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Huang J, Huang Y. A novel three-step DNA extraction method for mixed bloodstains. Electrophoresis 2024; 45:474-479. [PMID: 37946572 DOI: 10.1002/elps.202300094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Mixed DNA samples from at least two contributors can be present at a crime scene, which could be the most crucial piece of genetic evidence. The mixed stains in sexual assault cases are typically separated using differential lysis procedures (a two-step method). Blood mixed stains, however, are usually difficult to separate. In this work, we propose that a mixed stain comprises three layers, that is, (1) the upper layer which is primarily made up of cells from one contributor; (2) the middle layer which is a similar mixture from two contributors; and (3) the lower layer which primarily comprises cells from the other contributor. Based on this concept, a novel three-step DNA extraction method was proposed to solve the challenge involving bloodstains from two contributors. In the experiment, we extracted three layers DNA from mixed bloodstains using three steps. As a result, single-source DNA and approximate single-source DNA were detected from steps 1 and 3, respectively. This study demonstrates that the DNA from some mixed blood stains could be effectively separated following an appropriate extraction strategy, providing valuable insights, and serving as a reference for future examination of blood mixtures.
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Affiliation(s)
- Jian Huang
- Department of Forensic genetics, Brain Hospital of Hunan Province, The Second People's Hospital of Hunan Province, Changsha, P. R. China
| | - Yushong Huang
- Department of Forensic genetics, Brain Hospital of Hunan Province, The Second People's Hospital of Hunan Province, Changsha, P. R. China
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2
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Jäger R. New Perspectives for Whole Genome Amplification in Forensic STR Analysis. Int J Mol Sci 2022; 23:ijms23137090. [PMID: 35806097 PMCID: PMC9267064 DOI: 10.3390/ijms23137090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Modern PCR-based analytical techniques have reached sensitivity levels that allow for obtaining complete forensic DNA profiles from even tiny traces containing genomic DNA amounts as small as 125 pg. Yet these techniques have reached their limits when it comes to the analysis of traces such as fingerprints or single cells. One suggestion to overcome these limits has been the usage of whole genome amplification (WGA) methods. These methods aim at increasing the copy number of genomic DNA and by this means generate more template DNA for subsequent analyses. Their application in forensic contexts has so far remained mostly an academic exercise, and results have not shown significant improvements and even have raised additional analytical problems. Until very recently, based on these disappointments, the forensic application of WGA seems to have largely been abandoned. In the meantime, however, novel improved methods are pointing towards a perspective for WGA in specific forensic applications. This review article tries to summarize current knowledge about WGA in forensics and suggests the forensic analysis of single-donor bioparticles and of single cells as promising applications.
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Affiliation(s)
- Richard Jäger
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany;
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
- Institute of Safety and Security Research, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
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3
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Díaz-Rojas AR, Angeles-Estrada L, Pérez Vielma NM, Sánchez-Monroy V. Short tandem repeat (STR) instability in the oral mucosa of patients submitted to fixed orthodontic therapy: a limitation of STR profile quality for human identification. Forensic Sci Med Pathol 2022; 18:57-63. [PMID: 35098422 DOI: 10.1007/s12024-021-00451-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 11/26/2022]
Abstract
The purpose of this study was to evaluate changes in short tandem repeat (STR) profile quality before and after fixed orthodontic therapy. Samples of oral epithelial cells were obtained from 28 volunteers who had an indication for orthodontic treatment. The samples were collected before and three months after starting orthodontic treatment with fixed appliances. DNA extraction and integrity were evaluated by electrophoresis, and STR profiles were obtained by polymerase chain reaction amplification and STR typing via capillary electrophoresis. DNA electrophoresis showed a higher proportion (7/28, 25%) of DNA degradation in the samples collected after fixed orthodontic treatment compared to those obtained before starting orthodontic therapy (3/28, 11%), however, changes in DNA were not significant (p=0.289). In concordance all STR profiles showed complete genotyping; however, imbalances in the size of heterozygotes and in the signal were detected in 25% of STR profiles after orthodontic therapy. Moreover, STR instability was demonstrated by an increase in stutter bands detected in 60% of the DNA profiles after treatment and a spurious allele of the D195433 marker was found in one sample after treatment. The STR profiles of samples obtained from the oral cavity with orthodontic appliances should be interpreted with caution. STR instability increases the incidence of artifacts that could compromise the quality of the results of tests performed in forensic DNA laboratories.
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Affiliation(s)
- Arturo Rafael Díaz-Rojas
- Unidad de Especialidades Odontológicas, Secretaría de la Defensa Nacional, Estado de México, Mexico City, México
| | - Lucía Angeles-Estrada
- Unidad de Especialidades Odontológicas, Secretaría de la Defensa Nacional, Estado de México, Mexico City, México
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Estado de México, Naucalpan de Juárez, México
| | - Nadia Mabel Pérez Vielma
- Sección de Estudios de Posgrado e Investigación, Centro Interdisciplinario de Ciencias de la Salud Unidad Santo Tómas, Instituto Politécnico Nacional, Ciudad de México, México
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Vašek J, Čílová D, Melounová M, Svoboda P, Zdeňková K, Čermáková E, Ovesná J. OpiumPlex is a novel microsatellite system for profiling opium poppy (Papaver somniferum L.). Sci Rep 2021; 11:12799. [PMID: 34140548 PMCID: PMC8211840 DOI: 10.1038/s41598-021-91962-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Opium poppy (Papaver somniferum L.) is a versatile plant exploited by the pharmaceutical and food industries. Unfortunately, it is also infamously known as a source of highly addictive narcotics, primarily heroin. Drug abuse has devastating consequences for users and also has many direct or indirect negative impacts on human society as a whole. Therefore, developing a molecular genetic tool for the individualization of opium poppy, raw opium or heroin samples could help in the fight against the drug trade by retrieving more information about the source of narcotics and linking isolated criminal cases. Bioinformatic analysis provided insight into the distribution, density and other characteristics of roughly 150 thousand microsatellite loci within the poppy genome and indicated underrepresentation of microsatellites with the desired attributes. Despite this fact, 27 polymorphic STR markers, divided into three multiplexed assays, were developed in this work. Internal validation confirmed species-specific amplification, showed that the optimal amount of DNA is within the range of 0.625-1.25 ng per reaction, and indicate relatively well balanced assays according to the metrics used. Moreover, the stutter ratio (mean + 3 SD 2.28-15.59%) and allele-specific stutters were described. The analysis of 187 individual samples led to the identification of 158 alleles in total, with a mean of 5.85 alleles and a range of 3-14 alleles per locus. Most of the alleles (151) were sequenced by the Sanger method, which enabled us to propose standardized nomenclature and create three allelic ladders. The OpiumPlex system discriminates most of the varieties from each other and pharmaceutical varieties from the others (culinary, dual and ornamental).
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Affiliation(s)
- Jakub Vašek
- grid.15866.3c0000 0001 2238 631XDepartment of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Daniela Čílová
- grid.15866.3c0000 0001 2238 631XDepartment of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Martina Melounová
- grid.15866.3c0000 0001 2238 631XDepartment of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Pavel Svoboda
- grid.417626.00000 0001 2187 627XDivision of Crop Genetics and Breeding, Crop Research Institute, Prague, Czech Republic
| | - Kamila Zdeňková
- grid.448072.d0000 0004 0635 6059Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Eliška Čermáková
- grid.448072.d0000 0004 0635 6059Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Jaroslava Ovesná
- grid.417626.00000 0001 2187 627XDivision of Crop Genetics and Breeding, Crop Research Institute, Prague, Czech Republic
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Kim J, Yun W, Park YJ, Seo J, Lee RDW, Shin S, Lee HJ, Kim IS, Choi JR, Lee ST. Chimerism Assay Using Single Nucleotide Polymorphisms Adjacent and in Linkage-Disequilibrium Enables Sensitive Disease Relapse Monitoring after Hematopoietic Stem-Cell Transplantation. Clin Chem 2021; 67:781-787. [PMID: 33582770 DOI: 10.1093/clinchem/hvab010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/31/2020] [Indexed: 11/14/2022]
Abstract
BACKGROUND Short tandem repeat (STR)-based chimerism analysis has been widely used for chimerism monitoring after hematopoietic stem-cell transplantation (HSCT), but technical artifacts can be problematic. We designed a chimerism assay using single nucleotide polymorphisms (SNPs) adjacent and in linkage-disequilibrium (CASAL), which doubly checked for SNP pairs, and thus could reduce background errors and increase analytical sensitivity. METHODS CASAL targeted 84 SNP pairs within 10 bp distance and in perfect linkage-disequilibrium. Using undiluted and serially diluted samples, baseline error rates, and linearity was calculated. Clinical performance of CASAL was evaluated in comparison with a conventional STR assay, using 191 posttransplant samples from 42 patients with HSCT. RESULTS CASAL had ∼10 times lower baseline error rates compared to that of ordinary next-generation sequencing. Limit of detection and quantification of CASAL were estimated to be 0.09 and 0.39%, respectively, with a linear range of 0.1-100%. CASAL correlated well with STR assay (r2 = 0.99) and the higher sensitivity enabled detection of low-level recipient chimerism and earlier prediction of relapse. CONCLUSIONS CASAL is a simple, analytically sensitive and accurate assay that can be used in clinical samples after HSCT with a higher performance compared to that of traditional assays. It should also be useful in other forensic and archeological testing.
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Affiliation(s)
- JinJu Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Woobin Yun
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | - Yu Jin Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Department of Laboratory Medicine, Armed Forces Yangju Hospital, Gyeonggi-do, South Korea
| | - Jieun Seo
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | | | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyun-Ji Lee
- Department of Laboratory Medicine, Pusan National University, Yangsan Hospital, Yangsan, South Korea
| | - In Suk Kim
- Department of Laboratory Medicine, Pusan National University, School of Medicine, Pusan, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Dxome Co. Ltd, Seongnam-si, Gyeonggi-do, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
- Dxome Co. Ltd, Seongnam-si, Gyeonggi-do, South Korea
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Inokuchi S, Fujii K, Nakanishi H, Takada A, Saito K, Mizuno N. Modeling the minus two base pair stutter ratio of the D1S1656 locus: A sequence-based mixture distribution model. Forensic Sci Int Genet 2020; 51:102450. [PMID: 33387945 DOI: 10.1016/j.fsigen.2020.102450] [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: 07/23/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022]
Abstract
In this study, we propose a stutter ratio for a minus two base pair stutter (-2bpSR) model of the D1S1656 locus in capillary electrophoresis (CE)-based short tandem repeat (STR) typing. DNA from a total of 108 Japanese individuals was analyzed via massively parallel sequencing to investigate the length of the longest uninterrupted stretch of two base repeat motif (2bpLUS value) within repetitive structures involving the flanking region. Additionally, -2bpSR data was collected using the GlobalFiler Kit on a 3500xL Genetic Analyzer. As a result of sequencing analysis, all alleles were classified into two types by their 2bpLUS values. The -2bpSR differed significantly between the types. Then, we modeled the -2bpSR with a mixture log-normal distribution using the classification of alleles based on the 2bpLUS values. Furthermore, probabilities of the sequence type within each repeat number in the mixture log-normal distribution model were estimated using logistic regression for each of the five major detected populations. This study is expected to enable interpretation of STR typing while considering minus two base pair stutter at the D1S1656 locus.
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Affiliation(s)
- Shota Inokuchi
- Department of Forensic Medicine, Graduate School of Medicne, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan; National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, Japan; Forensic Science Laboratory, Tokyo Metropolitan Police Department, 3-35-21 Shakujiidai, Nerima-ku, Tokyo, Japan.
| | - Koji Fujii
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, Japan
| | - Hiroaki Nakanishi
- Department of Forensic Medicine, Graduate School of Medicne, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, 38 Moroyamamachimorohongo, Saitama, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Graduate School of Medicne, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan; Department of Forensic Medicine, Saitama Medical University, 38 Moroyamamachimorohongo, Saitama, Japan
| | - Natsuko Mizuno
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, Japan
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A reference allelic ladder for Western Capercaillie (Tetrao urogallus) and Black Grouse (Tetrao tetrix) enables linking grouse genetic data across studies. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractRapid anthropogenic climate change and progressing habitat degradation are considered top threats to biodiversity. The employment of demanding umbrella species as indicators for ecosystem health is a popular and cost-effective strategy that facilitates continuous monitoring and evaluation within a long-term conservation management scheme. The Western Capercaillie (Tetrao urogallus) and the Black Grouse (Tetrao tetrix) are both considered viable candidates due to their extensive habitat requirements, the possibility for conservative, non-invasive sampling, and their broad popular appeal. Regional population surveys based on genetic data from Short Sequence Repeat (SSR) analysis are being conducted throughout the Palearctic. However, to ensure reliable comparability among laboratories, standardization is required. Here, we report a catalogue of fifty fully characterized reference alleles from twelve SSR loci and the construction of a customizable allelic ladder for genotyping and individualization in Western Capercaillie and Black Grouse. This methodological improvement will help to cost-efficiently generate and collate supraregional data from different grouse surveys and thereby contribute to conservation management. Reference alleles and ladders can be obtained on demand.
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Machida M, Kibayashi K. Effectiveness of whole genome amplification prior to short tandem repeat analysis for degraded DNA. Forensic Sci Int Genet 2020; 49:102373. [PMID: 32871489 DOI: 10.1016/j.fsigen.2020.102373] [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: 07/07/2020] [Accepted: 08/14/2020] [Indexed: 01/27/2023]
Abstract
Short tandem repeat (STR) analysis is prone to failure as DNA is frequently damaged by various environmental factors; hence, increasing the number of starting templates may constitute a feasible approach to improve STR profiling success. Whole genome amplification (WGA) is often applied to bolster starting template quantity. Moreover, WGA can reportedly be used on degraded DNA samples in forensics. Therefore, we utilized a PCR-based WGA method, termed "modified improved primer extension preamplification" (mIPEP), prior to STR analysis of degraded DNA, as this method is less affected by DNA quantity and quality than most others. Saliva from four volunteers was dried on glass fiber filter papers (paper) and glass slides (glass) and irradiated with UVA light (365 nm). The mIPEP method was initiated using 5, 0.5, and 0.05 ng of DNA following DNA extraction. The DNA degradation index (DI) was calculated based on the ratio of 129 to 41 bp DNA fragments; lower numbers indicate higher degradation. Following mIPEP, STR analysis was performed using the AmpFlSTR Identifiler PCR amplification kit. The number of detectable STR loci, with and without mIPEP, decreased according to reduced DI in a different manner for the various DNA concentrations extracted from paper and glass. Specifically, for the 5 ng DNA sample on paper, at a DI < 0.2, the number of detectable STR loci was greater with mIPEP than without it, owing to fewer locus drop-outs. Similarly, the 0.05 ng DNA sample deposited on paper, at DI ≥ 0.7, exhibited higher numbers of detectable STR loci when prepared using mIPEP owing to fewer allele drop-outs. Moreover, among samples deposited on glass, the 0.05 ng DNA sample at DI ≥ 0.4 afforded a larger number of detectable STR loci when prepared using mIPEP than those without mIPEP, owing to fewer locus drop-outs. These findings suggest that performing mIPEP in accordance with sample DNA condition (e.g., quantity and quality) may lead to increased success of STR analysis. Notably, the conditions identified as most responsive to mIPEP were consistent across both UVA-irradiated and environmentally-damaged sample states. Taken together, our results suggest that applying mIPEP would be beneficial to obtain improved STR profiles under conditions involving severely degraded samples with large quantities of DNA, or with small quantities of DNA albeit with slight degradation.
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Affiliation(s)
- Mitsuyo Machida
- Department of Legal Medicine, School of Medicine, Tokyo Women's Medical University, Tokyo 162-8666, Japan.
| | - Kazuhiko Kibayashi
- Department of Legal Medicine, School of Medicine, Tokyo Women's Medical University, Tokyo 162-8666, Japan
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9
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Understanding the characteristics of sequence-based single-source DNA profiles. Forensic Sci Int Genet 2020; 44:102192. [DOI: 10.1016/j.fsigen.2019.102192] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/17/2019] [Accepted: 10/20/2019] [Indexed: 01/18/2023]
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10
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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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Fujii K, Fukagawa T, Watahiki H, Mita Y, Kitayama T, Mizuno N. Ratios and distances of pull-up peaks observed in GlobalFiler kit data. Leg Med (Tokyo) 2018; 34:58-63. [PMID: 30193238 DOI: 10.1016/j.legalmed.2018.08.005] [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: 03/02/2018] [Revised: 07/12/2018] [Accepted: 08/22/2018] [Indexed: 10/28/2022]
Abstract
Short tandem repeat (STR) analysis is widely used for forensic examinations with a capillary electrophoresis instrument such as the 3500xL Genetic Analyzer. This instrument adapts multi-locus STR kits to examine up to 27 loci using a 6-fluorescent dye system and corrects the spectral overlap between each dye. However, inaccurate spectral correction can cause pull-up peaks. Here, we examined the pull-up peaks observed in GlobalFiler kit data in terms of their peak height ratios and distances from their parent allele peaks when using the 3500xL and the 3130xl Genetic Analyzers. With the 3500xL, 546 pull-up peaks were observed, and their pull-up ratios averaged 1.03 ± 0.32% (range 0.260-2.80%). Of the 546 pull-up peaks, 534 peaks (97.8%) were within ±1 bp from their parent allele peaks. Overall, the pull-up peaks toward adjacent shorter wavelength channels (e.g., from yellow to green) tended to be observed in the left side (shorter bp) of the corresponding parent allele peaks, and the opposite side tendency was observed for those pull-up peaks toward adjacent longer wavelength channels. These tendencies were also observed in the GlobalFiler data generated with the 3130xl and in the data obtained by injecting a J6 matrix standard with LIZ 500 or 600 v2 size standard into the 3500xL and 3130xl. Inspection of raw data revealed that the shift of pull-up peaks from their parent allele peaks was derived from sigmoid, pull-down, or slightly shifted pull-up shapes. Based on the obtained data, we propose a standard for assessment of questionable pull-up peaks.
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Affiliation(s)
- Koji Fujii
- Fourth Biology Section, 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.
| | - Takashi Fukagawa
- Fourth Biology Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Haruhiko Watahiki
- Fourth Biology Section, 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
| | - Yusuke Mita
- Fourth Biology Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tetsushi Kitayama
- Fourth Biology Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- Fourth Biology Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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12
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Hirata S, Kojima K, Misawa K, Gervais O, Kawai Y, Nagasaki M. Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population. Heliyon 2018; 4:e00625. [PMID: 29872759 PMCID: PMC5986539 DOI: 10.1016/j.heliyon.2018.e00625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/22/2018] [Accepted: 05/08/2018] [Indexed: 11/29/2022] Open
Abstract
Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.
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Affiliation(s)
- Satoshi Hirata
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Kaname Kojima
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Kazuharu Misawa
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Olivier Gervais
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Yosuke Kawai
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Masao Nagasaki
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
- Corresponding author.
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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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14
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Oldoni F, Castella V, Grosjean F, Hall D. Sensitive DIP-STR markers for the analysis of unbalanced mixtures from “touch” DNA samples. Forensic Sci Int Genet 2017; 28:111-117. [DOI: 10.1016/j.fsigen.2017.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/27/2017] [Accepted: 02/09/2017] [Indexed: 01/31/2023]
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15
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Moore D, Clayton T, Thomson J. Description of artefacts in the PowerPlex Y23(®) system associated with excessive quantities of background female DNA. Forensic Sci Int Genet 2016; 24:44-50. [PMID: 27288717 DOI: 10.1016/j.fsigen.2016.05.009] [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: 12/21/2015] [Revised: 05/06/2016] [Accepted: 05/14/2016] [Indexed: 10/21/2022]
Abstract
Male on female sexual assault cases that involve azoospermic individuals, those where the male has penetrated but failed to ejaculate, those where there has been an extended interval between the sexual assault and sample collection or where there has been only digital penetration are often difficult to investigate by employing traditional autosomal STR testing. Such cases often involve minimal amounts of male DNA either being deposited initially or remaining after the passage of time. These cases are often further complicated by the presence of large amounts of female DNA compared to the relatively small amounts of male DNA on the intimate samples taken. Y-STR kits provide a solution that allows targeting of male DNA in a mixed male/female sample. However, large quantities of excess female DNA have the potential to generate non-specific artefact peaks. Here we characterise a number of previously reported artefacts observed in the PowerPlex(®) Y23 system. We demonstrate that some of these artefacts can impact on profile interpretation and that they are highly dependent on the levels of female DNA present. These artefacts have been characterised to assist practitioners with the interpretation of such samples.
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16
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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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17
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SkydancerPlex: A novel STR multiplex validated for forensic use in the hen harrier (Circus cyaneus). Forensic Sci Int Genet 2016; 22:100-109. [PMID: 26881329 DOI: 10.1016/j.fsigen.2016.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 11/21/2022]
Abstract
The hen harrier (Circus cyaneus) is a bird of prey which is heavily persecuted in the UK because it preys on the game bird red grouse (Lagopus lagopus scoticus). To help investigations into illegal killings of hen harrier, a STR multiplex kit containing eight short tandem repeat (STR) markers and a chromohelicase DNA binding protein 1 (CHD 1) sexing marker was developed. The multiplex kit was tested for species specificity, sensitivity, robustness, precision, accuracy and stability. Full profiles were obtained with as little as 0.25 ng of template DNA. Concurrent development of an allelic ladder to ensure reliable and accurate allele designation across laboratories makes the SkydancerPlex the first forensic DNA profiling system in a species of wildlife to be fully validated according to SWGDAM and ISFG recommendations. An average profile frequency of 3.67 × 10(-8), a PID estimate of 5.3 × 10(-9) and a PID-SIB estimate of 9.7 × 10(-4) make the SkydancerPlex an extremely powerful kit for individualisation.
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Tsai LC, Lee CC, Chen CC, Lee JCI, Wang SM, Huang NE, Linacre A, Hsieh HM. The Influence of Selected Fingerprint Enhancement Techniques on Forensic DNA Typing of Epithelial Cells Deposited on Porous Surfaces. J Forensic Sci 2015; 61 Suppl 1:S221-5. [PMID: 26259019 DOI: 10.1111/1556-4029.12893] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 12/09/2014] [Accepted: 12/30/2014] [Indexed: 11/28/2022]
Abstract
Fingerprints deposited at crime scene can be a source of DNA. Previous reports on the effects of fingerprint enhancement methods have focused mainly on fingermarks deposited in blood or saliva. Here, we evaluate the effects of fingerprint enhancement methods on fingerprints deposited on porous surfaces. We performed real-time quantification and STR typing, the results of which indicated that two methods (iodine fuming and 1,2-indanedione in ethyl acetate enhancement) had no effect on the quantity of DNA isolated and resultant STR alleles when compared to control samples. DNA quantities and allele numbers were lower for samples enhanced with silver nitrate and 1,2-indanedione in acetic acid when compared to control samples. Based on DNA quantity, quality, and observable stochastic effects, our data indicated that iodine fuming and 1,2-indanedione in ethyl acetate were the preferred options for the enhancement of fingerprints on porous surfaces.
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Affiliation(s)
- Li-Chin Tsai
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan
| | - Cheng-Chang Lee
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan.,Forensic Science Center, New Taipei City Police Department, No. 32, Fuzhong Rd., Banqiao District, New Taipei City, 22005, Taiwan
| | - Chun-Chieh Chen
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan.,Forensic Science Section, Changhua County Police Bureau, 778, Sec. 2, Jhong-jheng Rd., Changhua City, 50004, Taiwan
| | - James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No. 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan
| | - Sheng-Meng Wang
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan
| | - Nu-En Huang
- Forensic Science Center, New Taipei City Police Department, No. 32, Fuzhong Rd., Banqiao District, New Taipei City, 22005, Taiwan
| | - Adrian Linacre
- School of Biological Sciences, Flinders University, Adelaide, SA, 5001, Australia
| | - Hsing-Mei Hsieh
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan
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19
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Gill P, Haned H, Bleka O, Hansson O, Dørum G, Egeland T. Genotyping and interpretation of STR-DNA: Low-template, mixtures and database matches-Twenty years of research and development. Forensic Sci Int Genet 2015; 18:100-17. [PMID: 25866376 DOI: 10.1016/j.fsigen.2015.03.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 03/19/2015] [Accepted: 03/24/2015] [Indexed: 12/17/2022]
Abstract
The introduction of Short Tandem Repeat (STR) DNA was a revolution within a revolution that transformed forensic DNA profiling into a tool that could be used, for the first time, to create National DNA databases. This transformation would not have been possible without the concurrent development of fluorescent automated sequencers, combined with the ability to multiplex several loci together. Use of the polymerase chain reaction (PCR) increased the sensitivity of the method to enable the analysis of a handful of cells. The first multiplexes were simple: 'the quad', introduced by the defunct UK Forensic Science Service (FSS) in 1994, rapidly followed by a more discriminating 'six-plex' (Second Generation Multiplex) in 1995 that was used to create the world's first national DNA database. The success of the database rapidly outgrew the functionality of the original system - by the year 2000 a new multiplex of ten-loci was introduced to reduce the chance of adventitious matches. The technology was adopted world-wide, albeit with different loci. The political requirement to introduce pan-European databases encouraged standardisation - the development of European Standard Set (ESS) of markers comprising twelve-loci is the latest iteration. Although development has been impressive, the methods used to interpret evidence have lagged behind. For example, the theory to interpret complex DNA profiles (low-level mixtures), had been developed fifteen years ago, but only in the past year or so, are the concepts starting to be widely adopted. A plethora of different models (some commercial and others non-commercial) have appeared. This has led to a confusing 'debate' about the 'best' to use. The different models available are described along with their advantages and disadvantages. A section discusses the development of national DNA databases, along with details of an associated controversy to estimate the strength of evidence of matches. Current methodology is limited to searches of complete profiles - another example where the interpretation of matches has not kept pace with development of theory. STRs have also transformed the area of Disaster Victim Identification (DVI) which frequently requires kinship analysis. However, genotyping efficiency is complicated by complex, degraded DNA profiles. Finally, there is now a detailed understanding of the causes of stochastic effects that cause DNA profiles to exhibit the phenomena of drop-out and drop-in, along with artefacts such as stutters. The phenomena discussed include: heterozygote balance; stutter; degradation; the effect of decreasing quantities of DNA; the dilution effect.
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Affiliation(s)
- Peter Gill
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway; Department of Forensic Medicine, Sognsvannsveien 20, Rikshospitalet, 0372 Oslo, Norway.
| | - Hinda Haned
- Netherlands Forensic Institute, Department of Human Biological Traces, The Hague, The Netherlands
| | - Oyvind Bleka
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway
| | - Oskar Hansson
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway
| | - Guro Dørum
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Aas, Norway
| | - Thore Egeland
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Aas, Norway
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20
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Abstract
Whole genome amplification (WGA) is a widely used molecular technique that is becoming increasingly necessary in genetic research on a range of sample types including individual cells, fossilized remains and entire ecosystems. Multiple methods of WGA have been developed, each with specific strengths and weaknesses, but with a common defect in that each method distorts the initial template DNA during the course of amplification. The type, extent, and circumstance of the bias vary with the WGA method and particulars of the template DNA. In this review, we endeavor to discuss the types of bias introduced, the susceptibility of common WGA techniques to these bias types, and the interdependence between bias and characteristics of the template DNA. Finally, we attempt to illustrate some of the criteria specific to the analytical platform and research application that should be considered to enable combination of the appropriate WGA method, template DNA, sequencing platform, and intended use for optimal results.
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Affiliation(s)
| | - John H Leamon
- CyVek Inc., 2 Barnes Industrial Road South, Wallingford, CT, 06492, USA.
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21
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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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22
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Murigneux V, Dufour AB, Lobry JR, Pène L. Analysis of Positive Control STR Experiments Reveals that Results Obtained for FGA, D3S1358, and D13S317 Condition the Success Rate of the Analysis of Routine Reference Samples. J Forensic Sci 2014; 59:1074-9. [DOI: 10.1111/1556-4029.12360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 01/21/2013] [Accepted: 02/09/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Valentine Murigneux
- Laboratoire de Police Scientifique de Lyon; Institut National de Police Scientifique; F-69134 Ecully France
| | - Anne-Béatrice Dufour
- Université de Lyon; F-69000 Lyon France
- Université Lyon 1; F-69622 Villeurbanne France
- Laboratoire de Biométrie et Biologie Evolutive; CNRS, UMR5558; F-69622 Villeurbanne France
| | - Jean R. Lobry
- Laboratoire de Police Scientifique de Lyon; Institut National de Police Scientifique; F-69134 Ecully France
| | - Laurent Pène
- Laboratoire de Police Scientifique de Lyon; Institut National de Police Scientifique; F-69134 Ecully France
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23
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Chen JW, Uboh CE, Soma LR, You Y, Jiang Z, Li X, Guan F, Liu Y. Identification of sample donor by 24-plex short tandem repeat in a post-race equine plasma containing dexamethasone. SPRINGERPLUS 2014; 3:94. [PMID: 24600547 PMCID: PMC3935034 DOI: 10.1186/2193-1801-3-94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/14/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Animal sport such as horseracing is tainted with drug abuse as are human sports. Treatment of racehorses on race day with therapeutic medications in most cases is banned, and thus, it is essential to monitor the illicit use of drugs in the racing horse to maintain integrity of racing, ensure fair competition and protect the health, safety and welfare of the horse, jockeys and drivers. In the event of a dispute over the identity of the sample donor, if the regulator can provide evidence that the DNA genotype profile of the post-race sample matched that of the alleged donor, then the potential drug violation case might be easily resolved without legal challenges. CASE DESCRIPTION We present a case study of a racehorse sample that tested positive for dexamethasone in a post-race plasma sample in Pennsylvania (PA) but the result was challenged by the trainer of the horse. Dexamethasone is a synthetic glucocorticoid widely used in the management of musculoskeletal problems in horses but its presence in the horse during competition is banned by the PA Racing Commissions. The presence of dexamethasone in the post-competition plasma sample was confirmed using liquid chromatography-tandem mass spectrometry. However, this finding was challenged by the trainer of the horse alleging that the post-race sample was not collected from his/her horse and thus petitioned the Commission to be absolved of any wrong-doing. To resolve the dispute, a DNA test was ordered by the PA Racing Commission to identify the correct donor of the dexamethasone positive sample. For this purpose, a 24-plex short tandem repeat analysis to detect 21 equine markers and three human markers was employed. The results indicated that all the samples tested had identical DNA profiles and thus, it was concluded that the samples were collected from the same horse and that the probability of drawing a false conclusion was approximately zero (1.5 × 10(-15)). CONCLUSIONS The plasma sample confirmed for the presence of dexamethasone was collected from the alleged horse.
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Affiliation(s)
- Jin-Wen Chen
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Cornelius E Uboh
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA ; Pennsylvania Equine Toxicology & Research Center, Department of Chemistry, West Chester University, 220 E Rosedale Avenue, West Chester, PA 19382 USA
| | - Lawrence R Soma
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Youwen You
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Zibin Jiang
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Xiaoqing Li
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Fuyu Guan
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
| | - Ying Liu
- University of Pennsylvania School of Veterinary Medicine, New Bolton Center Campus, 382 West Street Road, Kennett Square, PA 19348 USA
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24
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Pascali VL, Merigioli S. ‘Stochastic’ effects at balanced mixtures: A calibration study. Forensic Sci Int Genet 2014; 8:113-25. [DOI: 10.1016/j.fsigen.2013.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 05/23/2013] [Accepted: 06/13/2013] [Indexed: 10/26/2022]
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25
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Mameli A, Piras G, Delogu G. The Successful Recovery of Low Copy Number and Degraded DNA from Bones Exposed to Seawater Suitable for Generating a DNA STR Profile. J Forensic Sci 2013; 59:470-3. [DOI: 10.1111/1556-4029.12323] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 11/25/2012] [Accepted: 12/16/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Alessandro Mameli
- Reparto Investigazioni Scientifiche Carabinieri di Cagliari; Piazza San Bartolomeo 29 09126 Cagliari Italy
| | - Gavino Piras
- Reparto Investigazioni Scientifiche Carabinieri di Cagliari; Piazza San Bartolomeo 29 09126 Cagliari Italy
| | - Giovanni Delogu
- Reparto Investigazioni Scientifiche Carabinieri di Cagliari; Piazza San Bartolomeo 29 09126 Cagliari Italy
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Kirkham A, Haley J, Haile Y, Grout A, Kimpton C, Al-Marzouqi A, Gill P. High-throughput analysis using AmpFlSTR® Identifiler® with the Applied Biosystems 3500xl Genetic Analyser. Forensic Sci Int Genet 2013; 7:92-7. [DOI: 10.1016/j.fsigen.2012.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 07/02/2012] [Accepted: 07/07/2012] [Indexed: 11/30/2022]
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Manabe S, Mori Y, Kawai C, Ozeki M, Tamaki K. Mixture interpretation: Experimental and simulated reevaluation of qualitative analysis. Leg Med (Tokyo) 2012; 15:66-71. [PMID: 23089142 DOI: 10.1016/j.legalmed.2012.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/09/2012] [Accepted: 09/11/2012] [Indexed: 11/29/2022]
Abstract
We present here analytical data using the 15 STR typing (Identifiler) kit regarding heterozygote balance in experimental DNA samples including one or two persons. Surprisingly, the allelic imbalance was observed even in samples consisting of only one person but adequate DNA for the standard protocol. The variance of heterozygote balance was more expanded in two-person mixtures than in one-person samples. Therefore, it is not suitable to use allelic peak heights/areas for estimating the genotypes of the contributors such as the quantitative analysis. We also reevaluated the effectiveness of qualitative analysis by simulation, i.e. consideration of the probability of all possible genotype combinations from the typing results of a mixed DNA sample. As demonstrated, the qualitative analysis using 15 STR loci is still extremely effective even in a mixture from two or three individuals.
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Affiliation(s)
- Sho Manabe
- Department of Forensic Medicine and Molecular Pathology, Kyoto University, Graduate School of Medicine, Kyoto 606-8501, Japan
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28
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Tvedebrink T, Mogensen HS, Stene MC, Morling N. Performance of two 17 locus forensic identification STR kits—Applied Biosystems's AmpFℓSTR® NGMSElect™ and Promega's PowerPlex® ESI17 kits. Forensic Sci Int Genet 2012; 6:523-31. [DOI: 10.1016/j.fsigen.2011.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/21/2011] [Accepted: 12/27/2011] [Indexed: 10/14/2022]
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29
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Westen AA, Haned H, Grol LJW, Harteveld J, van der Gaag KJ, de Knijff P, Sijen T. Combining results of forensic STR kits: HDplex validation including allelic association and linkage testing with NGM and Identifiler loci. Int J Legal Med 2012; 126:781-9. [DOI: 10.1007/s00414-012-0724-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/12/2012] [Indexed: 10/28/2022]
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30
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Andreassen R, Schregel J, Kopatz A, Tobiassen C, Knappskog PM, Hagen SB, Kleven O, Schneider M, Kojola I, Aspi J, Rykov A, Tirronen KF, Danilov PI, Eiken HG. A forensic DNA profiling system for Northern European brown bears (Ursus arctos). Forensic Sci Int Genet 2012; 6:798-809. [PMID: 22483764 DOI: 10.1016/j.fsigen.2012.03.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 02/10/2012] [Accepted: 03/11/2012] [Indexed: 11/29/2022]
Abstract
A set of 13 dinucleotide STR loci (G1A, G10B, G1D, G10L, MU05, MU09, MU10, MU15, MU23, MU26, MU50, MU51, MU59) were selected as candidate markers for a DNA forensic profiling system for Northern European brown bear (Ursus arctos). We present results from validation of the markers with respect to their sensitivity, species specificity and performance (precision, heterozygote balance and stutter ratios). All STRs were amplified with 0.6ng template input, and there were no false bear genotypes in the cross-species amplification tests. The validation experiments showed that stutter ratios and heterozygote balance was more pronounced than in the tetranucleotide loci used in human forensics. The elevated ratios of stutter and heterozygote balance at the loci validated indicate that these dinucleotide STRs are not well suited for interpretation of individual genotypes in mixtures. Based on the results from the experimental validations we discuss the challenges related to genotyping dinucleotide STRs in single source samples. Sequence studies of common alleles showed that, in general, the size variation of alleles corresponded with the variation in number of repeats. The samples characterized by sequence analysis may serve as standard DNA samples for inter laboratory calibration. A total of 479 individuals from eight Northern European brown bear populations were analyzed in the 13 candidate STRs. Locus MU26 was excluded as a putative forensic marker after revealing large deviations from expected heterozygosity likely to be caused by null-alleles at this locus. The remaining STRs did not reveal significant deviations from Hardy-Weinberg equilibrium expectations except for loci G10B and MU10 that showed significant deviations in one population each, respectively. There were 9 pairwise locus comparisons that showed significant deviation from linkage equilibrium in one or two out of the eight populations. Substantial genetic differentiation was detected in some of the pairwise population comparisons and the average estimate of population substructure (F(ST)) was 0.09. The average estimate of inbreeding (F(IS)) was 0.005. Accounting for population substructure and inbreeding the total average probability of identity in each of the eight populations was lower than 1.1×10(-9) and the total average probability of sibling identity was lower than 1.3×10(-4). The magnitude of these measurements indicates that if applying these twelve STRs in a DNA profiling system this would provide individual specific evidence.
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Affiliation(s)
- R Andreassen
- Faculty of Health Sciences, Oslo and Akershus University College, Oslo, Norway.
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31
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Puch-Solis R, Kirkham A, Gill P, Read J, Watson S, Drew D. Practical determination of the low template DNA threshold. Forensic Sci Int Genet 2011; 5:422-7. [DOI: 10.1016/j.fsigen.2010.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 08/12/2010] [Accepted: 09/01/2010] [Indexed: 11/29/2022]
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32
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Neumann C, Ramotowski R, Genessay T. Forensic examination of ink by high-performance thin layer chromatography—The United States Secret Service Digital Ink Library. J Chromatogr A 2011; 1218:2793-811. [DOI: 10.1016/j.chroma.2010.12.070] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 12/12/2010] [Accepted: 12/14/2010] [Indexed: 11/30/2022]
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33
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Characterising stutter in forensic STR multiplexes. Forensic Sci Int Genet 2011; 6:58-63. [PMID: 21388903 DOI: 10.1016/j.fsigen.2011.02.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/23/2010] [Accepted: 02/01/2011] [Indexed: 11/20/2022]
Abstract
Stutter is an artefact seen when amplifying short tandem repeats and typically occurs at one repeat unit shorter in length than the parent allele. In forensic analysis, stutter complicates the analysis of DNA profiles from multiple contributors, known as mixed profiles, a common profile type. Consequently it is important to both understand and predict stutter behaviour in order to improve our understanding of the resolution and interpretation of these profiles. Whilst stutter is well recognised and documented, little information is available that identifies and quantifies what influences the formation of stutter. In this work we use a novel approach to examine this. We have used synthetic oligonucleotides comprising multiple repeat units to test; the influence of repeat number, the influence of repeat sequence and the impact of interruptions to the repeat sequence length. Using multiple replicates allows detailed statistical analysis. We have confirmed a linear relationship between stutter ratio and repeat number. We have shown that increased A-T content increases stutter ratio and that interruptions in repeating sequences decreased stutter ratios to levels similar to the longest uninterrupted repeat stretch. We also found that there was no relationship between stutter ratio and repeat number for a repeat unit with an A-T content of 1/4 and that half of the interrupted repeat sequences stuttered significantly less than their longest uninterrupted repeat stretches. We have applied the knowledge gained to examine specific features of the loci present in the AmpFlSTR(®) SGM Plus(®) multiplex kit used in our laboratory.
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34
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Petricevic S, Whitaker J, Buckleton J, Vintiner S, Patel J, Simon P, Ferraby H, Hermiz W, Russell A. Validation and development of interpretation guidelines for low copy number (LCN) DNA profiling in New Zealand using the AmpFlSTR® SGM Plus™ multiplex. Forensic Sci Int Genet 2010; 4:305-10. [DOI: 10.1016/j.fsigen.2009.11.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 10/30/2009] [Accepted: 11/14/2009] [Indexed: 11/29/2022]
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35
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Hong YL, Lee HJ, Lee JW. Interpreting Mixtures Using Allele Peak Areas. KOREAN JOURNAL OF APPLIED STATISTICS 2010. [DOI: 10.5351/kjas.2010.23.1.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Rho SY. Technical Improvements of the Projection of Household Health Care Expenditure. KOREAN JOURNAL OF APPLIED STATISTICS 2010. [DOI: 10.5351/kjas.2010.23.1.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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38
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Neumann C, Margot P. New perspectives in the use of ink evidence in forensic science: Part I. Development of a quality assurance process for forensic ink analysis by HPTLC. Forensic Sci Int 2009; 185:29-37. [DOI: 10.1016/j.forsciint.2008.11.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2007] [Revised: 11/23/2008] [Accepted: 11/29/2008] [Indexed: 11/26/2022]
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39
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Gill P, Puch-Solis R, Curran J. The low-template-DNA (stochastic) threshold—Its determination relative to risk analysis for national DNA databases. Forensic Sci Int Genet 2009; 3:104-11. [DOI: 10.1016/j.fsigen.2008.11.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 09/10/2008] [Accepted: 11/03/2008] [Indexed: 10/21/2022]
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40
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Howard C, Gilmore S, Robertson J, Peakall R. Developmental validation of a Cannabis sativa STR multiplex system for forensic analysis. J Forensic Sci 2008; 53:1061-7. [PMID: 18624889 DOI: 10.1111/j.1556-4029.2008.00792.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A developmental validation study based on recommendations of the Scientific Working Group on DNA Analysis Methods (SWGDAM) was conducted on a multiplex system of 10 Cannabis sativa short tandem repeat loci. Amplification of the loci in four multiplex reactions was tested across DNA from dried root, stem, and leaf sources, and DNA from fresh, frozen, and dried leaf tissue with a template DNA range of 10.0-0.01 ng. The loci were amplified and scored consistently for all DNA sources when DNA template was in the range of 10.0-1.0 ng. Some allelic dropout and PCR failure occurred in reactions with lower template DNA amounts. Overall, amplification was best using 10.0 ng of template DNA from dried leaf tissue indicating that this is the optimal source material. Cross species amplification was observed in Humulus lupulus for three loci but there was no allelic overlap. This is the first study following SWGDAM validation guidelines to validate short tandem repeat markers for forensic use in plants.
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Affiliation(s)
- Christopher Howard
- School of Botany and Zoology, The Australian National University, Canberra, Australia
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41
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Power T, McCabe B, Harbison SA. FaSTR DNA: A new expert system for forensic DNA analysis. Forensic Sci Int Genet 2008; 2:159-65. [DOI: 10.1016/j.fsigen.2007.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 10/17/2007] [Accepted: 11/15/2007] [Indexed: 11/26/2022]
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42
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Graham EAM, Bowyer VL, Martin VJ, Rutty GN. Investigation into the usefulness of DNA profiling of earprints. Sci Justice 2008; 47:155-9. [PMID: 18229756 DOI: 10.1016/j.scijus.2007.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA profiling of biological trace evidence has been used for many years. The application of this technique specifically to the DNA profiling of earprints has not to date been thoroughly investigated. This report presents the results of 60 earprints collected from three healthy adult volunteers under controlled laboratory conditions. DNA profile analysis revealed that high levels of non-donor alleles are observed when earprints are collected for DNA profiling. The source of these non-donor alleles is investigated and the impact that their presence within the profile may have on the use of this technique is discussed.
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Affiliation(s)
- E A M Graham
- Forensic Pathology Unit, University of Leicester, Robert Kilpatrick Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
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43
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Gill P, Curran J, Neumann C, Kirkham A, Clayton T, Whitaker J, Lambert J. Interpretation of complex DNA profiles using empirical models and a method to measure their robustness. Forensic Sci Int Genet 2008; 2:91-103. [DOI: 10.1016/j.fsigen.2007.10.160] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Revised: 09/03/2007] [Accepted: 10/09/2007] [Indexed: 12/01/2022]
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44
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Abstract
Although not directly related, circumstances do occur in forensic investigations whereby cancer studies and forensic science cross paths. This review takes a look at the circumstances under which this may occur, and investigates some potential problems that can arise when tumor tissue is submitted for DNA profile analysis. A background to the underlying molecular biology of tumors is described, highlighting the genetic instabilities that are observed in DNA sequences of similar or identical primary structure to the short tandem repeat markers used in forensic DNA profiling kits.
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45
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Wang T, Xue N, Birdwell JD. Least-Square Deconvolution: A Framework for Interpreting Short Tandem Repeat Mixtures. J Forensic Sci 2006; 51:1284-97. [PMID: 17199614 DOI: 10.1111/j.1556-4029.2006.00268.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interpreting mixture short tandem repeat DNA data is often a laborious process, involving trying different genotype combinations mixed at assumed DNA mass proportions, and assessing whether the resultant is supported well by the relative peak-height information of the mixture sample. If a clear pattern of major-minor alleles is apparent, it is feasible to identify the major alleles of each locus and form a composite genotype profile for the major contributor. When alleles are shared between the two contributors, and/or heterozygous peak imbalance is present, it becomes complex and difficult to deduce the profile of the minor contributor. The manual trial and error procedures performed by an analyst in the attempt to resolve mixture samples have been formalized in the least-square deconvolution (LSD) framework reported here for two-person mixtures, with the allele peak height (or area) information as its only input. LSD operates on the peak-data information of each locus separately, independent of all other loci, and finds the best-fit DNA mass proportions and calculates error residual for each possible genotype combination. The LSD mathematical result for all loci is then to be reviewed by a DNA analyst, who will apply a set of heuristic interpretation guidelines in an attempt to form a composite DNA profile for each of the two contributors. Both simulated and forensic peak-height data were used to support this approach. A set of heuristic guidelines is to be used in forming a composite profile for each of the mixture contributors in analyzing the mathematical results of LSD. The heuristic rules involve the checking of consistency of the best-fit mass proportion ratios for the top-ranked genotype combination case among all four- and three-allele loci, and involve assessing the degree of fit of the top-ranked case relative to the fit of the second-ranked case. A different set of guidelines is used in reviewing and analyzing the LSD mathematical results for two-allele loci. Resolution of two-allele loci is performed with less confidence than for four- and three-allele loci. This paper gives a detailed description of the theory of the LSD methodology, discusses its limitations, and the heuristic guidelines in analyzing the LSD mathematical results. A 13-loci sample case study is included. The use of the interpretation guidelines in forming composite profiles for each of the two contributors is illustrated. Application of LSD in this case produced correct resolutions at all loci. Information on obtaining access to the LSD software is also given in the paper.
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Affiliation(s)
- Tsewei Wang
- Department of Chemical Engineering and Laboratory for Information Technologies, The University of Tennessee, Knoxville, TN 37996-2200, USA.
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46
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Duewer DL, Kline MC, Redman JW, Butler JM. NIST mixed stain study 3: signal intensity balance in commercial short tandem repeat multiplexes. Anal Chem 2006; 76:6928-34. [PMID: 15571343 DOI: 10.1021/ac049178k] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Short-tandem repeat (STR) allelic intensities were collected from more than 60 forensic laboratories for a suite of seven samples as part of the National Institute of Standards and Technology-coordinated 2001 Mixed Stain Study 3 (MSS3). These interlaboratory challenge data illuminate the relative importance of intrinsic and user-determined factors affecting the locus-to-locus balance of signal intensities for currently used STR multiplexes. To varying degrees, seven of the eight commercially produced multiplexes used by MSS3 participants displayed very similar patterns of intensity differences among the different loci probed by the multiplexes for all samples, in the hands of multiple analysts, with a variety of supplies and instruments. These systematic differences reflect intrinsic properties of the individual multiplexes, not user-controllable measurement practices. To the extent that quality systems specify minimum and maximum absolute intensities for data acceptability and data interpretation schema require among-locus balance, these intrinsic intensity differences may decrease the utility of multiplex results and surely increase the cost of analysis.
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Affiliation(s)
- David L Duewer
- Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8394, USA.
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47
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Gill P, Brenner CH, Buckleton JS, Carracedo A, Krawczak M, Mayr WR, Morling N, Prinz M, Schneider PM, Weir BS. DNA commission of the International Society of Forensic Genetics: Recommendations on the interpretation of mixtures. Forensic Sci Int 2006; 160:90-101. [PMID: 16750605 DOI: 10.1016/j.forsciint.2006.04.009] [Citation(s) in RCA: 244] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 04/10/2006] [Indexed: 11/21/2022]
Abstract
The DNA commission of the International Society of Forensic Genetics (ISFG) was convened at the 21st congress of the International Society for Forensic Genetics held between 13 and 17 September in the Azores, Portugal. The purpose of the group was to agree on guidelines to encourage best practice that can be universally applied to assist with mixture interpretation. In addition the commission was tasked to provide guidance on low copy number (LCN) reporting. Our discussions have highlighted a significant need for continuing education and research into this area. We have attempted to present a consensus from experts but to be practical we do not claim to have conveyed a clear vision in every respect in this difficult subject. For this reason, we propose to allow a period of time for feedback and reflection by the scientific community. Then the DNA commission will meet again to consider further recommendations.
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Affiliation(s)
- P Gill
- Forensic Science Service, Trident Court, 2960 Solihull Parkway, Birmingham, UK.
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48
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Daniel R, Walsh SJ. The Continuing Evolution of Forensic DNA Profiling - From STRS to SNPS. AUST J FORENSIC SCI 2006. [DOI: 10.1080/00450610609410633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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49
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Gill P, Kirkham A, Curran J. LoComatioN: a software tool for the analysis of low copy number DNA profiles. Forensic Sci Int 2006; 166:128-38. [PMID: 16759831 DOI: 10.1016/j.forsciint.2006.04.016] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Accepted: 04/11/2006] [Indexed: 11/26/2022]
Abstract
Previously, the interpretation of low copy number (LCN) STR profiles has been carried out using the biological or 'consensus' method-essentially, alleles are not reported, unless duplicated in separate PCR analyses [P. Gill, J. Whitaker, C. Flaxman, N. Brown, J. Buckleton, An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA, Forens. Sci. Int. 112 (2000) 17-40]. The method is now widely used throughout Europe. Although a probabilistic theory was simultaneously introduced, its time-consuming complexity meant that it could not be easily applied in practice. The 'consensus' method is not as efficient as the probabilistic approach, as the former wastes information in DNA profiles. However, the theory was subsequently extended to allow for DNA mixtures and population substructure in a programmed solution by Curran et al. [J.M. Curran, P. Gill, M.R. Bill, Interpretation of repeat measurement DNA evidence allowing for multiple contributors and population substructure, Forens. Sci. Int. 148 (2005) 47-53]. In this paper, we describe an expert interpretation system (LoComatioN) which removes this computational burden, and enables application of the full probabilistic method. This is the first expert system that can be used to rapidly evaluate numerous alternative explanations in a likelihood ratio approach, greatly facilitating court evaluation of the evidence. This would not be possible with manual calculation. Finally, the Gill et al. and Curran et al. papers both rely on the ability of the user to specify two quantities: the probability of allelic drop-out, and the probability of allelic contamination ("drop-in"). In this paper, we offer some guidelines on how these quantities may be specified.
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Affiliation(s)
- Peter Gill
- Forensic Science Service, Trident Court, 2960 Solihull Parkway, Solihull B37 7YN, UK.
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50
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Cowell RG, Lauritzen SL, Mortera J. Identification and separation of DNA mixtures using peak area information. Forensic Sci Int 2006; 166:28-34. [PMID: 16650704 DOI: 10.1016/j.forsciint.2006.03.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Revised: 03/28/2006] [Accepted: 03/29/2006] [Indexed: 11/18/2022]
Abstract
We introduce a new methodology, based upon probabilistic expert systems, for analysing forensic identification problems involving DNA mixture traces using quantitative peak area information. Peak area is modelled with conditional Gaussian distributions. The expert system can be used for ascertaining whether individuals, whose profiles have been measured, have contributed to the mixture. It can also be used to predict DNA profiles of unknown contributors by separating the mixture into its individual components. The potential of our probabilistic methodology is illustrated on case data examples and compared with alternative approaches. The advantages are that identification and separation issues can be handled in a unified way within a single probabilistic model and the uncertainty associated with the analysis is quantified. Further work, required to bring the methodology to a point where it could be applied to the routine analysis of casework, is discussed.
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Affiliation(s)
- R G Cowell
- Faculty of Actuarial Science and Statistics, Cass Business School, London, UK.
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