1
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Stephens KM, Barta R, Fleming K, Perez JC, Wu SF, Snedecor J, Holt CL, LaRue B, Budowle B. Developmental validation of the ForenSeq MainstAY kit, MiSeq FGx sequencing system and ForenSeq Universal Analysis Software. Forensic Sci Int Genet 2023; 64:102851. [PMID: 36907074 DOI: 10.1016/j.fsigen.2023.102851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
For human identification purposes, forensic genetics has primarily relied upon a core set of autosomal (and to a lesser extent Y chromosome) short tandem repeat (STR) markers that are enriched by amplification using the polymerase chain reaction (PCR) that are subsequently separated and detected using capillary electrophoresis (CE). While STR typing conducted in this manner is well-developed and robust, advances in molecular biology that have occurred over the last 15 years, in particular massively parallel sequencing (MPS) [1-7], offer certain advantages as compared to CE-based typing. First and foremost is the high throughput capacity of MPS. Current bench top high throughput sequencers enable larger batteries of markers to be multiplexed and multiple samples to be sequenced simultaneously (e.g., millions to billions of nucleotides can be sequenced in one run). Second, compared to the length-based CE approach, sequencing STRs increases discrimination power, enhances sensitivity of detection, reduces noise due to instrumentation, and improves mixture interpretation [4,8-23]. Third, since detection of STRs is based on sequence and not fluorescence, amplicons can be designed that are shorter in length and of similar lengths among loci, where possible, which can improve amplification efficiency and analysis of degraded samples. Lastly, MPS offers a single format approach that can be applied to analysis of a wide variety of genetic markers of forensic interest (e.g., STRs, mitochondrial DNA, single nucleotide polymorphisms, insertion/deletions). These features make MPS a desirable technology for casework [14,15,24,25-48]. The developmental validation of the ForenSeq MainstAY library preparation kit with the MiSeq FGx Sequencing System and ForenSeq Universal Software is reported here to assist with validation of this MPS system for casework [49]. The results show that the system is sensitive, accurate and precise, specific, and performs well with mixtures and mock case-type samples.
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Affiliation(s)
| | - Richelle Barta
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Keenan Fleming
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | | | - Shan-Fu Wu
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - June Snedecor
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Cydne L Holt
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Bobby LaRue
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Bruce Budowle
- University of Helsinki, Department of Forensic Medicine, Haartmaninkatu 8, P.O. Box 63, Helsinki 00014, Finland
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2
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Dash HR, Vajpayee K, Shukla R, Srivastava A, Shrivastava P, Das S. Sequence-based assessment of expediency of tri-, tetra-, and penta-nucleotides repeat autosomal STR markers in the central Indian population using Next Generation Sequencing (NGS). Meta Gene 2022. [DOI: 10.1016/j.mgene.2021.100983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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3
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Garafutdinov RR, Sakhabutdinova AR, Slominsky PA, Aminev FG, Chemeris AV. A new digital approach to SNP encoding for DNA identification. Forensic Sci Int 2020; 317:110520. [PMID: 33031982 DOI: 10.1016/j.forsciint.2020.110520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/21/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
Identification of individuals has become an urgent problem for mankind. In the last three decades, STR-based DNA identification has actively evolved along with traditional biometric methods. Nonetheless, single-nucleotide polymorphisms (SNPs) are now of great interest and a number of relevant SNP panels have been proposed for DNA identification. Here, a simple approach to SNP data digitization that can provide assigning a unique genetic identification number (GIN) to each person is proposed. The key points of this approach are as follows: 1) SNP data are digitized as whole 4-bit boxes in the most convenient binary format, where character "1" (YES) is assigned to revealed nucleotides, and character "0" (NO) to missing nucleotides after SNP-typing; 2) all SNPs should be considered tetra-allelic. Calculations showed that a 72-plex SNP panel is enough to provide the population with unique GINs, which can be represented in digital (binary or hexadecimal) or graphic (linear or two-dimensional) formats. Simple software for SNP data processing and GINs creation in any format was written. It is likely that the national and global GIN databases will facilitate the solution of problems related to identification of individuals or human biological materials. The proposed approach may be extended to other living organisms as well.
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Affiliation(s)
- Ravil R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, 450054, prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, 450054, prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia
| | - Petr A Slominsky
- Institute of Molecular Genetics, Russian Academy of Sciences, 123182, Kurchatov sq. 2, Moscow, Russia
| | - Farit G Aminev
- Bashkir State University, 450076, Zaki Validi str., 32, Ufa, Bashkortostan, Russia
| | - Alexey V Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, 450054, prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia
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4
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Li HX, Peng D, Wang Y, Wu RG, Zhang YM, Li R, Sun HY. Evaluation of genetic parameters of 23 autosomal STR loci in a Southern Chinese Han population. Ann Hum Biol 2018; 45:359-364. [DOI: 10.1080/03014460.2018.1480731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Hai-xia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, PR China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Ying Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Ri-ga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Yin-ming Zhang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Hong-yu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, PR China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, PR China
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5
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Gettings KB, Borsuk LA, Steffen CR, Kiesler KM, Vallone PM. Sequence-based U.S. population data for 27 autosomal STR loci. Forensic Sci Int Genet 2018; 37:106-115. [PMID: 30144646 DOI: 10.1016/j.fsigen.2018.07.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/26/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
Abstract
This manuscript reports Short Tandem Repeat (STR) sequence-based allele frequencies for 1036 samples across 27 autosomal STR loci: D1S1656, TPOX, D2S441, D2S1338, D3S1358, D4S2408, FGA, D5S818, CSF1PO, D6S1043, D7S820, D8S1179, D9S1122, D10S1248, TH01, vWA, D12S391, D13S317, Penta E, D16S539, D17S1301, D18S51, D19S433, D20S482, D21S11, Penta D, and D22S1045. Sequence data were analyzed by two bioinformatic pipelines and all samples have been evaluated for concordance with alleles derived from CE-based analysis at all loci. Each reported sequence includes high-quality flanking sequence and is properly formatted according to the most recent guidance of the International Society for Forensic Genetics. In addition, GenBank accession numbers are reported for each sequence, and associated records are available in the STRSeq BioProject (https://www.ncbi.nlm.nih.gov/bioproject/380127). The D3S1358 locus demonstrates the greatest average increase in heterozygosity across populations (approximately 10 percentage points). Loci demonstrating average increase in heterozygosity from 10 to 5 percentage points include (in descending order) D9S1122, D13S317, D8S1179, D21S11, D5S818, D12S391, and D2S441. The remaining 19 loci each demonstrate less than 5 percentage point increase in average heterozygosity. Discussion includes the utility of this data in understanding traditional CE results, such as informing stutter models and understanding migration challenges, and considerations for population sampling strategies in light of the marked increase in rare alleles for several of the sequence-based STR loci. This NIST 1036 data set is expected to support the implementation of STR sequencing forensic casework by providing high-confidence sequence-based allele frequencies for the same sample set which are already the basis for population statistics in many U.S. forensic laboratories.
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Affiliation(s)
- Katherine Butler Gettings
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
| | - Lisa A Borsuk
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
| | - Carolyn R Steffen
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
| | - Kevin M Kiesler
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
| | - Peter M Vallone
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
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6
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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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7
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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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8
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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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9
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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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10
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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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11
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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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12
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Gopinath S, Zhong C, Nguyen V, Ge J, Lagacé RE, Short ML, Mulero JJ. Developmental validation of the Yfiler® Plus PCR Amplification Kit: An enhanced Y-STR multiplex for casework and database applications. Forensic Sci Int Genet 2016; 24:164-175. [DOI: 10.1016/j.fsigen.2016.07.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 06/23/2016] [Accepted: 07/07/2016] [Indexed: 11/25/2022]
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13
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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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14
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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: 22] [Impact Index Per Article: 2.8] [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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15
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Friis SL, Buchard A, Rockenbauer E, Børsting C, Morling N. Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs. Forensic Sci Int Genet 2015; 21:68-75. [PMID: 26722765 DOI: 10.1016/j.fsigen.2015.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/05/2015] [Accepted: 12/10/2015] [Indexed: 10/22/2022]
Abstract
This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report with the assigned SNP-STR alleles. The main output file from STRinNGS contains all sequences with read counts above 1% of the total number of reads per locus. STR sequences are automatically named according to the nomenclature used previously and according to the repeat unit definitions in STRBase (http://www.cstl.nist.gov/strbase/). The sequences are named with (1) the locus name, (2) the length of the repeat region divided by the length of the repeat unit, (3) the sequence(s) of the repeat unit(s) followed by the number of repeats and (4) variations in the flanking regions. Lower case letters in the main output file are used to flag sequences with previously unknown variations in the STRs. SNPs in the flanking regions are named by their "rs" numbers and the nucleotides in the SNP position. Data from 207 Danes sequenced with the Ion Torrent™ HID STR 10-plex that amplified nine STRs (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D16S539, TH01, TPOX, vWA), and Amelogenin was analysed with STRinNGS. Sequencing uncovered five common SNPs near four STRs and revealed 20 new alleles in the 207 Danes. Three short homopolymers in the D8S1179 flanking regions caused frequent sequencing errors. In 29 of 3726 allele calls (0.8%), sequences with homopolymer errors were falsely assigned as true alleles. An in-house developed script in R compensated for these errors by compiling sequence reads that had identical STR sequences and identical nucleotides in the five common SNPs. In the output file from the R script, all SNP-STR haplotype calls were correct. The 207 samples and six additional samples were sequenced for D3S1358, D12S391, and D21S11 using the 454 GS Junior platform in this and a previous work. Overall, next generation sequencing (NGS) of the 11 STRs lowered the mean match probability 386 times and increased the typical paternity indexes (i.e. the geometric mean) for trios and duos 47 and 23 times, respectively, compared to the traditional PCR-CE typing of the same population.
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Affiliation(s)
- Susanne L Friis
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Anders Buchard
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Eszter Rockenbauer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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16
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Gettings KB, Kiesler KM, Faith SA, Montano E, Baker CH, Young BA, Guerrieri RA, Vallone PM. Sequence variation of 22 autosomal STR loci detected by next generation sequencing. Forensic Sci Int Genet 2015; 21:15-21. [PMID: 26701720 DOI: 10.1016/j.fsigen.2015.11.005] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/22/2015] [Accepted: 11/17/2015] [Indexed: 11/30/2022]
Abstract
Sequencing short tandem repeat (STR) loci allows for determination of repeat motif variations within the STR (or entire PCR amplicon) which cannot be ascertained by size-based PCR fragment analysis. Sanger sequencing has been used in research laboratories to further characterize STR loci, but is impractical for routine forensic use due to the laborious nature of the procedure in general and additional steps required to separate heterozygous alleles. Recent advances in library preparation methods enable high-throughput next generation sequencing (NGS) and technological improvements in sequencing chemistries now offer sufficient read lengths to encompass STR alleles. Herein, we present sequencing results from 183 DNA samples, including African American, Caucasian, and Hispanic individuals, at 22 autosomal forensic STR loci using an assay designed for NGS. The resulting dataset has been used to perform population genetic analyses of allelic diversity by length compared to sequence, and exemplifies which loci are likely to achieve the greatest gains in discrimination via sequencing. Within this data set, six loci demonstrate greater than double the number of alleles obtained by sequence compared to the number of alleles obtained by length: D12S391, D2S1338, D21S11, D8S1179, vWA, and D3S1358. As expected, repeat region sequences which had not previously been reported in forensic literature were identified.
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Affiliation(s)
- Katherine Butler Gettings
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
| | - Kevin M Kiesler
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
| | - Seth A Faith
- North Carolina State University, College of Veterinary Medicine and Forensic Science Institute, 1060 William Moore Drive, Raleigh, NC 27607, USA.
| | - Elizabeth Montano
- Battelle Memorial Institute, 505 King Avenue, Columbus, OH 43201, USA.
| | - Christine H Baker
- Battelle Memorial Institute, 505 King Avenue, Columbus, OH 43201, USA.
| | - Brian A Young
- Battelle Memorial Institute, 505 King Avenue, Columbus, OH 43201, USA.
| | | | - Peter M Vallone
- U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA.
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17
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Børsting C, Morling N. Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 2015; 18:78-89. [DOI: 10.1016/j.fsigen.2015.02.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/12/2015] [Accepted: 02/11/2015] [Indexed: 12/13/2022]
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18
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A novel set of DIP-STR markers for improved analysis of challenging DNA mixtures. Forensic Sci Int Genet 2015; 19:156-164. [PMID: 26232274 DOI: 10.1016/j.fsigen.2015.07.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 01/09/2023]
Abstract
Currently available molecular biology tools allow forensic scientists to characterize DNA evidence found at crime scenes for a large variety of samples, including those of limited quantity and quality, and achieve high levels of individualization. Yet, standard forensic markers provide limited or no results when applied to mixed DNA samples where the contributors are present in very different proportions (unbalanced DNA mixtures). This becomes an issue mostly for the analysis of trace samples collected on the victim or from touched objects. To this end, we recently proposed an innovative type of genetic marker, named DIP-STR that relies on pairing deletion/insertion polymorphisms (DIP) with standard short tandem repeats (STR). This novel compound marker allows detection of the minor DNA contributor in a DNA mixture of any gender and cellular origin with unprecedented resolution (beyond a DNA ratio of 1:1000). To provide a novel analytical tool useful in practice to common forensic laboratories, this article describes the first set of 10 DIP-STR markers selected according to forensic technical standards. The novel DIP-STR regions are short (between 146 and 271 bp), include only highly polymorphic tri-, tetra- and pentanucleotide tandem repeats and are located on different chromosomes or chromosomal arms to provide statistically independent results. This novel set of DIP-STR can target the amplification of 0.03-0.1 ng of DNA when mixed with a 1000-fold excess of major DNA. DIP-STR relative allele frequencies are estimated based on a survey of 103 Swiss individuals. Finally, this study provides an estimate of the occurrence of informative alleles and a calculation of the corresponding random match probability of the detected minor DIP-STR genotype assessed across 10,506 pairwise conceptual mixtures.
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19
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Olofsson JK, Mogensen HS, Buchard A, Børsting C, Morling N. Forensic and population genetic analyses of Danes, Greenlanders and Somalis typed with the Yfiler ® Plus PCR amplification kit. Forensic Sci Int Genet 2015; 16:232-236. [DOI: 10.1016/j.fsigen.2015.02.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/09/2015] [Accepted: 02/15/2015] [Indexed: 11/29/2022]
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20
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Fujii K, Iwashima Y, Kitayama T, Nakahara H, Mizuno N, Sekiguchi K. Validation of STR typing method using a PowerPlex Fusion System for forensic purposes. ACTA ACUST UNITED AC 2015. [DOI: 10.3408/jafst.683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Koji Fujii
- National Research Institute of Police Science
| | - Yasuki Iwashima
- Forensic Science Laboratory, Kyoto Prefectural Police H.Q
- National Research Institute of Police Science
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21
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Fordyce SL, Mogensen HS, Børsting C, Lagacé RE, Chang CW, Rajagopalan N, Morling N. Second-generation sequencing of forensic STRs using the Ion Torrent™ HID STR 10-plex and the Ion PGM™. Forensic Sci Int Genet 2015; 14:132-40. [DOI: 10.1016/j.fsigen.2014.09.020] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/20/2014] [Accepted: 09/23/2014] [Indexed: 01/07/2023]
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22
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Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples. Forensic Sci Int Genet 2014; 15:8-15. [PMID: 25438934 DOI: 10.1016/j.fsigen.2014.11.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/03/2014] [Indexed: 12/30/2022]
Abstract
Though shed hairs are one of the most commonly encountered evidence types, they are among the most limited in terms of DNA quantity and quality. As a result, DNA testing has historically focused on the recovery of just about 600 base pairs of the mitochondrial DNA control region. Here, we describe our success in recovering complete mitochondrial genome (mtGenome) data (∼16,569bp) from single shed hairs. By employing massively parallel sequencing (MPS), we demonstrate that particular hair samples yield DNA sufficient in quantity and quality to produce 2-3kb mtGenome amplicons and that entire mtGenome data can be recovered from hair extracts even without PCR enrichment. Most importantly, we describe a small amplicon multiplex assay comprised of sixty-two primer sets that can be routinely applied to the compromised hair samples typically encountered in forensic casework. In all samples tested here, the MPS data recovered using any one of the three methods were consistent with the control Sanger sequence data developed from high quality known specimens. Given the recently demonstrated value of complete mtGenome data in terms of discrimination power among randomly sampled individuals, the possibility of recovering mtGenome data from the most compromised and limited evidentiary material is likely to vastly increase the utility of mtDNA testing for hair evidence.
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23
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Børsting C, Fordyce SL, Olofsson J, Mogensen HS, Morling N. Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing. Forensic Sci Int Genet 2014; 12:144-54. [DOI: 10.1016/j.fsigen.2014.06.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 06/04/2014] [Accepted: 06/06/2014] [Indexed: 12/18/2022]
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24
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Scheible M, Loreille O, Just R, Irwin J. Short tandem repeat typing on the 454 platform: Strategies and considerations for targeted sequencing of common forensic markers. Forensic Sci Int Genet 2014; 12:107-19. [DOI: 10.1016/j.fsigen.2014.04.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/12/2014] [Accepted: 04/22/2014] [Indexed: 01/05/2023]
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25
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Phillips C, Gelabert-Besada M, Fernandez-Formoso L, García-Magariños M, Santos C, Fondevila M, Ballard D, Syndercombe Court D, Carracedo Á, Victoria Lareu M. “New turns from old STaRs”: Enhancing the capabilities of forensic short tandem repeat analysis. Electrophoresis 2014; 35:3173-87. [DOI: 10.1002/elps.201400095] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/25/2014] [Accepted: 05/15/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Christopher Phillips
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Miguel Gelabert-Besada
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Luis Fernandez-Formoso
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | | | - Carla Santos
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Manuel Fondevila
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - David Ballard
- Department of Forensic and Analytical Science; King's College London; London UK
| | | | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
- Center of Excellence in Genomic Medicine Research; King Abdulaziz University; Jeddah Saudi Arabia
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
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26
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Fujii K, Iwashima Y, Kitayama T, Nakahara H, Mizuno N, Sekiguchi K. Allele frequencies for 22 autosomal short tandem repeat loci obtained by PowerPlex Fusion in a sample of 1501 individuals from the Japanese population. Leg Med (Tokyo) 2014; 16:234-7. [DOI: 10.1016/j.legalmed.2014.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/03/2014] [Accepted: 03/25/2014] [Indexed: 10/25/2022]
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27
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Gelardi C, Rockenbauer E, Dalsgaard S, Børsting C, Morling N. Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles. Forensic Sci Int Genet 2014; 12:38-41. [PMID: 24893347 DOI: 10.1016/j.fsigen.2014.04.016] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/29/2014] [Accepted: 04/30/2014] [Indexed: 11/27/2022]
Abstract
Second generation sequencing (SGS) may revolutionize the field of forensic STR typing. Two of the essential requirements for implementation of an SGS based approach for forensic investigations are (1) establishment of adequate frequency databases and (2) adoption of a new STR nomenclature. We report the STR sequences and allele frequencies of three STR loci: D3S1358, D12S391 and D21S11 in 197 unrelated Danes. We used a new STR nomenclature that depicts the locus name used in forensic genetics, the length of the repeat region divided by the repeat length (typically 4 nucleotides) and detailed sequence information of possible sub-repeats and SNPs within the amplified fragment.
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Affiliation(s)
- Chiara Gelardi
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark; Faculty of Mathematical, Physical and Natural Sciences, University of Palermo, Palermo, Italy
| | - Eszter Rockenbauer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Sigrun Dalsgaard
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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28
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Kim EH, Jung SE, Shin KJ, Yang WI, Yang IS. Sequence Generation and Genotyping of 15 Autosomal STR Markers Using Next Generation Sequencing. ACTA ACUST UNITED AC 2014. [DOI: 10.7580/kjlm.2014.38.2.48] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eun Hye Kim
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
| | - Sang-Eun Jung
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
| | - Woo Ick Yang
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - In Seok Yang
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
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