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Sapan V, Simsek SZ, Filoğlu G, Bulbul O. Forensic DNA phenotyping using Oxford Nanopore Sequencing system. Electrophoresis 2024. [PMID: 38794987 DOI: 10.1002/elps.202300252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 05/27/2024]
Abstract
In forensic science, the demand for precision, consistency, and cost-effectiveness has driven the exploration of next-generation sequencing technologies. This study investigates the potential of Oxford Nanopore Sequencing (ONT) Technology for analyzing the HIrisPlex-S panel, a set of 41 single nucleotide polymorphism (SNP) markers used to predict eye, hair, and skin color. Using ONT sequencing, we assessed the accuracy and reliability of ONT-generated data by comparing it with conventional capillary electrophoresis (CE) in 18 samples. The Guppy v6.1 was used as a basecaller, and sample profiles were obtained using Burrows-Wheeler Aligner, Samtools, BCFtools, and Python. Comparing accuracy with CE, we found that 62% of SNPs in ONT-unligated samples were correctly genotyped, with 36% showing allele dropout, and 2% being incorrectly genotyped. In the ONT-ligated samples, 85% of SNPs were correctly genotyped, with 10% showing allele dropout, and 5% being incorrectly genotyped. Our findings indicate that ONT, particularly when combined with ligation, enhances genotyping accuracy and coverage, thereby reducing allele dropouts. However, challenges associated with the technology's error rates and the impact on genotyping accuracy are recognized. Phenotype predictions based on ONT data demonstrate varying degrees of success, with the technology showing high accuracy in several cases. Although ONT technology holds promise in forensic genetics, further optimization and quality control measures are essential to harness its full potential. This study contributes to the ongoing efforts to refine sequence read tuning and improve correction tools in the context of ONT technology's application in forensic genetics.
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Affiliation(s)
- Veysel Sapan
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Sumeyye Zulal Simsek
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Gonul Filoğlu
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ozlem Bulbul
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
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Deymenci E, Sarı O I, Filoglu G, Polat E, Bulbul O. Eye and hair color prediction of human DNA recovered from Lucilia sericata larvae. Int J Legal Med 2024; 138:627-637. [PMID: 37934208 DOI: 10.1007/s00414-023-03112-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023]
Abstract
Forensic entomological evidence is employed to estimate minimum postmortem interval (PMImin), location, and identification of fly samples or human remains. Traditional forensic DNA analysis (i.e., STR, mitochondrial DNA) has been used for human identification from the larval gut contents. Forensic DNA phenotyping (FDP), predicting human appearance from DNA-based crime scene evidence, has become an established approach in forensic genetics in the past years. In this study, we aimed to recover human DNA from Lucilia sericata (Meigen 1826) (Diptera: Calliphoridae) gut contents and predict the eye and hair color of individuals using the HIrisPlex system. Lucilia sericata larvae and reference blood samples were collected from 30 human volunteers who were under maggot debridement therapy. The human DNA was extracted from the crop contents and quantified. HIrisPlex multiplex analysis was performed using the SNaPshot minisequencing procedure. The HIrisPlex online tool was used to assess the prediction of the eye and hair color of the larval and reference samples. We successfully genotyped 25 out of 30 larval samples, and the most SNP genotypes (87.13%) matched those of reference samples, though some alleles were dropped out, producing partial profiles. The prediction of the eye colors was accurate in 17 out of 25 larval samples, and only one sample was misclassified. Fourteen out of 25 larval samples were correctly predicted for hair color, and eight were misclassified. This study shows that SNP analysis of L. sericata gut contents can be used to predict eye and hair color of a corpse.
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Affiliation(s)
- Emre Deymenci
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Adli Tıp ve Adli Bilimler Enstitüsü, Büyükçekmece Yerleşkesi, 34500 Büyükçekmece, Istanbul, Turkey
| | - Ilksen Sarı O
- Department of Medical Services and Techniques, Vocational School of Health Services, Istanbul Gelisim University, 34310, Istanbul, Turkey
| | - Gonul Filoglu
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Adli Tıp ve Adli Bilimler Enstitüsü, Büyükçekmece Yerleşkesi, 34500 Büyükçekmece, Istanbul, Turkey
| | - Erdal Polat
- Department of Medical Microbiology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ozlem Bulbul
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpasa, Adli Tıp ve Adli Bilimler Enstitüsü, Büyükçekmece Yerleşkesi, 34500 Büyükçekmece, Istanbul, Turkey.
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Soldati G, Turrina S, Treccani M, Saccardo C, Ausania F, De Leo D. Concordance study on Y-STRs typing between SeqStudio™ genetic analyzer for HID and MiSeq™ FGx forensic genomics system. Mol Biol Rep 2023; 50:9779-9789. [PMID: 37812349 PMCID: PMC10676315 DOI: 10.1007/s11033-023-08808-4] [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: 07/25/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Massively Parallel Sequencing (MPS) allowed an increased number of information to be retrieved from short tandem repeat (STR) analysis, expanding them not only to the size, as already performed in Capillary Electrophoresis (CE), but also to the sequence. MPS requires constant development and validation of the analytical parameters to ensure that the genotyping results of STRs correspond to those obtained by CE. Given the increased frequency of usage of Y-STRs as supplementary markers to the autosomal STRs analysis, it is urgent to validate the concordance of the typing results between CE and MPS analyses. METHODS AND RESULTS DNA extracted from 125 saliva samples of unrelated males was genotyped using Yfiler™ Plus PCR Amplification Kit and ForenSeq™ DNA Signature Prep Kit, which were analyzed by SeqStudio™ Genetic Analyzer for HID and MiSeq™ FGx Forensic Genomics System, respectively. For each shared Y-STR, allele designation, number of length- and sequence-based alleles per locus, stutter percentage, and the intra-locus balance of multicopy Y-STRs were screened. CONCLUSIONS Although the number of forensic genetics laboratories that are applying the MPS technique in routine analysis is small and does not allow a global assessment of MPS limitations, this comparative study highlights the ability of MPS to produce reliable profiles despite the generation of large amounts of raw data.
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Affiliation(s)
- Giulia Soldati
- Department of Diagnostics and Public Health, Section of Forensic Medicine, Forensic Genetics Lab, University of Verona, Verona, Italy.
| | - Stefania Turrina
- Department of Diagnostics and Public Health, Section of Forensic Medicine, Forensic Genetics Lab, University of Verona, Verona, Italy
| | - Mirko Treccani
- GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Chiara Saccardo
- Department of Diagnostics and Public Health, Section of Forensic Medicine, Forensic Genetics Lab, University of Verona, Verona, Italy
| | - Francesco Ausania
- Department of Diagnostics and Public Health, Section of Forensic Medicine, Forensic Genetics Lab, University of Verona, Verona, Italy
| | - Domenico De Leo
- Department of Diagnostics and Public Health, Section of Forensic Medicine, Forensic Genetics Lab, University of Verona, Verona, Italy
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Kayser M, Branicki W, Parson W, Phillips C. Recent advances in Forensic DNA Phenotyping of appearance, ancestry and age. Forensic Sci Int Genet 2023; 65:102870. [PMID: 37084623 DOI: 10.1016/j.fsigen.2023.102870] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Forensic DNA Phenotyping (FDP) comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry and age from DNA of crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified with forensic STR-profiling. In recent years, FDP has advanced considerably in all of its three components, which we summarize in this review article. Appearance prediction from DNA has broadened beyond eye, hair and skin color to additionally comprise other traits such as eyebrow color, freckles, hair structure, hair loss in men, and tall stature. Biogeographic ancestry inference from DNA has progressed from continental ancestry to sub-continental ancestry detection and the resolving of co-ancestry patterns in genetically admixed individuals. Age estimation from DNA has widened beyond blood to more somatic tissues such as saliva and bones as well as new markers and tools for semen. Technological progress has allowed forensically suitable DNA technology with largely increased multiplex capacity for the simultaneous analysis of hundreds of DNA predictors with targeted massively parallel sequencing (MPS). Forensically validated MPS-based FDP tools for predicting from crime scene DNA i) several appearance traits, ii) multi-regional ancestry, iii) several appearance traits together with multi-regional ancestry, and iv) age from different tissue types, are already available. Despite recent advances that will likely increase the impact of FDP in criminal casework in the near future, moving reliable appearance, ancestry and age prediction from crime scene DNA to the level of detail and accuracy police investigators may desire, requires further intensified scientific research together with technical developments and forensic validations as well as the necessary funding.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland,; Institute of Forensic Research, Kraków, Poland
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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Wen D, Shi J, Liu Y, He W, Qu W, Wang C, Xing H, Cao Y, Li J, Zha L. DNA methylation analysis for smoking status prediction in the Chinese population based on the methylation-sensitive single-nucleotide primer extension method. Forensic Sci Int 2022; 339:111412. [DOI: 10.1016/j.forsciint.2022.111412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/04/2022]
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Developments in forensic DNA analysis. Emerg Top Life Sci 2021; 5:381-393. [PMID: 33792660 PMCID: PMC8457771 DOI: 10.1042/etls20200304] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/20/2022]
Abstract
The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.
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Zhao GB, Ma GJ, Zhang C, Kang KL, Li SJ, Wang L. BGISEQ-500RS sequencing of a 448-plex SNP panel for forensic individual identification and kinship analysis. Forensic Sci Int Genet 2021; 55:102580. [PMID: 34454122 DOI: 10.1016/j.fsigen.2021.102580] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/13/2021] [Accepted: 08/17/2021] [Indexed: 01/23/2023]
Abstract
Next generation sequencing (NGS)-based single nucleotide polymorphism (SNP) genotyping is widely used in the field of forensics. SNP genotyping data from several NGS platforms have been published, but forensic application trials of DNA nanoball sequencing platforms have been very limited. In this work, we developed a 448-plex SNP panel on the BGISEQ-500RS platform. The sequencing metrics of a total of 261 samples that were sequenced with this panel are reported in detail. The average sequencing depth was 8373 × and the average heterozygosity of the 448-plex assay was 0.85. Sensitivity analysis showed that 325 SNPs were successfully genotyped with as little as 50 pg of genomic DNA, with the mean quality score of the sequencing data above Q30. Forensic parameters were calculated based on the data of 142 unrelated Chinese Han individuals and the combined matching probability was as low as 5.21 × 10-101. Kinship analyses based on experiments and computer simulations showed that the 448-panel was as effective as the ForenSeq™ DNA Signature Prep Kit for second-degree kinship identification, and when the two panels were merged, the related pairs were almost completely distinguished from unrelated pairs. The 448-plex SNP panel on the BGISEQ-500RS platform provides a powerful tool for forensic individual identification and kinship analysis.
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Affiliation(s)
- Guang-Bin Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
| | - Guan-Ju Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Chi Zhang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
| | - Ke-Lai Kang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
| | - Shu-Jin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China.
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8
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Frégeau CJ. Validation of the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B for phenotypic and biogeographical ancestry predictions using the Micro MiSeq® Flow Cells. Forensic Sci Int Genet 2021; 53:102533. [PMID: 34058534 DOI: 10.1016/j.fsigen.2021.102533] [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: 10/16/2020] [Revised: 03/17/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
In anticipation of offering phenotypic and biogeographical ancestry predictions to help resolve cases, the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B was evaluated in the context of Micro MiSeq® Flow Cells. These flow cells were determined as the best format for a quick turnaround time response and cost effective approach compared to standard flow cells. The phenotype informative SNPs (piSNPs) and ancestry informative SNPs (aiSNPs) were thoroughly examined through sensitivity, reproducibility and repeatability, concordance, robustness (mock casework) and low level DNA mixture studies purposely selecting individuals with different phenotypes (hair and eye color) when possible and different biogeographical ancestry. SNP locus-specific interpretation thresholds were established for the Universal Analysis Software (UAS) based on surviving alleles and SNP predictor rank to minimize false homozygous genotypes and maximize the information that can be derived from an unknown sample. Dropin alleles' intensity determined an appropriate threshold to minimize false heterozygous SNP genotypes. The selection of inappropriate interpretation thresholds was shown to have major consequences on phenotypic predictions. A 3.2% and 4.8% minor DNA component contribution to a DNA mixture had no impact on ancestry predictions whereas a 9.1% contribution did. The multi-locus SNP genotypes generated using the ForenSeq™ DNA Signature Prep kit/Primer Mix B were shown to be reliable, reproducible, concordant and resulted in predictions that were also reliable, reproducible and concordant based on the limited number of donors (N = 19) used in this study.
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Affiliation(s)
- Chantal J Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Biology Policy & Program Support, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada.
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Tao R, Wang S, Chen A, Xia R, Zhang X, Yang Q, Qu Y, Zhang S, Li C. Parallel sequencing of 87 STR and 294 SNP markers using the prototype of the SifaMPS panel on the MiSeq FGx™ system. Forensic Sci Int Genet 2021; 52:102490. [PMID: 33689955 DOI: 10.1016/j.fsigen.2021.102490] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022]
Abstract
Massively parallel sequencing (MPS), or next generation sequencing (NGS), is a promising methodology for the detection of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) in forensic genetics. Here, the prototype SifaMPS Panel is designed to simultaneously target 87 STRs and 294 SNPs with forensic interest in a single multiplex in conjunction with the TruSeq™ Custom Amplicon workflow and MiSeq FGx™ System. Two in-house python scripts are adopted for the fastq-to-genotype interpretation of MPS data concerning STR and SNP, respectively. In the present study, by sequencing 50 Chinese Hans and many other DNA samples involved in validation studies, system parameters including the depth of coverage (DoC), heterozygote balance (Hb) and sequence coverage ratios (SCRs), as well as different forensic parameters of STRs and SNPs in a population study, were calculated to evaluate the overall performance of this new panel and its practicality in forensic application. In general, except for two STRs (DYS505 and DYS449) and one SNP (rs4288409) that performed poorly, the other 85 STRs and 293 SNPs in our panel had good performance that could strengthen efficiency for human identification and paternity testing. In addition, discordant STR genotype results between those generated from capillary electrophoresis (CE) and from the MPS platform were clearly illustrated, and these results could be a useful reference for applying these particular non-CODIS STRs in forensic practice.
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Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China
| | - Shouyu Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, PR China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Xiaochun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Qi Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, PR China.
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Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples. Genes (Basel) 2020; 11:genes11121398. [PMID: 33255693 PMCID: PMC7760956 DOI: 10.3390/genes11121398] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/19/2020] [Accepted: 11/22/2020] [Indexed: 12/21/2022] Open
Abstract
As the field of forensic DNA analysis has started to transition from genetics to genomics, new methods to aid in crime scene investigations have arisen. The development of informative single nucleotide polymorphism (SNP) markers has led the forensic community to question if DNA can be a reliable "eye-witness" and whether the data it provides can shed light on unknown perpetrators. We have developed an assay called the Ion AmpliSeq™ PhenoTrivium Panel, which combines three groups of markers: 41 phenotype- and 163 ancestry-informative autosomal SNPs together with 120 lineage-specific Y-SNPs. Here, we report the results of testing the assay's sensitivity and the predictions obtained for known reference samples. Moreover, we present the outcome of a blind study performed on real casework samples in order to understand the value and reliability of the information that would be provided to police investigators. Furthermore, we evaluated the accuracy of admixture prediction in Converge™ Software. The results show the panel to be a robust and sensitive assay which can be used to analyze casework samples. We conclude that the combination of the obtained predictions of phenotype, biogeographical ancestry, and male lineage can serve as a potential lead in challenging police investigations such as cold cases or cases with no suspect.
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11
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Liu Y, Jin X, Mei S, Lan Q, Fang Y, Liu C, Zhu B. A set of novel multi‐allelic SNPs for forensic application developed through massively parallel sequencing and its examples of population genetic studies. Electrophoresis 2020; 41:2036-2046. [DOI: 10.1002/elps.202000128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/10/2020] [Accepted: 08/23/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Yanfang Liu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- College of Forensic Medicine Xi'an Jiaotong University Health Science Center Shaanxi P. R. China
| | - Shuyan Mei
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Qiong Lan
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Yating Fang
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Chao Liu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
| | - Bofeng Zhu
- Multi‐Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics School of Forensic Medicine Southern Medical University Guangzhou P. R. China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases College of Stomatology Xi'an Jiaotong University Shaanxi P. R. China
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12
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Ancestry and phenotype predictions from touch DNA using massively parallel sequencing. Int J Legal Med 2020; 135:81-89. [PMID: 32815052 DOI: 10.1007/s00414-020-02398-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 08/10/2020] [Indexed: 01/11/2023]
Abstract
Direct PCR can be used to successfully generate full STR profiles from DNA present on the surface of objects. STR profiles are only of use in cases where a potential donor profile is available for comparison, and DNA is of sufficient DNA quality and quantity to generate a reliable profile. Often, no donor information is available and only trace DNA is present on items. As a result, alternative techniques are required to generate genetic data that can provide investigative leads. Massively parallel sequencing (MPS) offers the ability to detect trace levels of DNA and improve DNA analysis success from touched items. Here, we present the first application of direct PCR coupled with MPS to generate forensic intelligence SNP data from latent DNA. The panels assessed are (1) the HIrisplex System that targets 24 SNPs to simultaneously predict hair and eye, and (2) the Precision ID Ancestry Panel that targets 165 autosomal SNPs indicative of biogeographic ancestry. For each panel, we analysed 60 touched samples across five individuals and four substrates (glass slide, fuse, zip-lock bag and wire) using Ion AmpliSeq Library Preparation Kit on the automated Ion Chef System and Ion Torrent PGM. We examine the SNP recovery, concordance with reference samples and the genotype reproducibility from different substrates and donors. The results demonstrate the application of this approach for obtaining informative genetic from trace amounts of DNA.
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Kukla-Bartoszek M, Szargut M, Pośpiech E, Diepenbroek M, Zielińska G, Jarosz A, Piniewska-Róg D, Arciszewska J, Cytacka S, Spólnicka M, Branicki W, Ossowski A. The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system. Forensic Sci Int Genet 2020; 47:102301. [PMID: 32387914 DOI: 10.1016/j.fsigen.2020.102301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/02/2020] [Accepted: 04/10/2020] [Indexed: 10/24/2022]
Abstract
Identification of human remains is an important part of human DNA analysis studies. STR and mitochondrial DNA markers are well suited for the analysis of degraded biological samples including bone material. However, these DNA markers may be useless when reference material is not available. In these cases, predictive DNA analysis can support the process of human identification by providing investigative leads. Forensic DNA phenotyping has progressed significantly by offering new methods based on massively parallel sequencing technology, but the frequent degradation processes observed in skeletal remains can make analysis of such samples challenging. In this study, we demonstrate the usefulness of a recently established Ion AmpliSeqTM HIrisPlex-S panel using Ion Torrent technology for analyzing bone samples that show different levels of DNA degradation. In total, 63 bone samples at post-mortem intervals up to almost 80 years were genotyped and eye, hair and skin colour predictions were performed using the HIrisPlex-S models. Following the recommended coverage thresholds, it was possible to establish full DNA profiles comprising of 41 DNA variants for 35 samples (55.6%). For 5 samples (7.9%) no DNA profiles were generated. The remaining 23 samples (36.5%) produced partial profiles and showed a clear underperformance of 3 HIrisPlex-S SNPs - rs1545397 (OCA2), rs1470608 (OCA2) and rs10756819 (BNC2), all used for skin colour prediction only. None of the 23 samples gave complete genotypes needed for skin colour prediction was obtained, and in 7 of them (25.9%) the 3 underperformed SNPs were the cause. At the same time, the prediction of eye and hair colour using complete IrisPlex and HIrisPlex profiles could be made for these 23 samples in 20 (87.0%) and 12 cases (52.2%), respectively. Complete HIrisPlex-S profiles were generated from as little as 49 pg of template DNA. Five samples for which the HIrisPlex-S analysis failed, consistently failed in standard STR analysis. Importantly, the 3 underperforming SNPs produced significantly lower number of reads in good quality samples. Nonetheless, the AUC loss resulting from missing data for these 3 SNPs is not considered large (≤0.004) and the prediction of pigmentation from partial profiles is also available in the current HPS tool. The study shows that DNA degradation and the resulting loss of data are the most serious challenge to DNA phenotyping of skeletal remains. Although the newly developed HIrisPlex-S panel has been successfully validated in the current research, primer redesign for the 3 underperforming SNPs in the MPS design should be considered in the future.
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Affiliation(s)
- Magdalena Kukla-Bartoszek
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-387, Kraków, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland
| | - Maria Szargut
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland
| | - Marta Diepenbroek
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; Institut für Rechtsmedizin der Universität München, Nußbaumstr. 26, 80336, München, Germany
| | - Grażyna Zielińska
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Agata Jarosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland
| | - Danuta Piniewska-Róg
- Department of Forensic Medicine, Jagiellonian University Medical College, Grzegórzecka St. 16, 31-531, Kraków, Poland
| | - Joanna Arciszewska
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Sandra Cytacka
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Magdalena Spólnicka
- Biology Department, Central Forensic Laboratory of the Police, Aleje Ujazdowskie 7, 00-583, Warszawa, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland; Department of Forensic Medicine, Jagiellonian University Medical College, Grzegórzecka St. 16, 31-531, Kraków, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
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Butler JM, Willis S. Interpol review of forensic biology and forensic DNA typing 2016-2019. Forensic Sci Int Synerg 2020; 2:352-367. [PMID: 33385135 PMCID: PMC7770417 DOI: 10.1016/j.fsisyn.2019.12.002] [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: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 12/23/2022]
Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2016 to 2019 as a part of the 19th Interpol International Forensic Science Managers Symposium. The review papers are also available at the Interpol website at: https://www.interpol.int/content/download/14458/file/Interpol%20Review%20Papers%202019.pdf.
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