1
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Guo LL, Yuan JH, Zhang C, Zhao J, Yao YR, Guo KL, Meng Y, Ji AQ, Kang KL, Wang L. Developmental validation of the STRSeqTyper122 kit for massively parallel sequencing of forensic STRs. Int J Legal Med 2024; 138:1255-1264. [PMID: 38416217 DOI: 10.1007/s00414-024-03195-2] [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: 12/22/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024]
Abstract
Massively parallel sequencing allows for integrated genotyping of different types of forensic markers, which reduces DNA consumption, simplifies experimental processes, and provides additional sequence-based genetic information. The STRseqTyper122 kit genotypes 63 autosomal STRs, 16 X-STRs, 42 Y-STRs, and the Amelogenin locus. Amplicon sizes of 117 loci were below 300 bp. In this study, MiSeq FGx sequencing metrics for STRseqTyper122 were presented. The genotyping accuracy of this kit was examined by comparing to certified genotypes of NIST standard reference materials and results from five capillary electrophoresis-based kits. The sensitivity of STRseqTyper122 reached 125 pg, and > 80% of the loci were correctly called with 62.5 pg and 31.25 pg input genomic DNA. Repeatability, species specificity, and tolerance for DNA degradation and PCR inhibitors of this kit were also evaluated. STRseqTyper122 demonstrated reliable performance with routine case-work samples and provided a powerful tool for forensic applications.
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Affiliation(s)
- Li-Liang Guo
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jia-Hui Yuan
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Chi Zhang
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jie Zhao
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Yi-Ren Yao
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Ke-Li Guo
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Yang Meng
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - An-Quan Ji
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Ke-Lai Kang
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Le Wang
- Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China.
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2
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Dierig L, Kunz SN, Wiegand P. Comparison of massively parallel sequencing to capillary electrophoresis for short tandem repeat genotyping of trace DNA. Electrophoresis 2024; 45:451-462. [PMID: 38085164 DOI: 10.1002/elps.202300145] [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: 07/01/2023] [Revised: 09/08/2023] [Accepted: 10/23/2023] [Indexed: 03/20/2024]
Abstract
In forensic genetics, massively parallel sequencing (MPS) offers several advantages over the current golden standard, capillary electrophoresis (CE): additional sequence information, shorter amplicon lengths, and the simultaneous analysis of many markers. These benefits result in a reduced number of reactions necessary while improving the amount of data obtained, thereby conserving valuable sample extracts. This proves particularly advantageous for the analysis of trace DNA. This study assessed the suitability of MPS for short tandem repeat (STR) typing of low template samples compared with results obtained through CE. The MPS genotypes showed higher concordance to reference genotypes, with donor alleles being more frequently assigned to be the major contributor, meeting the requirements for database entry. However, the MPS workflow is more time-consuming and associated with higher costs.
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Affiliation(s)
- Lisa Dierig
- Institute of Legal Medicine, Ulm University, Ulm, Germany
| | | | - Peter Wiegand
- Institute of Legal Medicine, Ulm University, Ulm, Germany
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3
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Pilli E, Tarallo R, Riccia PL, Berti A, Novelletto A. Kinship assignment with the ForenSeq™ DNA Signature Prep Kit: Sources of error in simulated and real cases. Sci Justice 2022; 62:1-9. [PMID: 35033321 DOI: 10.1016/j.scijus.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 08/31/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022]
Abstract
Kinship recognition between anonymous DNA samples is becoming a relevant issue in forensics, more so with the increasing number of DNA profiles in databanks. Also, NGS-based genotyping is being increasingly used in routine personal identification, to simultaneously type large numbers of markers of different kind. In the present work, we explored computationally and experimentally the performance of the ForenSeq™ DNA Signature Prep Kit in identifying the true relationship between two anonymous samples, distinguishing it from other possible relationships. We analyzed with Familias R series of 10,000 pairs with 9 different simulated relationships, corresponding to different degrees of autosomal sharing. For each pair we obtained likelihood ratios for five kinship hypotheses vs. unrelatedness, and used their ranking to identify the preferred relationship. We also typed 21 subjects from two pedigrees, representing from parent-child to 4th cousins relationships. As expected, the power for identifying the true relationship decays in the order of autosomal sharing. Parent-child and full siblings can be robustly identified against other relationships. For half-siblings the chance of reaching a significant conclusion is already small. For more distant relationships the proportion of cases correctly and significantly identified is 10% or less. Bidirectional errors in kinship attribution include the suggestion of relatedness when this does not exist (10-50%), and the suggestion of independence in pairs of individuals more than 4 generations apart (25-60%). The real cases revealed a relevant effect of genotype miscalling at some loci, which could only be partly avoided by modulating the analysis parameters. In conclusion, with the exception of first degree relatives, the kit can be useful to inform additional investigations, but does not usually provide probatory results.
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Affiliation(s)
- Elena Pilli
- Department of Biology, University of Florence, Florence, Italy.
| | - Roberta Tarallo
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Pietro La Riccia
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche, Sezione di Biologia, Roma, Italy
| | - Andrea Novelletto
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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4
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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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5
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Cusick MF, Clark L, Tu T, Goforth J, Zhang X, LaRue B, Gutierrez R, Jindra PT. Performance characteristics of chimerism testing by next generation sequencing. Hum Immunol 2021; 83:61-69. [PMID: 34728094 DOI: 10.1016/j.humimm.2021.10.004] [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: 07/30/2021] [Revised: 09/23/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022]
Abstract
Chimerism testing provides informative clinical data regarding the status of a biological sample mixture. For years, this testing was achieved by measuring the peaks of informative short tandem repeat (STR) loci using capillary electrophoresis (CE). With the advent of next generation sequencing (NGS) technology, the quantification of the percentage of donor/recipient mixtures is more easily done using sequence reads in large batches of samples run on a single flow cell. In this study, we present data on using a FORENSIC NGS chimerism platform to accurately measure the percentage of donor/recipient mixtures. We were able to detect chimerism to a limit threshold of 1% using both STR and single nucleotide polymorphism (SNP) informative loci. Importantly, a significant correlation was observed between NGS and CE chimerism methods when compared at donor detection ranges from 1% to 10%. Furthermore, 100% accuracy was achieved through proficiency testing over six surveys. Its usefulness was expanded beyond this to help identify suitable donors for solid organ transplant patients using ancestry SNP profiles. In summary, the NGS method provides a sensitive and reliable alternative to traditional CE for chimerism testing of clinical samples.
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Affiliation(s)
- Matthew F Cusick
- Department of Pathology, University of Michigan Medicine, 2800 Plymouth Rd., Building 36, Ann Arbor, MI 48109, USA.
| | - Lauren Clark
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - Thuydung Tu
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - John Goforth
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA
| | - Xiaohai Zhang
- HLA and Immunogenetics, Laboratory, Cedars-Sinai Medical Center, Lab-SSB 197, 8723 Alden D, Los Angeles, CA 90048, USA
| | - Bobby LaRue
- Department of Forensic Science, 1003 Bowers Blvd, Sam Houston, State University Huntsville, TX 77340, USA
| | - Ryan Gutierrez
- Department of Forensic Science, 1003 Bowers Blvd, Sam Houston, State University Huntsville, TX 77340, USA
| | - Peter T Jindra
- Department of Surgery, Baylor College of Medicine, One Baylor Plaza, MS:BCM 504, Houston, TX 77030, USA.
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6
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STRNaming: Generating simple, informative names for sequenced STR alleles in a standardised and automated manner. Forensic Sci Int Genet 2021; 52:102473. [PMID: 33607395 DOI: 10.1016/j.fsigen.2021.102473] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 11/20/2022]
Abstract
The introduction of Massively Parallel Sequencing in the forensic domain has exposed the need for comprehensive nomenclature of sequenced Short Tandem Repeat (STR) alleles. In general, three strategies are at hand: 1) the full sequence mapped to the human genome reference sequence, which ensures exact data exchange; 2) shortened, human-readable formats for forensic reporting and data presentation and 3) very short codes that enable compact figures and tables but do not convey any sequence information. Here, we describe an algorithm of the second type: STRNaming, which generates human-readable names for sequenced STR alleles. STRNaming is guided by a reference sequence at each locus and then functions independently to automatically assign a unique, sequence-descriptive name that also includes the capillary electrophoresis allele number. STRNaming settings were established based on preferences that were surveyed internationally in the forensic community. These settings ensure that a small change in the sequence corresponds to a small change in the allele name, which is helpful for recognising for instance stutter products. Sequence variants outside of the repeat units are indicated as simple variant calls. Since the STR name is sequence-descriptive, the sequence can be traced back from the allele name. Because STRNaming is fully guided by an assignable reference sequence, no central coordination or configuration is required and the method will work for any STR locus, be it autosomal, Y-, X-chromosomal in current or future use. The algorithm is publicly available online and offline.
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7
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Allelic diversity and forensic estimations of the Beijing Hans: Comparative data on sequence-based and length-based STRs. Forensic Sci Int Genet 2020; 51:102424. [PMID: 33248347 DOI: 10.1016/j.fsigen.2020.102424] [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: 03/31/2019] [Revised: 10/25/2020] [Accepted: 11/01/2020] [Indexed: 11/24/2022]
Abstract
Short tandem repeat (STR) profiling is routinely used in forensic genetics. At present, STR analysis is mainly performed by capillary electrophoresis (CE). However, due to limitations associated with the CE method, STR genotyping has been limited to length polymorphisms only. Because next generation sequencing (NGS) is capable of providing full resolution STR data at the sequence variation level, the individual identification capability of forensic STR loci could be significantly improved. Here we present sequence-based STR data for the Beijing Han population in which 291 individuals were screened for 23 commonly used forensic STRs using the SeqTypeR24 CASE kit on an Ion PGM platform. In total, 234 length-based alleles and 356 sequence-based alleles, which included 22 novel core repeat sequences, were observed. The sequence-based matching probability and power of discrimination were superior to the length-based numbers for 16 loci bearing micro-variant alleles. Combined matching probability reached 8.2 × 10-29 for 23 STR loci at the sequence level. This was two orders of magnitude higher than the parameters at length level and provides a data base for sequence-based STR casework applications.
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8
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Simayijiang H, Morling N, Børsting C. Sequencing of human identification markers in an Uyghur population using the MiSeq FGxTM Forensic Genomics System. Forensic Sci Res 2020; 7:154-162. [PMID: 35784409 PMCID: PMC9246034 DOI: 10.1080/20961790.2020.1779967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Massively parallel sequencing (MPS) offers a useful alternative to capillary electrophoresis (CE) based analysis of human identification markers in forensic genetics. By sequencing short tandem repeats (STRs) instead of determining the fragment lengths by CE, the sequence variation within the repeat region and the flanking regions may be identified. In this study, we typed 264 Uyghur individuals using the MiSeq FGx™ Forensic Genomics System and Primer Mix A of the ForenSeq™ DNA Signature Prep Kit that amplifies 27 autosomal STRs, 25 Y-STRs, seven X-STRs, and 94 HID-SNPs. STRinNGS v.1.0 and GATK 3.6 were used to analyse the STR regions and HID-SNPs, respectively. Increased allelic diversity was observed for 33 STRs with the PCR-MPS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were 3–4 times larger than those of alleles determined by repeat length alone. A relatively large number of flanking region variants (28 SNPs and three InDels) were observed in the Uyghur population. Seventeen of the flanking region SNPs were rare, and 12 of these SNPs had no accession number in dbSNP. The combined mean match probability and typical paternity index based on 26 sequenced autosomal STRs were 3.85E−36 and 1.49E + 16, respectively. This was 10 000 times lower and 1 000 times higher, respectively, than the same parameters calculated from STR repeat lengths.Key Points Sequencing data on STRs and SNPs used for human identification are presented for the Uyghur population. STRinNGS v.1.0 was used to analyse the flanking regions of STRs. The concordance between PCR-CE and PCR-MPS results was 99.86%. Detection of sequence variation in STRs and their flanking regions increased the allelic diversity.
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Affiliation(s)
- Halimureti Simayijiang
- Faculty of Health and Medical Sciences, Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
- Faculty of Criminal Science and Technology, Xinjiang Police College, Xinjiang, China
| | - Niels Morling
- Faculty of Health and Medical Sciences, Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Claus Børsting
- Faculty of Health and Medical Sciences, Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
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9
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Wu H, Ji AC, Liu YC, Kang KL, Zhang C, Li ZW, Ji AQ, Ye J, Nie SJ, Wang L. Massively parallel sequencing of STRs using a 29-plex panel reveals stutter sequence characteristics. Electrophoresis 2020; 41:2029-2035. [PMID: 32770833 DOI: 10.1002/elps.202000093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/20/2020] [Accepted: 08/05/2020] [Indexed: 12/21/2022]
Abstract
Massively parallel sequencing of forensic STRs simultaneously provides length-based genotypes and core repeat sequences as well as flanking sequence variations. Here, we report primer sequences and concentrations of a next-generation sequencing (NGS)-based in-house panel covering 28 autosomal STR loci (CSF1PO, D1GATA113, D1S1627, D1S1656, D1S1677, D2S441, D2S1776, D3S3053, D5S818, D6S474, D6S1017, D6S1043, D8S1179, D9S2157, D10S1435, D11S4463, D13S317, D14S1434, D16S539, D18S51, D18S853, D20S482, D20S1082, D22S1045, FGA, TH01, TPOX, and vWA) and the sex determinant locus Amelogenin. Preliminary evaluation experiments showed that the panel yielded intralocus- and interlocus-balanced sequencing data with a sensitivity as low as 62.5 pg input DNA. A total of 203 individuals from Yunnan Bai population were sequenced with this panel. Comparative forensic genetic analyses showed that sequence-based matching probability of this 29-plex panel reached 2.37 × 10-29 , which was 23 times lower than the length-based data. Compound stutter sequences of eight STRs were compared with parental alleles. For seven loci, repeat motif insertions or deletions occurred in the longest uninterrupted repeat sequences (LUS). However, LUS and non-LUS stutters co-existed in the locus D6S474 with different sequencing depth ratios. These results supplemented our current knowledge of forensic STR stutters, and provided a sound basis for DNA mixture deconvolution.
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Affiliation(s)
- Hao Wu
- 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, P. R. China
| | - Ai-Cen Ji
- 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, P. R. China.,School of Forensic Medicine, Kunming Medical University, Kunming, P. R. China
| | - Yi-Cheng Liu
- 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, P. R. 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, P. R. 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, P. R. China
| | - Zhi-Wen Li
- 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, P. R. China.,Public Security Bureau of Ximeng County in Pu'er City, Pu'er, P. R. China
| | - An-Quan Ji
- 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, P. R. China
| | - Jian Ye
- 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, P. R. China
| | - Sheng-Jie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, P. R. 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, P. R. China
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10
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STRinNGS v2.0: Improved tool for analysis and reporting of STR sequencing data. Forensic Sci Int Genet 2020; 48:102331. [DOI: 10.1016/j.fsigen.2020.102331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/23/2020] [Accepted: 06/04/2020] [Indexed: 11/18/2022]
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11
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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: 51] [Impact Index Per Article: 12.8] [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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12
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Silva DSBS, Scheible MK, Bailey SF, Williams CL, Allwood JS, Just RS, Schuetter J, Skomrock N, Minard-Smith A, Barker-Scoggins N, Eichman C, Meiklejohn K, Faith SA. Sequence-based autosomal STR characterization in four US populations using PowerSeq™ Auto/Y system. Forensic Sci Int Genet 2020; 48:102311. [PMID: 32531758 DOI: 10.1016/j.fsigen.2020.102311] [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: 08/20/2019] [Revised: 04/21/2020] [Accepted: 05/14/2020] [Indexed: 11/30/2022]
Abstract
The forensic science community is poised to utilize modern advances in massively parallel sequencing (MPS) technologies to better characterize biological samples with higher resolution. A critical component towards the advancement of forensic DNA analysis with these technologies is a comprehensive understanding of the diversity and population distribution of sequence-based short tandem repeat (STR) alleles. Here we analyzed 786 samples of individuals from different population groups, including four of the mostly commonly encountered in forensic casework in the USA. DNA samples were amplified with the PowerSeq™ Auto/Y System Prototype Kit (Promega Corp.), and sequencing was performed on an Illumina® MiSeq instrument. Sequence data were analyzed using a bioinformatics processing tool, Altius. For additional data analysis and profile comparison, capillary electrophoresis (CE) size-based STR genotypes were generated for a subset of individuals, and where possible, also with a second commercially available MPS STR assay. Autosomal STR loci were analyzed and frequencies were calculated based on sequence composition. Also, population genetics studies were performed, with Hardy-Weinberg equilibrium, polymorphic information content (PIC), and observed and expected heterozygosity all assessed. Overall, sequence-based allelic variants of the repeat region were observed in 20 out of 22 different STR loci commonly used in forensic DNA genotyping, with the highest number of sequence variation observed at locus D12S391. The highest increase in allelic diversity and in PIC through sequence-based genotyping was observed at loci D3S1358 and D8S1179. Such detailed sequence analysis, as the one performed in the present study, is important to help understand the diversity of sequence-based STR alleles across different populations and to demonstrate how such allelic variation can improve statistics used for forensic casework.
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Affiliation(s)
- Deborah S B S Silva
- Battelle Memorial Institute, 505 King Ave., Columbus, OH, 43201, USA; NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA.
| | - Melissa K Scheible
- NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA; NC State University, Population Health and Pathobiology, 1060 William Moore Dr., Raleigh, NC, 27607, USA
| | - Sarah F Bailey
- NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA
| | - Christopher L Williams
- NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA
| | - Julia S Allwood
- NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA
| | - Rebecca S Just
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135, USA
| | - Jared Schuetter
- Battelle Memorial Institute, 505 King Ave., Columbus, OH, 43201, USA
| | - Nicholas Skomrock
- Battelle Memorial Institute, 505 King Ave., Columbus, OH, 43201, USA
| | | | - Nicole Barker-Scoggins
- NC State University, College of Veterinary Medicine, Office of Information Technology, 1060 William Moore Dr., Raleigh, NC, 27607, USA
| | - Christopher Eichman
- NC State University, College of Veterinary Medicine, Office of Information Technology, 1060 William Moore Dr., Raleigh, NC, 27607, USA
| | - Kelly Meiklejohn
- NC State University, Population Health and Pathobiology, 1060 William Moore Dr., Raleigh, NC, 27607, USA
| | - Seth A Faith
- Battelle Memorial Institute, 505 King Ave., Columbus, OH, 43201, USA; NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA; Penn State University Forensic Science Program, 329 Whitmore Laboratory, University Park, PA, 16802, USA
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13
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Wang Z, Wang L, Liu J, Ye J, Hou Y. Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations. Electrophoresis 2020; 41:194-201. [PMID: 31916267 DOI: 10.1002/elps.201900278] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/25/2019] [Accepted: 12/08/2019] [Indexed: 11/11/2022]
Abstract
Massively parallel sequencing (MPS) technologies have the ability to reveal sequence variations within STR alleles as well as their nominal allele lengths, which have traditionally been detected by CE instruments. Recently, Thermo Fisher Scientific has updated the MPS-STR panel, named the Precision ID GlobalFiler next-generation sequencing (NGS) STR Panel version 2, with primers redesigned to add two pentanucleotide tandem repeat loci and profile interpretation supported by the Converge software. Using the Ion Chef System, the Ion S5XL System, and the Converge software, genetic variations were characterized within STR repeat and flanking regions of 30 autosomal STR markers in 115 unrelated individuals from two Chinese population groups (58 Tibetans and 57 Hans). Nineteen STRs demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. In total, 390 alleles were identified by their sequences compared with 258 alleles that were identified by length. Of these 92 sequence variants found within the STR repeat regions, 40 variants were located in STR flanking regions. Additionally, the agreement of the results with CE data was evaluated, as was the ability of this new MPS panel to analyze case-type (11 samples) and artificially degraded samples (seven samples in triplicate). The results generated from this study illustrate that extensive sequence variation exists in commonly used STR markers in the selected population samples and indicate that this NGS STR panel has the potential to be used as an effective tool for human forensics.
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Affiliation(s)
- Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China.,Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, P. R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
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14
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High polymorphism detected by massively parallel sequencing of autosomal STRs using old blood samples from a Chinese Han population. Sci Rep 2019; 9:18959. [PMID: 31831766 PMCID: PMC6908607 DOI: 10.1038/s41598-019-55282-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 10/31/2019] [Indexed: 12/02/2022] Open
Abstract
The development of massively parallel sequencing (MPS) has quickly changed forensic short tandem repeat (STR) genotyping. By providing detailed sequence information, MPS technology may be used as an alternative or additional method to overcome the limitations of capillary electrophoresis-based STR profiling. Most current NGS processes are labour-intensive with regard to library preparation and require high-quality DNA template. In this study, a 16-plex STR typing system (SeqType®R16) was used to achieve direct library preparation without DNA extraction and adaptor ligation. The efficiency of this system was tested in 601 individuals, including 593 old blood samples from the Chinese Han population and eight positive controls. It took approximately 4 hours for library preparation, including blood direct multiplex PCR (1.5 hours), mixing of the product (15 minutes), single tube purification (2 hours) and quantification (15 minutes). The results showed that MPS presented a broader allele range and higher discrimination power. Except for FGA and D19S433, the allele number almost doubled or more than doubled at all complex STR loci and simple STR loci, including D13S317, D16S539, D5S818, and D7S820. The range of discrimination power increased from 0.8008–0.9572 to 0.8401–0.9753, and the culminated matching probability decreased from 1.7 × 10−15 to 1.1 × 10−17.
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15
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A nomenclature for sequence-based forensic DNA analysis. Forensic Sci Int Genet 2019; 42:14-20. [DOI: 10.1016/j.fsigen.2019.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/11/2019] [Accepted: 06/05/2019] [Indexed: 12/19/2022]
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16
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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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17
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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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18
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Utility of ForenSeq™ DNA Signature Prep Kit in the research of pairwise 2nd-degree kinship identification. Int J Legal Med 2019; 133:1641-1650. [PMID: 30687898 DOI: 10.1007/s00414-019-02003-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/15/2019] [Indexed: 10/27/2022]
Abstract
The scope of forensic kinship analysis is being extended to more distant or complex relationships. However, current methods and standards in this field do not meet the needs of casework. The next-generation sequencing (NGS) technology may hold an advantage in this field to traditional methods due to its strong power to get much more genetic information. To evaluate the effectiveness of NGS to identify the 2nd-degree kinship pairs, DNA samples of 227 individuals from 49 Hebei Han pedigrees were tested by Goldeneye™ 20A kit using capillary electrophoresis (CE) to confirm the relationships within each pedigree, and those of 111 individuals within 97 confirmed grandparent-grandchild or avuncular pairs were analyzed by ForenSeq™ DNA Signature Prep Kit using MiSeq® FGx™ DNA sequencing platform. We calculated the likelihood ratio (LR) based on ITO method and the identical by state (IBS) score of 97 kinship pairs and compared with those of 97 unrelated pairs. According to the results summarized and analyzed by Fisher discriminant analysis and leave-one-out cross-validation (LOOCV) method, ITO method showed higher accuracy than IBS method, even with less information. Therefore, we proposed a recommendation of the thresholds for pairwise 2nd-degree kinship identification for Hebei Han population based on ITO method. When using ITO method based on 94 SNPs and the length information of 27 autosomal STRs, cumulative likelihood ratio (CLR) > 1 and CLR < 0.1 are recommended as the thresholds of confirming and excluding, respectively. The accuracy applying such thresholds is greater than 95%, indicating the promising application value of NGS in this field and providing a direction for further kinship identification strategy selection. Further studies are needed to get the population genetic data of loci contained in the kit based on all sequence information including flanking regions to make full use of the NGS data to improve the accuracy of kinship analysis.
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19
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Wu J, Li JL, Wang ML, Li JP, Zhao ZC, Wang Q, Yang SD, Xiong X, Yang JL, Deng YJ. Evaluation of the MiSeq FGx system for use in forensic casework. Int J Legal Med 2019; 133:689-697. [PMID: 30604102 DOI: 10.1007/s00414-018-01987-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 12/19/2018] [Indexed: 11/24/2022]
Abstract
Capillary electrophoresis (CE) is widely used in forensic genetics to study short tandem repeats (STRs). Recently, next-generation sequencing (NGS) platforms have facilitated the development of new strategies for forensic DNA typing. Several studies have shown that NGS successfully analyzes challenging samples. However, because NGS is complicated and time-consuming, it remains unclear whether NGS platforms offer significant advantages over CE for all forensic cases. Here, the MiSeq FGx system was used to test some cases that had previously been analyzed using CE. These cases included paternity test cases in which some samples exhibited locus inconsistencies; samples with off-ladder (OL) alleles; samples with triallelic patterns; and samples with amelogenin test abnormalities. The results generated by MiSeq FGx were compared to those previously generated by CE. The MiSeq FGx and CE results were consistent with the exception of three samples, where inconsistencies were observed at the Penta D locus. For all three incongruent samples, the MiSeq FGx results were correct. Sequence analysis indicated that, in two cases, mismatches were due to undetected alleles rather than mutations. In two additional cases, mutation sources were identified, and in a fifth case, mutation step size was reconsidered. MiSeq FGx was used to identify OL alleles and samples with amelogenin test abnormalities. For cases where verification was required via CE analysis, the simultaneous NGS amplification of several types of multiple genetic markers improved testing efficiency. In addition, we identified additional sequence variants at autosomal, Y chromosomal, and X chromosomal STR loci in the Han Chinese population from northern China. Our results will be useful for future forensic analyses of STR genotypes in Chinese populations. It is likely that NGS would be more widely used in forensic genetics if costs and procedure complexity were reduced.
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Affiliation(s)
- Jie Wu
- Institute of Beijing DNA Evidence, Beijing, 101318, People's Republic of China.
| | - Jing-Long Li
- Institute of Beijing DNA Evidence, Beijing, 101318, People's Republic of China
| | - Meng-Lei Wang
- Institute of Beijing DNA Evidence, Beijing, 101318, People's Republic of China
| | - Jian-Ping Li
- Institute of Beijing DNA Evidence, Beijing, 101318, People's Republic of China
| | - Zhi-Chao Zhao
- Institute of Beijing DNA Evidence, Beijing, 101318, People's Republic of China
| | - Qi Wang
- Institute of Beijing DNA Evidence, Beijing, 101318, People's Republic of China
| | - Shu-Dong Yang
- Institute of Beijing DNA Evidence, Beijing, 101318, People's Republic of China
| | - Xin Xiong
- Institute of Beijing DNA Evidence, Beijing, 101318, People's Republic of China
| | - Jing-Long Yang
- Institute of Beijing DNA Evidence, Beijing, 101318, People's Republic of China
| | - Ya-Jun Deng
- Institute of Beijing DNA Evidence, Beijing, 101318, People's Republic of China.
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20
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Plesivkova D, Richards R, Harbison S. A review of the potential of the MinION™ single‐molecule sequencing system for forensic applications. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/wfs2.1323] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Diana Plesivkova
- Forensic Science Programme, School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Rebecca Richards
- Forensic Science Programme, 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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21
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Kim SY, Lee HC, Chung U, Ham SK, Lee HY, Park SJ, Roh YJ, Lee SH. Massive parallel sequencing of short tandem repeats in the Korean population. Electrophoresis 2018; 39:2702-2707. [PMID: 30084488 DOI: 10.1002/elps.201800090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/28/2018] [Accepted: 07/16/2018] [Indexed: 11/10/2022]
Abstract
STR analysis using capillary electrophoresis has been the most widely used method for forensic DNA typing. Recently, massive parallel sequencing (MPS) technique has been emerging as an innovative tool to supplement or replace the conventional CE process. In this study, we evaluated the application of commercial MiSeqFGx™ forensic signature kit (Illumina Inc., San Diego, CA, USA) in the Korean population, including performance comparison with CE-based STR profiling kits. The genotyping results of 209 unrelated random Korean individuals were summarized according to the International Society for Forensic Genetics guideline. The study revealed that 26 novel sequence variations in autosomal STR were newly found that had not been previously reported in other forensic literature. This indicates that MPS may be an effective supplementary tool for forensic DNA typing and the database to increase the discriminatory power of individual identification.
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Affiliation(s)
- Se-Yong Kim
- Division of Forensic Genetics & Chemistry, Supreme Prosecutors' Office, Seoul, Republic of Korea.,Department of Forensic Sciences, Sungkyunkwan University, Seoul, Republic of Korea
| | - Han-Chul Lee
- Division of Forensic Genetics & Chemistry, Supreme Prosecutors' Office, Seoul, Republic of Korea
| | - Ukhee Chung
- Division of Forensic Genetics & Chemistry, Supreme Prosecutors' Office, Seoul, Republic of Korea
| | - Seon-Kyu Ham
- Division of Forensic Genetics & Chemistry, Supreme Prosecutors' Office, Seoul, Republic of Korea
| | - Ho Yeon Lee
- Department of Forensic Sciences, Sungkyunkwan University, Seoul, Republic of Korea
| | - Su Jeong Park
- Division of Forensic Genetics & Chemistry, Supreme Prosecutors' Office, Seoul, Republic of Korea
| | | | - Seung Hwan Lee
- Division of Forensic Genetics & Chemistry, Supreme Prosecutors' Office, Seoul, Republic of Korea
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22
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Moreno LI, Galusha MB, Just R. A closer look at Verogen's Forenseq™ DNA Signature Prep kit autosomal and Y-STR data for streamlined analysis of routine reference samples. Electrophoresis 2018; 39:2685-2693. [DOI: 10.1002/elps.201800087] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/05/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022]
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23
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Barbian HJ, Connell AJ, Avitto AN, Russell RM, Smith AG, Gundlapally MS, Shazad AL, Li Y, Bibollet‐Ruche F, Wroblewski EE, Mjungu D, Lonsdorf EV, Stewart FA, Piel AK, Pusey AE, Sharp PM, Hahn BH. CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees. Ecol Evol 2018; 8:7946-7963. [PMID: 30250675 PMCID: PMC6145012 DOI: 10.1002/ece3.4302] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/29/2022] Open
Abstract
Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.
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Affiliation(s)
- Hannah J. Barbian
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrew Jesse Connell
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Alexa N. Avitto
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Ronnie M. Russell
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrew G. Smith
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Madhurima S. Gundlapally
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Alexander L. Shazad
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Yingying Li
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Frederic Bibollet‐Ruche
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Emily E. Wroblewski
- Department of AnthropologyWashington University in St. LouisSt. LouisMissouri
| | | | | | - Fiona A. Stewart
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Alexander K. Piel
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Anne E. Pusey
- Department of Evolutionary AnthropologyDuke UniversityDurhamNorth Carolina
| | - Paul M. Sharp
- Institute of Evolutionary Biology and Centre for ImmunityInfection and EvolutionUniversity of EdinburghEdinburghUK
| | - Beatrice H. Hahn
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
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24
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Zhang QX, Yang M, Pan YJ, Zhao J, Qu BW, Cheng F, Yang YR, Jiao ZP, Liu L, Yan JW. Development of a massively parallel sequencing assay for investigating sequence polymorphisms of 15 short tandem repeats in a Chinese Northern Han population. Electrophoresis 2018; 39:2725-2731. [DOI: 10.1002/elps.201800071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/11/2018] [Accepted: 05/07/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Qing-Xia Zhang
- Forensic Science Service; Beijing Public Security Bureau; Beijing P. R. China
| | - Meng Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
| | | | - Jing Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | | | - Feng Cheng
- College of forensic medicine; Shanxi Medical University; Taiyuan P. R. China
| | - Ya-Ran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
| | - Zhang-Ping Jiao
- Forensic Science Service; Beijing Public Security Bureau; Beijing P. R. China
| | - Li Liu
- Forensic Science Service; Beijing Public Security Bureau; Beijing P. R. China
- College of forensic medicine; Shanxi Medical University; Taiyuan P. R. China
| | - Jiang-Wei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
- College of forensic medicine; Shanxi Medical University; Taiyuan P. R. China
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25
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Tao R, Wang S, Zhang J, Zhang J, Yang Z, Sheng X, Hou Y, Zhang S, Li C. Separation/extraction, detection, and interpretation of DNA mixtures in forensic science (review). Int J Legal Med 2018; 132:1247-1261. [PMID: 29802461 DOI: 10.1007/s00414-018-1862-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/11/2018] [Indexed: 02/08/2023]
Abstract
Interpreting mixed DNA samples containing material from multiple contributors has long been considered a major challenge in forensic casework, especially when encountering low-template DNA (LT-DNA) or high-order mixtures that may involve missing alleles (dropout) and unrelated alleles (drop-in), among others. In the last decades, extraordinary progress has been made in the analysis of mixed DNA samples, which has led to increasing attention to this research field. The advent of new methods for the separation and extraction of DNA from mixtures, novel or jointly applied genetic markers for detection and reliable interpretation approaches for estimating the weight of evidence, as well as the powerful massively parallel sequencing (MPS) technology, has greatly extended the range of mixed samples that can be correctly analyzed. Here, we summarized the investigative approaches and progress in the field of forensic DNA mixture analysis, hoping to provide some assistance to forensic practitioners and to promote further development involving this issue.
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Affiliation(s)
- Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Xiang Sheng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China. .,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
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26
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Hussing C, Bytyci R, Huber C, Morling N, Børsting C. The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit. Int J Legal Med 2018; 133:325-334. [PMID: 29797283 DOI: 10.1007/s00414-018-1854-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/11/2018] [Indexed: 10/24/2022]
Abstract
Some STR loci have internal sequence variations, which are not revealed by the standard STR typing methods used in forensic genetics (PCR and fragment length analysis by capillary electrophoresis (CE)). Typing of STRs with next-generation sequencing (NGS) uncovers the sequence variation in the repeat region and in the flanking regions. In this study, 363 Danish individuals were typed for 56 STRs (26 autosomal STRs, 24 Y-STRs, and 6 X-STRs) using the ForenSeq™ DNA Signature Prep Kit to establish a Danish STR sequence database. Increased allelic diversity was observed in 34 STRs by the PCR-NGS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were around four times larger than the numbers of alleles determined by repeat length alone. Thirteen SNPs and one InDel were identified in the flanking regions of 12 STRs. Furthermore, 36 single positions and five longer stretches in the STR flanking regions were found to have dubious genotyping quality. The combined match probability of the 26 autosomal STRs was 10,000 times larger using the PCR-NGS assay than by using PCR-CE. The typical paternity indices for trios and duos were 500 and 100 times larger, respectively, than those obtained with PCR-CE. The assay also amplified 94 SNPs selected for human identification. Eleven of these loci were not in Hardy-Weinberg equilibrium in the Danish population, most likely because the minimum threshold for allele calling (30 reads) in the ForenSeq™ Universal Analysis Software was too low and frequent allele dropouts were not detected.
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Affiliation(s)
- C Hussing
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark
| | - R Bytyci
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark
| | - C Huber
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark.
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27
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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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28
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Xue J, Wu R, Pan Y, Wang S, Qu B, Qin Y, Shi Y, Zhang C, Li R, Zhang L, Zhou C, Sun H. Integrated massively parallel sequencing of 15 autosomal STRs and Amelogenin using a simplified library preparation approach. Electrophoresis 2018; 39:1466-1473. [DOI: 10.1002/elps.201700429] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/22/2018] [Accepted: 03/27/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Jian Xue
- Forensic Science Service of the Beijing Public Security Bureau; Beijing P. R. China
| | - Riga Wu
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center; Sun Yat-sen University; Guangzhou Guangdong P. R. China
| | - Yajiao Pan
- IPE Biotechnology Co., Ltd.; Beijing P. R. China
| | - Shunxia Wang
- Forensic Science Service of the Beijing Public Security Bureau; Beijing P. R. China
| | - Baowang Qu
- IPE Biotechnology Co., Ltd.; Beijing P. R. China
| | - Ying Qin
- Zhuhai Municipal Public Security Forensic Science Center; Zhuhai P. R. China
| | - Yuequn Shi
- Zhuhai Municipal Public Security Forensic Science Center; Zhuhai P. R. China
| | - Chuchu Zhang
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Ran Li
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Liyan Zhang
- Zhuhai Municipal Public Security Forensic Science Center; Zhuhai P. R. China
| | - Cheng Zhou
- IPE Biotechnology Co., Ltd.; Beijing P. R. China
| | - Hongyu Sun
- Department of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center; Sun Yat-sen University; Guangzhou Guangdong P. R. China
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29
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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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30
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Wang L, Chen M, Wu B, Liu YC, Zhang GF, Jiang L, Xu XL, Zhao XC, Ji AQ, Ye J. Massively Parallel Sequencing of Forensic STRs Using the Ion Chef™ and the Ion S5™ XL Systems. J Forensic Sci 2018; 63:1692-1703. [PMID: 29494760 DOI: 10.1111/1556-4029.13767] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/25/2017] [Accepted: 02/05/2018] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing (NGS) has been used to genotype forensic short tandem repeat (STR) markers for individual identification and kinship analysis. STR data from several NGS platforms have been published, but forensic application trials using the Ion S5™ XL system have not been reported. In this work, we report sensitivity, reproducibility, mixture, simulated degradation, and casework sample data on the Ion Chef™ and S5™ XL systems using an early access 25-plex panel. Sensitivity experiments showed that over 97% of the alleles were detectable with down to 62 pg input of genomic DNA. In mixture studies, alleles from minor contributors were correctly assigned at 1:9 and 9:1 ratios. NGS successfully gave 12 full genotype results from 13 challenging casework samples, compared with five full results using the CE platform. In conclusion, the Ion Chef™ and the Ion S5™ XL systems provided an alternative and promising approach for forensic STR genotyping.
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Affiliation(s)
- Le Wang
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Man Chen
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Bo Wu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Yi-Cheng Liu
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Guang-Feng Zhang
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Li Jiang
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Xiu-Lan Xu
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Xing-Chun Zhao
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - An-Quan Ji
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science and MPS Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
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31
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Wang Z, Zhou D, Wang H, Jia Z, Liu J, Qian X, Li C, Hou Y. Massively parallel sequencing of 32 forensic markers using the Precision ID GlobalFiler™ NGS STR Panel and the Ion PGM™ System. Forensic Sci Int Genet 2017; 31:126-134. [DOI: 10.1016/j.fsigen.2017.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 08/26/2017] [Accepted: 09/06/2017] [Indexed: 01/04/2023]
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32
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STRSeq: A catalog of sequence diversity at human identification Short Tandem Repeat loci. Forensic Sci Int Genet 2017; 31:111-117. [PMID: 28888135 DOI: 10.1016/j.fsigen.2017.08.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/30/2017] [Indexed: 11/23/2022]
Abstract
The STR Sequencing Project (STRSeq) was initiated to facilitate the description of sequence-based alleles at the Short Tandem Repeat (STR) loci targeted in human identification assays. This international collaborative effort, which has been endorsed by the ISFG DNA Commission, provides a framework for communication among laboratories. The initial data used to populate the project are the aggregate alleles observed in targeted sequencing studies across four laboratories: National Institute of Standards and Technology (N=1786), Kings College London (N=1043), University of North Texas Health Sciences Center (N=839), and University of Santiago de Compostela (N=944), for a total of 4612 individuals. STRSeq data are maintained as GenBank records at the U.S. National Center for Biotechnology Information (NCBI), which participates in a daily data exchange with the DNA DataBank of Japan (DDBJ) and the European Nucleotide Archive (ENA). Each GenBank record contains the observed sequence of a STR region, annotation ("bracketing") of the repeat region and flanking region polymorphisms, information regarding the sequencing assay and data quality, and backward compatible length-based allele designation. STRSeq GenBank records are organized within a BioProject at NCBI (https://www.ncbi.nlm.nih.gov/bioproject/380127), which is sub-divided into: commonly used autosomal STRs, alternate autosomal STRs, Y-chromosomal STRs, and X-chromosomal STRs. Each of these categories is further divided into locus-specific BioProjects. The BioProject hierarchy facilitates access to the GenBank records by browsing, BLAST searching, or ftp download. Future plans include user interface tools at strseq.nist.gov, a pathway for submission of additional allele records by laboratories performing population sample sequencing and interaction with the STRidER web portal for quality control (http://strider.online).
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33
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Kim EH, Lee HY, Kwon SY, Lee EY, Yang WI, Shin KJ. Sequence-based diversity of 23 autosomal STR loci in Koreans investigated using an in-house massively parallel sequencing panel. Forensic Sci Int Genet 2017; 30:134-140. [DOI: 10.1016/j.fsigen.2017.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 01/13/2023]
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34
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Just RS, Moreno LI, Smerick JB, Irwin JA. Performance and concordance of the ForenSeq™ system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens. Forensic Sci Int Genet 2017; 28:1-9. [DOI: 10.1016/j.fsigen.2017.01.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/30/2016] [Accepted: 01/01/2017] [Indexed: 01/26/2023]
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35
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Statistical modelling of Ion PGM HID STR 10-plex MPS data. Forensic Sci Int Genet 2017; 28:82-89. [DOI: 10.1016/j.fsigen.2017.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/18/2017] [Accepted: 01/30/2017] [Indexed: 11/18/2022]
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36
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FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise. Forensic Sci Int Genet 2017; 27:27-40. [DOI: 10.1016/j.fsigen.2016.11.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/31/2016] [Accepted: 11/23/2016] [Indexed: 11/20/2022]
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37
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Massively parallel sequencing of 10 autosomal STRs in Chinese using the ion torrent personal genome machine (PGM). Forensic Sci Int Genet 2016; 25:34-38. [DOI: 10.1016/j.fsigen.2016.07.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/13/2016] [Accepted: 07/27/2016] [Indexed: 12/21/2022]
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38
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Characterization of genetic sequence variation of 58 STR loci in four major population groups. Forensic Sci Int Genet 2016; 25:214-226. [DOI: 10.1016/j.fsigen.2016.09.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/15/2016] [Accepted: 09/27/2016] [Indexed: 11/22/2022]
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39
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Fujii K, Watahiki H, Mita Y, Iwashima Y, Miyaguchi H, Kitayama T, Nakahara H, Mizuno N, Sekiguchi K. Next-generation sequencing analysis of off-ladder alleles due to migration shift caused by sequence variation at D12S391 locus. Leg Med (Tokyo) 2016; 22:62-7. [PMID: 27591542 DOI: 10.1016/j.legalmed.2016.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 08/03/2016] [Accepted: 08/10/2016] [Indexed: 10/21/2022]
Abstract
In short tandem repeat (STR) analysis, length polymorphisms are detected by capillary electrophoresis (CE). At most STR loci, mobility shift due to sequence variation in the repeat region was thought not to affect the typing results. In our recent population studies of 1501 Japanese individuals, off-ladder calls were observed at the D12S391 locus using PowerPlex Fusion in nine samples for allele 22, one sample for allele 25, and one sample for allele 26. However, these samples were typed as ordinary alleles within the bins using GlobalFiler. In this study, next-generation sequencing analysis using MiSeq was performed for the D12S391 locus from the 11 off-ladder samples and 33 other samples, as well as the allelic ladders of PowerPlex Fusion and GlobalFiler. All off-ladder allele 22 in the nine samples had [AGAT]11[AGAC]11 as a repeat structure, while the corresponding allele was [AGAT]15[AGAC]6[AGAT] for the PowerPlex Fusion ladder, and [AGAT]13[AGAC]9 for the GlobalFiler ladder. Overall, as the number of [AGAT] in the repeat structure decreased at the D12S391 locus, the peak migrated more slowly using PowerPlex Fusion, the reverse strand of which was labeled, and it migrated more rapidly using GlobalFiler, the forward strand of which was labeled. The allelic ladders of both STR kits were reamplified with our small amplicon D12S391 primers and their mobility was also examined. In conclusion, off-ladder observations of allele 22 at the D12S391 locus using PowerPlex Fusion were mainly attributed to a relatively large difference of the repeat structure between its allelic ladder and off-ladder allele 22.
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Affiliation(s)
- Koji Fujii
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan; Identification Center, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Haruhiko Watahiki
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yusuke Mita
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yasuki Iwashima
- Forensic Science Laboratory, Kyoto Prefectural Police Headquarters, 85-3, 85-4 Shimodachiuri-dori, Kamanza-higashiiru, Yabunouchi-cho, Kamigyo-ku, Kyoto 602-8550, Japan
| | - Hajime Miyaguchi
- Identification Center, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tetsushi Kitayama
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan; Identification Center, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Hiroaki Nakahara
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Kazumasa Sekiguchi
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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40
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Bodner M, Bastisch I, Butler JM, Fimmers R, Gill P, Gusmão L, Morling N, Phillips C, Prinz M, Schneider PM, Parson W. Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on quality control of autosomal Short Tandem Repeat allele frequency databasing (STRidER). Forensic Sci Int Genet 2016; 24:97-102. [DOI: 10.1016/j.fsigen.2016.06.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 06/11/2016] [Indexed: 01/20/2023]
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41
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Massively parallel sequencing of short tandem repeats—Population data and mixture analysis results for the PowerSeq™ system. Forensic Sci Int Genet 2016; 24:86-96. [DOI: 10.1016/j.fsigen.2016.05.016] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/25/2016] [Accepted: 05/29/2016] [Indexed: 11/17/2022]
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42
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Ma Y, Kuang JZ, Nie TG, Zhu W, Yang Z. Next generation sequencing: Improved resolution for paternal/maternal duos analysis. Forensic Sci Int Genet 2016; 24:83-85. [DOI: 10.1016/j.fsigen.2016.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 11/28/2022]
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43
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Evaluation of the Early Access STR Kit v1 on the Ion Torrent PGM™ platform. Forensic Sci Int Genet 2016; 23:111-120. [DOI: 10.1016/j.fsigen.2016.04.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/12/2016] [Accepted: 04/02/2016] [Indexed: 11/23/2022]
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44
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Darby BJ, Erickson SF, Hervey SD, Ellis-Felege SN. Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing. Ecol Evol 2016; 6:4502-12. [PMID: 27386092 PMCID: PMC4930997 DOI: 10.1002/ece3.2221] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/09/2016] [Accepted: 05/12/2016] [Indexed: 12/11/2022] Open
Abstract
High‐throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high‐throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high‐throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost‐effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence‐aware microsatellite data.
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Affiliation(s)
- Brian J Darby
- Department of Biology University of North Dakota 10 Cornell St. Stop 9019 Grand Forks North Dakota 58202
| | - Shay F Erickson
- Department of Biology University of North Dakota 10 Cornell St. Stop 9019 Grand Forks North Dakota 58202
| | - Samuel D Hervey
- Department of Biology University of North Dakota 10 Cornell St. Stop 9019 Grand Forks North Dakota 58202
| | - Susan N Ellis-Felege
- Department of Biology University of North Dakota 10 Cornell St. Stop 9019 Grand Forks North Dakota 58202
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45
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Kim EH, Lee HY, Yang IS, Jung SE, Yang WI, Shin KJ. Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons. Forensic Sci Int Genet 2016; 22:1-7. [DOI: 10.1016/j.fsigen.2016.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 12/09/2015] [Accepted: 01/05/2016] [Indexed: 11/26/2022]
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46
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Parson W, Ballard D, Budowle B, Butler JM, Gettings KB, Gill P, Gusmão L, Hares DR, Irwin JA, King JL, Knijff PD, Morling N, Prinz M, Schneider PM, Neste CV, Willuweit S, Phillips C. Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements. Forensic Sci Int Genet 2016; 22:54-63. [DOI: 10.1016/j.fsigen.2016.01.009] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 12/15/2022]
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47
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Abstract
The author's thoughts and opinions on where the field of forensic DNA testing is headed for the next decade are provided in the context of where the field has come over the past 30 years. Similar to the Olympic motto of 'faster, higher, stronger', forensic DNA protocols can be expected to become more rapid and sensitive and provide stronger investigative potential. New short tandem repeat (STR) loci have expanded the core set of genetic markers used for human identification in Europe and the USA. Rapid DNA testing is on the verge of enabling new applications. Next-generation sequencing has the potential to provide greater depth of coverage for information on STR alleles. Familial DNA searching has expanded capabilities of DNA databases in parts of the world where it is allowed. Challenges and opportunities that will impact the future of forensic DNA are explored including the need for education and training to improve interpretation of complex DNA profiles.
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Affiliation(s)
- John M Butler
- National Institute of Standards and Technology, Gaithersburg, MD, USA
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48
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Mo SK, Liu YC, Wang SQ, Bo XC, Li Z, Chen Y, Ni M. Exploring the efficacy of paternity and kinship testing based on single nucleotide polymorphisms. Forensic Sci Int Genet 2016; 22:161-168. [PMID: 26952733 DOI: 10.1016/j.fsigen.2016.02.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 02/22/2016] [Accepted: 02/24/2016] [Indexed: 11/17/2022]
Abstract
Short tandem repeats (STRs) are conventional genetic markers typically used for paternity and kinship testing. As supplementary markers of STRs, single nucleotide polymorphisms (SNPs) have less discrimination power but broader applicability to degraded samples. The rapid improvement of next-generation sequencing (NGS) and multiplex amplification technologies also make it possible now to simultaneously identify dozens or even hundreds of SNP loci in a single pool. However, few studies have been endeavored to kinship testing based on SNP loci. In this study, we genotyped 90 autosomal human identity SNP loci with NGS, and investigated their testing efficacies based on the likelihood ratio model in eight pedigree scenarios involving paternity, half/full-sibling, uncle/nephew, and first-cousin relationships. We found that these SNPs might be sufficient to discriminate paternity and full-sibling, but impractical for more distant relatives such as uncle and cousin. Furthermore, we conducted an in silico study to obtain the theoretical tendency of how testing efficacy varied with increasing number of SNP loci. For each testing battery in a given pedigree scenario, we obtained distributions of logarithmic likelihood ratio for both simulated relatives and unrelated controls. The proportion of the overlapping area between the two distributions was defined as a false testing level (FTL) to evaluate the testing efficacy. We estimated that 85, 127, 491, and 1,858 putative SNP loci were required to discriminate paternity, full-sibling, half-sibling/uncle-nephew, and first-cousin (FTL, 0.1%), respectively. To test a half-sibling or nephew, an additional uncle relative could be included to decrease the required number of putative SNP loci to ∼320 (FTL, 0.1%). As a systematic computation of paternity and kinship testing based only on SNPs, our results could be informative for further studies and applications on paternity and kinship testing using SNP loci.
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Affiliation(s)
- Shao-Kang Mo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China.
| | - Ya-Cheng Liu
- Beijing Tongda Shoucheng Institute of Forensic Science, 23 Yongtai Middle Road, Beijing 100192, People's Republic of China.
| | - Sheng-Qi Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China.
| | - Xiao-Chen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China.
| | - Zhen Li
- Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China.
| | - Ying Chen
- Department of Radiation Toxicology & Oncology, Beijing Institute of Radiation Medicine, Beijing 100850, People's Republic of China.
| | - Ming Ni
- Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China.
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49
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England R, Harbison S. Massively parallel sequencing for the forensic scientist – sequencing archived amplified products of AmpFlSTR Identifiler and PowerPlex Y multiplex kits to capture additional information. AUST J FORENSIC SCI 2016. [DOI: 10.1080/00450618.2015.1134658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ryan England
- Forensic Business Group, Institute of Environmental Science and Research Ltd, Auckland, New Zealand
| | - SallyAnn Harbison
- Forensic Business Group, Institute of Environmental Science and Research Ltd, Auckland, New Zealand
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50
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Wang Z, Zhou D, Cao Y, Hu Z, Zhang S, Bian Y, Hou Y, Li C. Characterization of microRNA expression profiles in blood and saliva using the Ion Personal Genome Machine ® System (Ion PGM™ System). Forensic Sci Int Genet 2016; 20:140-146. [DOI: 10.1016/j.fsigen.2015.10.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 10/27/2015] [Accepted: 10/27/2015] [Indexed: 11/24/2022]
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