analyses and provide new possibilities for human identification. Therefore, the growing relevance and demand in forensic casework display the need for reliable validation studies and experiences with challenging DNA samples. The presented validation of the MiSeq FGx system and the ForenSeq™ DNA Signature Prep Kit (1) investigated sensitivity, repeatability, reproducibility, concordance, pooling variations, DNA extraction method variances, DNA mixtures, degraded, and casework samples and (2) optimized the sequencing workflow for challenging samples from human corpses by testing additional PCR purification, pooling adjustments, and adapter volume reductions. Overall results indicate the system's reliability in concordance to traditional capillary electrophoresis (CE)‐based genotyping and reproducibility of sequencing data. Genotyping success rates of 100% were obtained down to 62.5 pg DNA input concentrations. Autosomal STR (aSTR) profiles of artificially degraded samples revealed significantly lower numbers of locus and allelic dropouts than CE. However, it was observed that the system still exposed drawbacks when sequencing highly degraded and inhibited samples from human remains. Due to the lack of studies evaluating the sequencing success of samples from decomposed or skeletonised corpses, the presented optimisation studies provide valuable recommendations such as an additional PCR purification, an increase in library pooling volumes, and a reduction of adapter volumes for samples with concentrations ≥31.2 pg. Thus, this research highlights the importance of all‐encompassing validation studies for implementing novel technologies in forensic casework and presents recommendations for challenging samples.
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Affiliation(s)
- Alina Senst
- Institute of Forensic Medicine, Basel, Switzerland
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University and University-Hospital Schleswig-Holstein, Kiel, Germany
| | - Eva Scheurer
- Institute of Forensic Medicine, Basel, Switzerland
| | - Iris Schulz
- Institute of Forensic Medicine, Basel, Switzerland
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Tyazhelova TV, Kuznetsova IL, Andreeva TV, Kunizheva SS, Rogaev EI. Application of Massive Parallel Sequencing Technology in Forensics: Comparative Analysis of Sequencing Platforms. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421120127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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9
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Predicting eye and hair colour in a Norwegian population using Verogen's ForenSeq™ DNA signature prep kit. Forensic Sci Int Genet 2021; 56:102620. [PMID: 34735941 DOI: 10.1016/j.fsigen.2021.102620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/24/2021] [Accepted: 10/21/2021] [Indexed: 01/01/2023]
Abstract
Prediction of eye and hair colour from DNA can be an important investigative tool in forensic cases if conventional DNA profiling fails to match DNA from any known suspects or cannot obtain a hit in a DNA database. The HIrisPlex model for simultaneous eye and hair colour predictions was developed for forensic usage. To genotype a DNA sample, massively parallel sequencing (MPS) has brought new possibilities to the analysis of forensic DNA samples. As part of an in-house validation, this study presents the genotyping and predictive performance of the HIrisPlex SNPs in a Norwegian study population, using Verogen's ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx system and the HIrisPlex webtool. DNA-profiles were successfully typed with DNA input down to 125 pg. In samples with DNA input < 125 pg, false homozygotes were observed with as many as 92 reads. Prediction accuracies in terms of AUC were high for red (0.97) and black (0.93) hair colours, as well as blue (0.85) and brown (0.94) eye colours. The AUCs for blond (0.72) and brown (0.70) hair colour were considerably lower. None of the individuals was predicted to have intermediate eye colour. Therefore, the error rates of the overall eye colour predictions were 37% with no predictive probability threshold (pmax) and 26% with a probability threshold of 0.7. We also observed that more than half of the incorrect predictions were for individuals carrying the rs12913832 GG genotype. For hair colour, 65% of the individuals were correctly predicted when using the highest probability category approach. The main error was observed for individuals with brown hair colour that were predicted to have blond hair. Utilising the prediction guide approach increased the correct predictions to 75%. Assessment of phenotype-genotype associations of eye colours using a quantitative eye colour score (PIE-score), revealed that rs12913832 AA individuals of Norwegian descent had statistically significantly higher PIE-score (less brown eye colour) than individuals of non-northern European descent. To our knowledge, this has not been reported in other studies. Our study suggests that careful assessment of the target population prior to the implementation of forensic DNA phenotyping to case work is beneficial.
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Chen C, Jin X, Zhang X, Zhang W, Guo Y, Tao R, Chen A, Xu Q, Li M, Yang Y, Zhu B. Comprehensive Insights Into Forensic Features and Genetic Background of Chinese Northwest Hui Group Using Six Distinct Categories of 231 Molecular Markers. Front Genet 2021; 12:705753. [PMID: 34721519 PMCID: PMC8555763 DOI: 10.3389/fgene.2021.705753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal short tandem repeats (A-STRs), into 90 unrelated male individuals from the Chinese Northwest Hui group to comprehensively explore its forensic characteristics and genetic background. Total of 451 length-based and 652 sequence-based distinct alleles were identified from 58 short tandem repeats (STRs) in 90 unrelated Northwest Hui individuals, denoting that the sequence-based genetic markers could pronouncedly provide more genetic information than length-based markers. The forensic characteristics and efficiencies of STRs and IISNPs were estimated, both of which externalized high polymorphisms in the Northwest Hui group and could be further utilized in forensic investigations. No significant departure from the Hardy-Weinberg equilibrium (HWE) expectation was observed after the Bonferroni correction. Additionally, four group sets of reference population data were exploited to dissect the genetic background of the Northwest Hui group separately from different perspectives, which contained 26 populations for 93 IISNPs, 58 populations for 17 Y-STRs, 26 populations for 55 AISNPs (raw data), and 109 populations for 55 AISNPs (allele frequencies). As a result, the analyses based on the Y-STRs indicated that the Northwest Hui group primarily exhibited intimate genetic relationships with reference Hui groups from Chinese different regions except for the Sichuan Hui group and secondarily displayed close genetic relationships with populations from Central and West Asia, as well as several Chinese groups. However, the AISNP analyses demonstrated that the Northwest Hui group shared more intimate relationships with current East Asian populations apart from reference Hui group, harboring the large proportion of ancestral component contributed by East Asia.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Min Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Department of Forensic Genetics, Multi-Omics Innovative Research Center of Forensic Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Hölzl-Müller P, Bodner M, Berger B, Parson W. Exploring STR sequencing for forensic DNA intelligence databasing using the Austrian National DNA Database as an example. Int J Legal Med 2021; 135:2235-2246. [PMID: 34436655 PMCID: PMC8523457 DOI: 10.1007/s00414-021-02685-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/12/2021] [Indexed: 11/29/2022]
Abstract
Here, we present the results from a population study that evaluated the performance of massively parallel sequencing (MPS) of short tandem repeats (STRs) with a particular focus on DNA intelligence databasing purposes. To meet this objective, 247 randomly selected reference samples, earlier being processed with conventional capillary electrophoretic (CE) STR sizing from the Austrian National DNA Database, were reanalyzed with the PowerSeq 46Y kit (Promega). This sample set provides MPS-based population data valid for the Austrian population to increase the body of sequence-based STR variation. The study addressed forensically relevant parameters, such as concordance and backward compatibility to extant amplicon-based genotypes, sequence-based stutter ratios, and relative marker performance. Of the 22 autosomal STR loci included in the PowerSeq 46GY panel, 99.98% of the allele calls were concordant between MPS and CE. Moreover, 25 new sequence variants from 15 markers were found in the Austrian dataset that are yet undescribed in the STRSeq online catalogue and were submitted for inclusion. Despite the high degree of concordance between MPS and CE derived genotypes, our results demonstrate the need for a harmonized allele nomenclature system that is equally applicable to both technologies, but at the same time can take advantage of the increased information content of MPS. This appears to be particularly important with regard to database applications in order to prevent false exclusions due to varying allele naming based on different analysis platforms and ensures backward compatibility.
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Affiliation(s)
- Petra Hölzl-Müller
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria.
- Forensic Science Program, The Pennsylvania State University, State College, PA, USA.
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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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13
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Strategy for STR typing of bones from the Second World War combining CE and NGS technology: A pilot study. Forensic Sci Int Genet 2020; 50:102401. [PMID: 33171316 DOI: 10.1016/j.fsigen.2020.102401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/21/2020] [Accepted: 09/26/2020] [Indexed: 01/23/2023]
Abstract
The genetic identification of skeletal remains found in Second World War mass graves is complicated because of the poor quality of the samples. The aim of this study was to set up a workflow for STR typing of such samples combining PCR/CE and PCR/NGS technologies. To this end, 57 DNA samples from an equal number of 75-year-old femurs were studied. After a first round of PCR typing using GlobalFiler CE, 42 samples yielded a full profile and were therefore submitted to our standard workflow. The 15 samples that yielded no or a limited number (2-17/21) of autosomal STR markers as well four bone control samples that provided a full profile with the conventional PCR/CE test were typed in duplicate by the GlobalFiler NGS kit. Despite the degradation of the samples, which resulted in lower coverage and a lower % of on-target reads, reliable sequencing data were obtained from 16/19 samples. The use of a threshold of 30× for the locus call led to a consensus profile (cp) of 20-31/31 STR autosomal loci in 10 samples and to a cp of 8-10/31 loci in two samples, whereas the four control samples yielded a cp of 26-31/31 loci. Finally, the data of the NGS typing were combined with those of the CE typing. This last task allowed us to recover (on average) three alleles per sample and to increase the number of the heterozygous patterns in 37 cases. In total, the combined approach proposed here made possible the genetic typing of 65-100% of the autosomal STR markers in 10/15 (66.6 %) skeletal remains that yielded no or very poor results with the conventional PCR/CE approach. However, because several artefacts (such as allelic drop-out and allelic drop-in) were scored, the risk of mistyping cannot be neglected.
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14
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Finaughty C, Reid KM, Alli IH, Heathfield LJ. A first for forensic genetics in Africa: successful identification of skeletal remains from the marine environment using massively parallel sequencing. Forensic Sci Int Genet 2020; 49:102370. [PMID: 32829148 DOI: 10.1016/j.fsigen.2020.102370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022]
Abstract
In unrelated circumstances, two young adult males allegedly went missing off the coast of Cape Town, South Africa, within two months of each other. Weeks after the second disappearance, a decomposed human lower limb was recovered from a beach in Cape Town, followed by a washed-up decomposed hand three days later. An item of female clothing was found with the remains, and preliminary analysis of the skeleton indicated a female, leading to confusion regarding the possible identity of the decedent. Consequently, DNA analyses were requested to determine the biological sex of the remains, and whether the two sets of remains originated from the same individual. Various samples were collected, including bone, nails and swabs of soft tissue. DNA quantity and quality varied between sample types, with better results obtained from metacarpal bone and swab lysates. DNA profiling revealed a male sex, which suggests cognitive bias may have played a role in initial sex estimations. In addition, massively parallel sequencing confidently matched the two sets of remains (random match probability: 1 in 2.70 x 1031). These results were a first for Africa where massively parallel sequencing was successfully used and assisted in the identification of human remains, thus, affording closure to the next-of-kin. Moreover, this constitutes the first global report where soft tissue lysates from a marine decomposition case yielded full DNA profiles with a massively parallel sequencing approach.
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Affiliation(s)
- Chandra Finaughty
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa.
| | - Kate Megan Reid
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa.
| | - Iekram Hoosen Alli
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa.
| | - Laura Jane Heathfield
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa.
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15
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Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing. Sci Rep 2020; 10:12225. [PMID: 32699278 PMCID: PMC7376188 DOI: 10.1038/s41598-020-69137-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/16/2020] [Indexed: 01/26/2023] Open
Abstract
Massively parallel sequencing (MPS) has rapidly become a promising method for forensic DNA typing, due to its ability to detect a large number of markers and samples simultaneously in a single reaction, and sequence information can be obtained directly. In the present study, two kinds of forensic genetic markers, short tandem repeat (STR) and identity-informative single nucleotide polymorphism (iiSNP) were analyzed simultaneously using ForenSeq DNA Signature Prep Kit, a commercially available kit on MPS platform. A total of 152 DNA markers, including 27 autosomal STR (A-STR) loci, 24 Y chromosomal STR (Y-STR) loci, 7 X chromosomal STR (X-STR) loci and 94 iiSNP loci were genotyped for 107 Tibetan individuals (53 males and 54 females). Compared with length-based STR typing methods, 112 more A-STR alleles, 41 more Y-STR alleles, and 24 more X-STR alleles were observed at 17 A-STRs, 9 Y-STRs, and 5 X-STRs using sequence-based approaches. Thirty-nine novel sequence variations were observed at 20 STR loci. When the flanking regions were also analyzed in addition to target SNPs at the 94 iiSNPs, 38 more alleles were identified. Our study provided an adequate genotype and frequencies data of the two types of genetic markers for forensic practice. Moreover, we also proved that this panel is highly polymorphic and informative in Tibetan population, and should be efficient in forensic kinship testing and personal identification cases.
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16
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Devesse L, Davenport L, Borsuk L, Gettings K, Mason-Buck G, Vallone PM, Syndercombe Court D, Ballard D. Classification of STR allelic variation using massively parallel sequencing and assessment of flanking region power. Forensic Sci Int Genet 2020; 48:102356. [PMID: 32712568 DOI: 10.1016/j.fsigen.2020.102356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
The application of massively parallel sequencing (MPS) to forensic genetics has led to improvements in multiple aspects of DNA analysis, however, additional complexities are concurrently associated with these advances. In relation to short tandem repeat (STR) typing, the move to sequence rather than length-based methodologies has highlighted the extent to which previous allelic variation was masked - both within and outside of the repeat regions (the flanking regions). In order to fully implement MPS for autosomal STR analysis, sequence-based allelic frequencies must be available, and concordance with previous typing techniques needs to be assessed. In this work, a series of samples (n = 1007) from five different population groups were genotyped using the MiSeq FGx™ Forensic Genomics System. Results were compared to those obtained using capillary electrophoresis (CE), and sequence variation has been characterised both within and outside STR repeat regions, with allelic frequencies provided for all variants observed within this database. Analysing and characterising flanking region sequence is currently less straightforward than studying repeat region variation alone, and the added value of doing so remains largely unexplored - this paper provides data to show that the gain in polymorphism achieved when analysing flanking regions is less than might be expected. In the White British population for example, including the sequence variation within repeat regions of 26 autosomal STRs made the average combined random match probability (RMP) over 700 times lower than with length-based alleles alone. Including the sequence variation within the flanking regions only resulted in a combined RMP that was a further 4 times lower.
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Affiliation(s)
- Laurence Devesse
- King's Forensics, King's College London, Franklin-Wilkins Building, 150 Stamford Street London, UK.
| | - Lucinda Davenport
- King's Forensics, King's College London, Franklin-Wilkins Building, 150 Stamford Street London, UK
| | - Lisa Borsuk
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Katherine Gettings
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Gabriella Mason-Buck
- King's Forensics, King's College London, Franklin-Wilkins Building, 150 Stamford Street London, UK
| | - Peter M Vallone
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Denise Syndercombe Court
- King's Forensics, King's College London, Franklin-Wilkins Building, 150 Stamford Street London, UK
| | - David Ballard
- King's Forensics, King's College London, Franklin-Wilkins Building, 150 Stamford Street London, UK
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17
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England R, Nancollis G, Stacey J, Sarman A, Min J, Harbison S. Compatibility of the ForenSeq™ DNA Signature Prep Kit with laser microdissected cells: An exploration of issues that arise with samples containing low cell numbers. Forensic Sci Int Genet 2020; 47:102278. [DOI: 10.1016/j.fsigen.2020.102278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/05/2020] [Accepted: 03/15/2020] [Indexed: 12/27/2022]
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18
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Ballard D, Winkler-Galicki J, Wesoły J. Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects. Int J Legal Med 2020; 134:1291-1303. [PMID: 32451905 PMCID: PMC7295846 DOI: 10.1007/s00414-020-02294-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 04/03/2020] [Indexed: 12/13/2022]
Abstract
In the last decade, next-generation sequencing (NGS) technology, alternatively massive parallel sequencing (MPS), was applied to all fields of biological research. Its introduction to the field of forensics was slower, mainly due to lack of accredited sequencers, kits, and relatively higher sequencing error rates as compared with standardized Sanger sequencing. Currently, a majority of the problematic issues have been solved, which is proven by the body of reports in the literature. Here, we discuss the utility of NGS sequencing in forensics, emphasizing the advantages, issues, the technical aspects of the experiments, commercial solutions, and the potentially interesting applications of MPS.
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Affiliation(s)
- David Ballard
- King's Forensic Genetics, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London, UK
| | - Jakub Winkler-Galicki
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz, University Poznan, 6 Uniwersytetu Poznanskiego Street, Poznan, Poland
| | - Joanna Wesoły
- Laboratory of High Throughput Technologies, Faculty of Biology, Adam Mickiewicz, University Poznan, 6 Uniwersytetu Poznanskiego Street, Poznan, Poland.
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19
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Hwa HL, Wu MY, Lee JCI, Yin HI, Hsu PM, Li SF, Hwu WL, Su CW. Analysis of nondegraded and degraded DNA mixtures of close relatives using massively parallel sequencing. Leg Med (Tokyo) 2020; 42:101631. [DOI: 10.1016/j.legalmed.2019.101631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/30/2019] [Accepted: 09/21/2019] [Indexed: 10/25/2022]
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20
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Zupanič Pajnič I, Obal M, Zupanc T. Identifying victims of the largest Second World War family massacre in Slovenia. Forensic Sci Int 2020; 306:110056. [DOI: 10.1016/j.forsciint.2019.110056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/25/2023]
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21
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Müller P, Sell C, Hadrys T, Hedman J, Bredemeyer S, Laurent FX, Roewer L, Achtruth S, Sidstedt M, Sijen T, Trimborn M, Weiler N, Willuweit S, Bastisch I, Parson W. Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA. Int J Legal Med 2019; 134:185-198. [PMID: 31745634 PMCID: PMC6949318 DOI: 10.1007/s00414-019-02201-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/29/2019] [Indexed: 12/30/2022]
Abstract
We present results from an inter-laboratory massively parallel sequencing (MPS) study in the framework of the SeqForSTRs project to evaluate forensically relevant parameters, such as performance, concordance, and sensitivity, using a standardized sequencing library including reference material, mixtures, and ancient DNA samples. The standardized library was prepared using the ForenSeq DNA Signature Prep Kit (primer mix A). The library was shared between eight European laboratories located in Austria, France, Germany, The Netherlands, and Sweden to perform MPS on their particular MiSeq FGx sequencers. Despite variation in performance between sequencing runs, all laboratories obtained quality metrics that fell within the manufacturer’s recommended ranges. Furthermore, differences in locus coverage did not inevitably adversely affect heterozygous balance. Inter-laboratory concordance showed 100% concordant genotypes for the included autosomal and Y-STRs, and still, X-STR concordance exceeded 83%. The exclusive reasons for X-STR discordances were drop-outs at DXS10103. Sensitivity experiments demonstrated that correct allele calling varied between sequencing instruments in particular for lower DNA amounts (≤ 125 pg). The analysis of compromised DNA samples showed the drop-out of one sample (FA10013B01A) while for the remaining three degraded DNA samples MPS was able to successfully type ≥ 87% of all aSTRs, ≥ 78% of all Y-STRs, ≥ 68% of all X-STRs, and ≥ 92% of all iSNPs demonstrating that MPS is a promising tool for human identity testing, which in return, has to undergo rigorous in-house validation before it can be implemented into forensic routine casework.
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Affiliation(s)
- Petra Müller
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria
| | | | - Thorsten Hadrys
- Institute of Forensic Sciences, DNA Department, Bavarian State Criminal Police Office, Munich, Germany
| | - Johannes Hedman
- Swedish National Forensic Centre (NFC), Linköping, Sweden.,Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Steffi Bredemeyer
- Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Francois-Xavier Laurent
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sabrina Achtruth
- The Police President in Berlin, Forensic Science Institute, Berlin, Germany
| | - Maja Sidstedt
- Swedish National Forensic Centre (NFC), Linköping, Sweden.,Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Titia Sijen
- Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB, The Hague, The Netherlands
| | - Marc Trimborn
- The Police President in Berlin, Forensic Science Institute, Berlin, Germany
| | - Natalie Weiler
- Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB, The Hague, The Netherlands
| | - Sascha Willuweit
- Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria. .,Forensic Science Program, The Pennsylvania State University, State College, PA, USA.
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22
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Massively parallel sequencing of autosomal STRs and identity-informative SNPs highlights consanguinity in Saudi Arabia. Forensic Sci Int Genet 2019; 43:102164. [PMID: 31585345 DOI: 10.1016/j.fsigen.2019.102164] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 01/13/2023]
Abstract
While many studies have been undertaken of Middle Eastern populations using autosomal STR profiling by capillary electrophoresis, little has so far been published from this region on the forensic use of massively parallel sequencing (MPS). Here, we carried out MPS of 27 autosomal STRs and 91 identity-informative SNPs (iiSNPs) with the Verogen ForenSeq™ DNA Signature Prep Kit on a representative sample of 89 Saudi Arabian males, and analysed the resulting sequence data using Verogen's ForenSeq Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0. This revealed sequence variation in the composition of complex STR arrays, and SNPs in their flanking regions, which raised the number of STR alleles from 238 distinct length variants to 357 sequence sub-variants. Similarly, between one and three additional polymorphic sites were observed within the amplicons of 37 of the 91 iiSNPs, forming up to six microhaplotypes per locus. These further enhance discrimination compared to the biallelic target SNP data presented by the primary UAS interface. In total, we observed twenty-two STR alleles previously unrecognised in the STRait Razor v3.0 default allele list, along with nine SNPs flanking target iiSNPs that were not highlighted by the UAS. Sequencing reduced the STR-based random match probability (RMP) from 2.62E-30 to 3.49E-34, and analysis of the iiSNP microhaplotypes reduced RMP from 9.97E-37 to 6.83E-40. The lack of significant linkage disequilibrium between STRs and target iiSNPs allowed the two marker types to be combined using the product rule, yielding a RMP of 2.39E-73. Evidence of consanguinity was apparent from both marker types. While TPOX was the only locus displaying a significant deviation from Hardy-Weinberg equilibrium, 23 out of 27 STRs and 63 out of 91 iiSNPs showed fewer than expected heterozygotes, demonstrating an overall homozygote excess probably reflecting the high frequency of first-cousin marriages in Saudi Arabia. We placed our data in a global context by considering the same markers in the Human Genome Diversity Panel (HGDP), revealing that the Saudi sample was typical of Middle Eastern populations, with a higher level of inbreeding than is seen in most European, African and Central/South Asian populations, correlating with known patterns of endogamy. Given reduced levels of diversity within endogamous groups, the ability to combine the discrimination power of both STRs and SNPs offers significant benefits in the analysis of forensic evidence in Saudi Arabia and the Middle East region more generally.
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23
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Szargut M, Diepenbroek M, Zielińska G, Cytacka S, Arciszewska J, Jałowińska K, Piątek J, Ossowski A. Is MPS always the answer? Use of two PCR-based methods for Y-chromosomal haplotyping in highly and moderately degraded bone material. Forensic Sci Int Genet 2019; 42:181-189. [PMID: 31374457 DOI: 10.1016/j.fsigen.2019.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/19/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022]
Abstract
Forensic and population genetics often rely on Y-chromosomal studies. Whether it is a human identification case, trace evidence examination or phylogenetic analysis, a Y-STR haplotype is an important tool in the hands of law enforcement agencies. A common obstacle in achieving satisfactory results in all of the above mentioned circumstances, is low DNA quantity and quality within samples obtained. In this study we have examined Y-STR haplotypes in 75 bone material samples, coming from different time periods. For this purpose we have chosen YFiler Plus PCR Amplification Kit (ThermoFisher Scientific) and ForenSeq Signature DNA Prep Kit (Verogen Inc.), which use two different allele calling technologies - capillary electrophoresis and Massively Parallel Sequencing respectively. Full profiles were obtained from DNA extracts with as little as 0.1896 ng (Degradation Index 1.3) (ForenSeq) and 0.0591 ng (Degradation Index 26.8) (YFiler Plus) DNA input. The results that we present in this paper show differences in amplification rates between common markers in both kits. The differences strictly reflect mean amplicon length of markers. This, however, does not seem to influence Y-haplogroup estimation results noticeably. In one sample a discordance occurred between haplotypes obtained with both methods, where a 24 allele was called in DYS390 marker by capillary electrophoresis, while for the same sample in this locus a 23 allele was shown with MPS. A reason for this is yet to be investigated. The sequence analysis revealed a significant variation between isometric alleles, especially within repetitive regions of studied Y-STR markers.
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Affiliation(s)
- Maria Szargut
- Department of Forensic Genetics of the Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland.
| | - Marta Diepenbroek
- Department of Forensic Genetics of the Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland; Institut für Rechtsmedizin der Universität München, Nußbaumstraße 26, 80336 München, Germany
| | - Grażyna Zielińska
- Department of Forensic Genetics of the Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Sandra Cytacka
- Department of Forensic Genetics of the Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Joanna Arciszewska
- Department of Forensic Genetics of the Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Katarzyna Jałowińska
- Department of Forensic Genetics of the Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Jarosław Piątek
- Department of Forensic Genetics of the Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics of the Pomeranian Medical University in Szczecin, Powstańców Wlkp. 72, 70-111 Szczecin, Poland
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24
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Zavala EI, Rajagopal S, Perry GH, Kruzic I, Bašić Ž, Parsons TJ, Holland MM. Impact of DNA degradation on massively parallel sequencing-based autosomal STR, iiSNP, and mitochondrial DNA typing systems. Int J Legal Med 2019; 133:1369-1380. [PMID: 31267160 DOI: 10.1007/s00414-019-02110-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
Biological samples, including skeletal remains exposed to environmental insults for extended periods of time, exhibit increasing levels of DNA damage and fragmentation. Human forensic identification methods typically use a combination of mitochondrial (mt) DNA sequencing and short tandem repeat (STR) analysis, which target segments of DNA ranging from 80 to 500 base pairs (bps). Larger templates are often unavailable as skeletal samples age and the associated DNA degrades. Single-nucleotide polymorphism (SNP) loci target shorter templates and may serve as a solution to the problem. Recently developed assays for STR and SNP analysis using a massively parallel sequencing approach, such as the ForenSeq kit (Verogen, San Diego, CA), offer a means for generating results from degraded samples as they target templates down to 60 to 170 bps. We performed a modeling study that demonstrates that SNPs can increase the significance of an identification when analyzing DNA down to an average size of 100 bps for input amounts between 0.375 and 1 ng of nuclear DNA. Observations from this study were then compared with human skeletal material results (n = 14, ninth to eighteenth centuries), which further demonstrated the utility of the ForenSeq kit for degraded samples. The robustness of the Promega PowerSeq™ Mito System was also tested with human skeletal remains (n = 70, ninth to eighteenth centuries), resulting in successful coverage of 99.29% of the mtDNA control region at 50× coverage or more. This was accompanied by modifications to a mainstream DNA extraction technique for skeletal remains that improved recovery of shorter templates.
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Affiliation(s)
- Elena I Zavala
- Department of Biochemistry and Molecular Biology, Forensic Science Program, Pennsylvania State University, State College, PA, USA.
| | - Swetha Rajagopal
- Department of Biochemistry and Molecular Biology, Forensic Science Program, Pennsylvania State University, State College, PA, USA.,Department of Forensic Science, John Jay College of Criminal Justice, New York, NY, USA
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, State College, PA, USA
| | - Ivana Kruzic
- University Department of Forensic Sciences, University of Split, Split, Croatia
| | - Željana Bašić
- University Department of Forensic Sciences, University of Split, Split, Croatia
| | - Thomas J Parsons
- International Commission on Missing Persons, The Hague, Netherlands
| | - Mitchell M Holland
- Department of Biochemistry and Molecular Biology, Forensic Science Program, Pennsylvania State University, State College, PA, USA
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25
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England R, Harbison S. A review of the method and validation of the MiSeq FGx™ Forensic Genomics Solution. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ryan England
- Forensic Science Program, School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Sallyann Harbison
- Institute of Environmental Science and Research Ltd Auckland New Zealand
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26
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Hollard C, Ausset L, Chantrel Y, Jullien S, Clot M, Faivre M, Suzanne É, Pène L, Laurent FX. Automation and developmental validation of the ForenSeq™ DNA Signature Preparation kit for high-throughput analysis in forensic laboratories. Forensic Sci Int Genet 2019; 40:37-45. [DOI: 10.1016/j.fsigen.2019.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/30/2018] [Accepted: 01/30/2019] [Indexed: 01/10/2023]
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27
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The impact of common PCR inhibitors on forensic MPS analysis. Forensic Sci Int Genet 2019; 40:182-191. [PMID: 30878722 DOI: 10.1016/j.fsigen.2019.03.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 11/21/2022]
Abstract
Massively parallel sequencing holds great promise for new possibilities in the field of forensic genetics, enabling simultaneous analysis of multiple markers as well as offering enhanced short tandem repeat allele resolution. A challenge in forensic DNA analysis is that the samples often contain low amounts of DNA in a background that may interfere with downstream analysis. PCR inhibition mechanisms of some relevant molecules have been studied applying e.g. real-time PCR and digital PCR. However, a detailed understanding of the effects of inhibitory molecules on forensic MPS, including mechanisms and ways to relieve inhibition, is missing. In this study, the effects of two well-characterized PCR inhibitors, humic acid and hematin, have been studied using the ForenSeq DNA Signature Prep kit. Humic acid and hematin resulted in lowered read numbers as well as specific negative effects on certain markers. Quality control of libraries with Fragment analyzer showed that increasing amounts of inhibitors caused a lowered amplicon quantity and that the larger amplicons were more likely to drop out. Further, the inhibitor tolerance could be improved 5-10 times by addition of bovine serum albumin in the initial PCR. On the contrary to the samples with inhibitors, low-template samples resulted in lowered read numbers for all markers. This difference strengthened the conclusion that the inhibitors have a negative effect on the DNA polymerase activity in the initial PCR. Additionally, a common capillary gel electrophoresis-based STR kit was shown to handle at least 200 times more inhibitors than the ForenSeq DNA Signature Prep kit. This suggests that there is room for improvement of the PCR components to ensure analytical success for challenging samples, which is needed for a broad application of MPS for forensic STR analysis.
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28
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An overall limited effect on the weight-of-evidence when taking STR DNA sequence polymorphism into account in kinship analysis. Forensic Sci Int Genet 2019; 39:44-49. [DOI: 10.1016/j.fsigen.2018.11.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 10/15/2018] [Accepted: 11/26/2018] [Indexed: 12/30/2022]
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29
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Li R, Li H, Peng D, Hao B, Wang Z, Huang E, Wu R, Sun H. Improved pairwise kinship analysis using massively parallel sequencing. Forensic Sci Int Genet 2019; 38:77-85. [DOI: 10.1016/j.fsigen.2018.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 09/24/2018] [Accepted: 10/09/2018] [Indexed: 01/16/2023]
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30
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Bruijns B, Tiggelaar R, Gardeniers H. Massively parallel sequencing techniques for forensics: A review. Electrophoresis 2018; 39:2642-2654. [PMID: 30101986 PMCID: PMC6282972 DOI: 10.1002/elps.201800082] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/07/2018] [Accepted: 07/23/2018] [Indexed: 11/09/2022]
Abstract
DNA sequencing, starting with Sanger's chain termination method in 1977 and evolving into the next generation sequencing (NGS) techniques of today that employ massively parallel sequencing (MPS), has become essential in application areas such as biotechnology, virology, and medical diagnostics. Reflected by the growing number of articles published over the last 2-3 years, these techniques have also gained attention in the forensic field. This review contains a brief description of first, second, and third generation sequencing techniques, and focuses on the recent developments in human DNA analysis applicable in the forensic field. Relevance to the forensic analysis is that besides generation of standard STR-profiles, DNA repeats can also be sequenced to look for polymorphisms. Furthermore, additional SNPs can be sequenced to acquire information on ancestry, paternity or phenotype. The current MPS systems are also very helpful in cases where only a limited amount of DNA or highly degraded DNA has been secured from a crime scene. If enough autosomal DNA is not present, mitochondrial DNA can be sequenced for maternal lineage analysis. These developments clearly demonstrate that the use of NGS will grow into an indispensable tool for forensic science.
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Affiliation(s)
- Brigitte Bruijns
- Mesoscale Chemical Systems, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
- Life ScienceEngineering & DesignSaxion University of Applied SciencesEnschedeThe Netherlands
| | - Roald Tiggelaar
- Mesoscale Chemical Systems, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
- NanoLab cleanroom, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
| | - Han Gardeniers
- Mesoscale Chemical Systems, MESA Institute for NanotechnologyUniversity of TwenteEnschedeThe Netherlands
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31
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Novroski NM, Woerner AE, Budowle B. Potential highly polymorphic short tandem repeat markers for enhanced forensic identity testing. Forensic Sci Int Genet 2018; 37:162-171. [DOI: 10.1016/j.fsigen.2018.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/02/2018] [Accepted: 08/21/2018] [Indexed: 01/22/2023]
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32
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Hwa HL, Wu MY, Chung WC, Ko TM, Lin CP, Yin HI, Lee TT, Lee JCI. Massively parallel sequencing analysis of nondegraded and degraded DNA mixtures using the ForenSeq™ system in combination with EuroForMix software. Int J Legal Med 2018; 133:25-37. [DOI: 10.1007/s00414-018-1961-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/24/2018] [Indexed: 01/19/2023]
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33
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Zhang Q, Zhou Z, Liu Q, Liu L, Shao L, Zhang M, Ding X, Gao Y, Wang S. Evaluation of the performance of Illumina's ForenSeq™ system on serially degraded samples. Electrophoresis 2018; 39:2674-2684. [DOI: 10.1002/elps.201800101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Qingzhen Zhang
- The Genomics Center of the AMMS; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Zhe Zhou
- The Genomics Center of the AMMS; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Qiqi Liu
- The Genomics Center of the AMMS; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Liyan Liu
- The Genomics Center of the AMMS; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Liting Shao
- The Genomics Center of the AMMS; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Minli Zhang
- The Genomics Center of the AMMS; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Xiaoran Ding
- The Genomics Center of the AMMS; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Yue Gao
- The Genomics Center of the AMMS; Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Shengqi Wang
- The Genomics Center of the AMMS; Beijing Institute of Radiation Medicine; Beijing P. R. China
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34
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Inter-laboratory validation study of the ForenSeq™ DNA Signature Prep Kit. Forensic Sci Int Genet 2018; 36:77-85. [DOI: 10.1016/j.fsigen.2018.05.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 11/19/2022]
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35
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King JL, Churchill JD, Novroski NM, Zeng X, Warshauer DH, Seah LH, Budowle B. Increasing the discrimination power of ancestry- and identity-informative SNP loci within the ForenSeq™ DNA Signature Prep Kit. Forensic Sci Int Genet 2018; 36:60-76. [DOI: 10.1016/j.fsigen.2018.06.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/03/2018] [Accepted: 06/05/2018] [Indexed: 11/26/2022]
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36
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Vlachos NT, Meiklejohn KA, Robertson JM. An automated independent workflow for the analysis of massively parallel sequence data from forensic SNP assays. Electrophoresis 2018; 39:2752-2756. [PMID: 30010201 DOI: 10.1002/elps.201800085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/15/2018] [Accepted: 07/01/2018] [Indexed: 12/30/2022]
Abstract
Illumina and Thermo Fisher Scientific have developed assays that permit the sequencing of forensically relevant single nucleotide polymorphisms (SNPs), along with software to determine the associated genotypes. Currently there is no method to either independently confirm the genotypes determined using the manufacturer's software, or to compare genotypes and quality metrics among samples processed using both platforms. This paper outlines an automated workflow developed in CLC Genomics Workbench that permits accurate, fast and independent analysis of SNP sequence data from either platform. To facilitate the straightforward comparison of genotypes generated from both the manufacturer's software and the independent CLC analysis, a Python script was written. Data for a total of 323 forensically relevant ancestry, identity and phenotypic SNPs can be analyzed, and the resulting genotypes, coverage, quality flags and major allele frequencies are easily compared across samples and platforms.
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Affiliation(s)
- Nicholas T Vlachos
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA
| | - Kelly A Meiklejohn
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA.,Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - James M Robertson
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, Quantico, VA, USA
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37
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Concordance of the ForenSeq™ system and characterisation of sequence-specific autosomal STR alleles across two major population groups. Forensic Sci Int Genet 2018; 34:57-61. [DOI: 10.1016/j.fsigen.2017.10.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/23/2017] [Accepted: 10/31/2017] [Indexed: 01/25/2023]
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38
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Bardan F, Higgins D, Austin JJ. A mini-multiplex SNaPshot assay for the triage of degraded human DNA. Forensic Sci Int Genet 2018; 34:62-70. [DOI: 10.1016/j.fsigen.2018.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/03/2018] [Accepted: 02/05/2018] [Indexed: 12/01/2022]
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39
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Hussing C, Huber C, Bytyci R, Mogensen HS, Morling N, Børsting C. Sequencing of 231 forensic genetic markers using the MiSeq FGx™ forensic genomics system - an evaluation of the assay and software. Forensic Sci Res 2018; 3:111-123. [PMID: 30483659 PMCID: PMC6197110 DOI: 10.1080/20961790.2018.1446672] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/26/2018] [Indexed: 02/07/2023] Open
Abstract
The MiSeq FGx™ Forensic Genomics System types 231 genetic markers in one multiplex polymerase chain reaction (PCR) assay. The markers include core forensic short tandem repeats (STRs) as well as identity, ancestry and phenotype informative short nucleotide polymorphisms (SNPs). In this work, the MiSeq FGx™ Forensic Genomics System was evaluated by analysing reproducibility, sensitivity, mixture identification and forensic phenotyping capabilities of the assay. Furthermore, the genotype calling of the ForenSeq™ Universal Analysis Software was verified by analysing fastq.gz files from the MiSeq FGx™ platform using the softwares STRinNGS and GATK. Overall, the performance of the MiSeq FGx™ Forensic Genomics System was high. However, locus and allele drop-outs were relatively frequent at six loci (two STRs and four human identification SNPs) due to low read depth or skewed heterozygote balances, and the stutter ratios were larger than those observed with conventional STR genotyping methods. The risk of locus and allele drop-outs increased dramatically when the amount of DNA in the first PCR was lower than 250 pg. Two-person 50:1 mixtures were identified as mixtures, whereas 100:1 and 1 000:1 mixtures were not. Y-chromosomal short tandem repeats (Y-STRs) alleles were detected in the 100:1 and 1 000:1 female/male mixtures. The ForenSeq™ Universal Analysis Software provided the data analyst with useful alerts that simplified the analysis of the large number of markers. Many of the alerts were due to user-defined, locus-specific criteria. The results shown here indicated that the default settings should be altered for some loci. Also, recommended changes to the assay and software are discussed.
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Affiliation(s)
- Christian Hussing
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christina Huber
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajmonda Bytyci
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Helle S Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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40
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Sukawutthiya P, Sathirapatya T, Vongpaisarnsin K. Considering a performance test of forensic genomics system on massively parallel sequencing technology. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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Sharma V, Chow HY, Siegel D, Wurmbach E. Qualitative and quantitative assessment of Illumina's forensic STR and SNP kits on MiSeq FGx™. PLoS One 2017; 12:e0187932. [PMID: 29121662 PMCID: PMC5679668 DOI: 10.1371/journal.pone.0187932] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/27/2017] [Indexed: 11/30/2022] Open
Abstract
Massively parallel sequencing (MPS) is a powerful tool transforming DNA analysis in multiple fields ranging from medicine, to environmental science, to evolutionary biology. In forensic applications, MPS offers the ability to significantly increase the discriminatory power of human identification as well as aid in mixture deconvolution. However, before the benefits of any new technology can be employed, a thorough evaluation of its quality, consistency, sensitivity, and specificity must be rigorously evaluated in order to gain a detailed understanding of the technique including sources of error, error rates, and other restrictions/limitations. This extensive study assessed the performance of Illumina’s MiSeq FGx MPS system and ForenSeq™ kit in nine experimental runs including 314 reaction samples. In-depth data analysis evaluated the consequences of different assay conditions on test results. Variables included: sample numbers per run, targets per run, DNA input per sample, and replications. Results are presented as heat maps revealing patterns for each locus. Data analysis focused on read numbers (allele coverage), drop-outs, drop-ins, and sequence analysis. The study revealed that loci with high read numbers performed better and resulted in fewer drop-outs and well balanced heterozygous alleles. Several loci were prone to drop-outs which led to falsely typed homozygotes and therefore to genotype errors. Sequence analysis of allele drop-in typically revealed a single nucleotide change (deletion, insertion, or substitution). Analyses of sequences, no template controls, and spurious alleles suggest no contamination during library preparation, pooling, and sequencing, but indicate that sequencing or PCR errors may have occurred due to DNA polymerase infidelities. Finally, we found utilizing Illumina’s FGx System at recommended conditions does not guarantee 100% outcomes for all samples tested, including the positive control, and required manual editing due to low read numbers and/or allele drop-in. These findings are important for progressing towards implementation of MPS in forensic DNA testing.
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Affiliation(s)
- Vishakha Sharma
- Department of Forensic Biology, Office of Chief Medical Examiner, New York, NY, United States of America
| | - Hoi Yan Chow
- Department of Forensic Biology, Office of Chief Medical Examiner, New York, NY, United States of America
| | - Donald Siegel
- Department of Forensic Biology, Office of Chief Medical Examiner, New York, NY, United States of America
| | - Elisa Wurmbach
- Department of Forensic Biology, Office of Chief Medical Examiner, New York, NY, United States of America
- * E-mail:
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42
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Guo F, Yu J, Zhang L, Li J. Massively parallel sequencing of forensic STRs and SNPs using the Illumina ® ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx™ Forensic Genomics System. Forensic Sci Int Genet 2017; 31:135-148. [DOI: 10.1016/j.fsigen.2017.09.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 08/06/2017] [Accepted: 09/06/2017] [Indexed: 12/13/2022]
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43
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Zeng X, King JL, Budowle B. Investigation of the STR loci noise distributions of PowerSeq™ Auto System. Croat Med J 2017; 58:214-221. [PMID: 28613038 PMCID: PMC5470120 DOI: 10.3325/cmj.2017.58.214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Aim To characterize the noise and stutter distribution of 23 short tandem repeats (STRs) included in the PowerSeqTM Auto System. Methods Raw FASTQ files were analyzed using STRait Razor v2s to display alleles and coverage. The sequence noise was divided into several categories: noise at allele position, noise at -1 repeat position, and artifact. The average relative percentages of locus coverage for each noise, stutter, and allele were calculated from the samples used for this locus noise analysis. Results Stutter products could be routinely observed at the -2 repeat position, -1 repeat position, and +1 repeat position of alleles. Sequence noise at the allele position ranged from 10.22% to 28.81% of the total locus coverage. At the allele position, individual noise reads were relatively low. Conclusion The data indicate that noise generally will be low. In addition, the PowerSeqTM Auto System could capture nine flanking region single nucleotide polymorphisms (SNPs) that would not be observed by other current kits for massively parallel sequencing (MPS) of STRs.
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Affiliation(s)
- Xiangpei Zeng
- Xiangpei Zeng, Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA,
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44
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Population and performance analyses of four major populations with Illumina's FGx Forensic Genomics System. Forensic Sci Int Genet 2017. [PMID: 28651097 DOI: 10.1016/j.fsigen.2017.06.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The MiSeq FGx Forensic Genomics System (Illumina) enables amplification and massively parallel sequencing of 59 STRs, 94 identity informative SNPs, 54 ancestry informative SNPs, and 24 phenotypic informative SNPs. Allele frequency and population statistics data were generated for the 172 SNP loci included in this panel on four major population groups (Chinese, African Americans, US Caucasians, and Southwest Hispanics). Single-locus and combined random match probability values were generated for the identity informative SNPs. The average combined STR and identity informative SNP random match probabilities (assuming independence) across all four populations were 1.75E-67 and 2.30E-71 with length-based and sequence-based STR alleles, respectively. Ancestry and phenotype predictions were obtained using the ForenSeq™ Universal Analysis System (UAS; Illumina) based on the ancestry informative and phenotype informative SNP profiles generated for each sample. Additionally, performance metrics, including profile completeness, read depth, relative locus performance, and allele coverage ratios, were evaluated and detailed for the 725 samples included in this study. While some genetic markers included in this panel performed notably better than others, performance across populations was generally consistent. The performance and population data included in this study support that accurate and reliable profiles were generated and provide valuable background information for laboratories considering internal validation studies and implementation.
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45
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Xavier C, Parson W. Evaluation of the Illumina ForenSeq™ DNA Signature Prep Kit – MPS forensic application for the MiSeq FGx™ benchtop sequencer. Forensic Sci Int Genet 2017; 28:188-194. [DOI: 10.1016/j.fsigen.2017.02.018] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/22/2017] [Accepted: 02/28/2017] [Indexed: 01/23/2023]
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46
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Mehta B, Venables S, Roffey P. Comparison between magnetic bead and qPCR library normalisation methods for forensic MPS genotyping. Int J Legal Med 2017; 132:125-132. [PMID: 28417259 DOI: 10.1007/s00414-017-1591-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/06/2017] [Indexed: 11/27/2022]
Abstract
Massively parallel sequencing (MPS) is fast approaching operational use in forensic science, with the capability to analyse hundreds of DNA identity and DNA intelligence markers in multiple samples simultaneously. The ForenSeq™ DNA Signature Kit on MiSeq FGx™ (Illumina) workflow can provide profiles for autosomal short tandem repeats (STRs), X chromosome and Y chromosome STRs, identity single nucleotide polymorphisms (SNPs), biogeographical ancestry SNPs and phenotype (eye and hair colour) SNPs from a sample. The library preparation procedure involves a series of steps including target amplification, library purification and library normalisation. This study highlights the comparison between the manufacturer recommended magnetic bead normalisation and quantitative polymerase chain reaction (qPCR) methods. Furthermore, two qPCR chemistries, KAPA® (KAPA Biosystems) and NEBNext® (New England Bio Inc.), have also been compared. The qPCR outperformed the bead normalisation method, while the NEBNext® kit obtained higher genotype concordance than KAPA®. The study also established an MPS workflow that can be utilised in any operational forensic laboratory.
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Affiliation(s)
- Bhavik Mehta
- National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics (ESTeM), University of Canberra, Canberra, Bruce, ACT 2617, Australia. .,Specialist Operations - Forensics, Australian Federal Police, Tambreet Street, Majura, ACT 2609, Australia.
| | - Samantha Venables
- National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics (ESTeM), University of Canberra, Canberra, Bruce, ACT 2617, Australia.,Specialist Operations - Forensics, Australian Federal Police, Tambreet Street, Majura, ACT 2609, Australia
| | - Paul Roffey
- National Centre for Forensic Studies, Faculty of Education, Science, Technology and Mathematics (ESTeM), University of Canberra, Canberra, Bruce, ACT 2617, Australia.,Specialist Operations - Forensics, Australian Federal Police, Tambreet Street, Majura, ACT 2609, Australia
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