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Huffman K, Ballantyne J. Single cell genomics applications in forensic science: Current state and future directions. iScience 2023; 26:107961. [PMID: 37876804 PMCID: PMC10590970 DOI: 10.1016/j.isci.2023.107961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
Standard methods of mixture analysis involve subjecting a dried crime scene sample to a "bulk" DNA extraction method such that the resulting isolate compromises a homogenized DNA mixture from the individual donors. If, however, instead of bulk DNA extraction, a sufficient number of individual cells from the mixed stain are subsampled prior to genetic analysis then it should be possible to recover highly probative single source, non-mixed scDNA profiles from each of the donors. This approach can detect low DNA level minor donors to a mixture that otherwise would not be identified using standard methods and can also resolve rare mixtures comprising first degree relatives and thereby also prevent the false inclusion of non-donor relatives. This literature landscape review and associated commentary reports on the history and increasing interest in current and potential future applications of scDNA in forensic genomics, and critically evaluates opportunities and impediments to further progress.
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Affiliation(s)
- Kaitlin Huffman
- Graduate Program in Chemistry, Department of Chemistry, University of Central Florida, PO Box 162366, Orlando, FL 32816-2366, USA
| | - Jack Ballantyne
- National Center for Forensic Science, PO Box 162367, Orlando, FL 32816-2367, USA
- Department of Chemistry, University of Central Florida, PO Box 162366, Orlando, FL 32816-2366, USA
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2
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England R, Nancollis G, Stacey J, Sarman A, Min J, Harbison S. Compatibility of the ForenSeq™ DNA Signature Prep Kit with laser microdissected cells: An exploration of issues that arise with samples containing low cell numbers. Forensic Sci Int Genet 2020; 47:102278. [DOI: 10.1016/j.fsigen.2020.102278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/05/2020] [Accepted: 03/15/2020] [Indexed: 12/27/2022]
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3
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Deconvolution of blood-blood mixtures using DEPArrayTM separated single cell STR profiling. Rechtsmedizin (Berl) 2018. [DOI: 10.1007/s00194-018-0291-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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4
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Whose blood is it? Application of DEPArray™ technology for the identification of individual/s who contributed blood to a mixed stain. Int J Legal Med 2018; 133:419-426. [DOI: 10.1007/s00414-018-1912-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 08/13/2018] [Indexed: 11/25/2022]
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5
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Tao R, Wang S, Zhang J, Zhang J, Yang Z, Sheng X, Hou Y, Zhang S, Li C. Separation/extraction, detection, and interpretation of DNA mixtures in forensic science (review). Int J Legal Med 2018; 132:1247-1261. [PMID: 29802461 DOI: 10.1007/s00414-018-1862-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/11/2018] [Indexed: 02/08/2023]
Abstract
Interpreting mixed DNA samples containing material from multiple contributors has long been considered a major challenge in forensic casework, especially when encountering low-template DNA (LT-DNA) or high-order mixtures that may involve missing alleles (dropout) and unrelated alleles (drop-in), among others. In the last decades, extraordinary progress has been made in the analysis of mixed DNA samples, which has led to increasing attention to this research field. The advent of new methods for the separation and extraction of DNA from mixtures, novel or jointly applied genetic markers for detection and reliable interpretation approaches for estimating the weight of evidence, as well as the powerful massively parallel sequencing (MPS) technology, has greatly extended the range of mixed samples that can be correctly analyzed. Here, we summarized the investigative approaches and progress in the field of forensic DNA mixture analysis, hoping to provide some assistance to forensic practitioners and to promote further development involving this issue.
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Affiliation(s)
- Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Xiang Sheng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China. .,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
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Abstract
The new opportunities of modern assays of molecular biology can only be exploited fully if the results can be accurately correlated to the tissue phenotype under investigation. This is a general problem of non-in situ techniques, whereas results from in situ techniques are often difficult to quantify. The use of bulk tissue, which is not precisely characterized in terms of histology, has long been the basis for molecular analysis. It has, however, become apparent, that this simple approach is not sufficient for a detailed analysis of molecular alterations, which might be restricted to a specific tissue phenotype (e.g., tumor or normal tissue, stromal or epithelial cells). Microdissection is a method to provide minute amounts of histologically characterized tissues for molecular analysis with non-in situ techniques and has become an indispensable research tool. If tissue diversity is moderate and negligible, manual microdissection can be an easy and cost-efficient method of choice. In contrast, the advantage of laser microdissection is a very exact selection down to the level of a single cell, but often with a considerable time exposure to get enough material for the following analyses. The latter issue and the method of tissue preparation needed for laser microdissection are the main problems to solve if RNA, highly sensitive to degradation, shall be analyzed. This chapter focuses on optimized procedures for manual microdissection and laser microdissection to analyze RNA of malignant and nonmalignant prostate tissue.
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Affiliation(s)
- Anja Rabien
- Research Division, Department of Urology, Charité-Universitätsmedizin Berlin, Campus Charité Mitte, Charitéplatz 1, 10117, Berlin, Germany.
| | - Glen Kristiansen
- Universitätsklinikum Bonn (AöR), Institut für Pathologie, Bonn, Germany
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Garvin AM, Fischer A, Schnee-Griese J, Jelinski A, Bottinelli M, Soldati G, Tubio M, Castella V, Monney N, Malik N, Madrid M. Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach. INVESTIGATIVE GENETICS 2012; 3:25. [PMID: 23211019 PMCID: PMC3546913 DOI: 10.1186/2041-2223-3-25] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/31/2012] [Indexed: 11/22/2022]
Abstract
Background Profiling sperm DNA present on vaginal swabs taken from rape victims often contributes to identifying and incarcerating rapists. Large amounts of the victim’s epithelial cells contaminate the sperm present on swabs, however, and complicate this process. The standard method for obtaining relatively pure sperm DNA from a vaginal swab is to digest the epithelial cells with Proteinase K in order to solubilize the victim’s DNA, and to then physically separate the soluble DNA from the intact sperm by pelleting the sperm, removing the victim’s fraction, and repeatedly washing the sperm pellet. An alternative approach that does not require washing steps is to digest with Proteinase K, pellet the sperm, remove the victim’s fraction, and then digest the residual victim’s DNA with a nuclease. Methods The nuclease approach has been commercialized in a product, the Erase Sperm Isolation Kit (PTC Labs, Columbia, MO, USA), and five crime laboratories have tested it on semen-spiked female buccal swabs in a direct comparison with their standard methods. Comparisons have also been performed on timed post-coital vaginal swabs and evidence collected from sexual assault cases. Results For the semen-spiked buccal swabs, Erase outperformed the standard methods in all five laboratories and in most cases was able to provide a clean male profile from buccal swabs spiked with only 1,500 sperm. The vaginal swabs taken after consensual sex and the evidence collected from rape victims showed a similar pattern of Erase providing superior profiles. Conclusions In all samples tested, STR profiles of the male DNA fractions obtained with Erase were as good as or better than those obtained using the standard methods.
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Affiliation(s)
- Alex M Garvin
- Confarma France SARL, Zone Industrielle Canal d'Alsace, Hombourg, 68490, France.
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9
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Schneider C, Müller U, Kilper R, Siebertz B. Low copy number DNA profiling from isolated sperm using the aureka®-micromanipulation system. Forensic Sci Int Genet 2011; 6:461-5. [PMID: 22155149 DOI: 10.1016/j.fsigen.2011.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 08/26/2011] [Accepted: 10/06/2011] [Indexed: 10/14/2022]
Abstract
A new cell isolation technique linked to the aureka® micromanipulation system (aureka®) was used to pick sperm from mixed samples containing sperm and epithelial cells. Both cell types were stained using the HY-LITER™ high-resolution, fluorescent staining kit. To isolate a single sperm of interest under a fluorescent microscope, a specific microsphere picking technique was used. This sensitive and reliable cell identification and isolation technique enables low-copy-number (LCN) DNA profiling, as few as 20 sperm are sufficient for obtaining a full short tandem repeat (STR) profile without any allelic drop out. The presented protocol covers the whole workflow, from sample staining and cell pick up to STR analysis.
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Affiliation(s)
- C Schneider
- Galantos Genetics GmbH, Johann-Joachim-Becher-Weg 30a, 55128 Mainz, Germany.
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10
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Vandewoestyne M, Deforce D. Laser capture microdissection for forensic DNA analysis. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.08.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Current genetic methodologies in the identification of disaster victims and in forensic analysis. J Appl Genet 2011; 53:41-60. [PMID: 22002120 PMCID: PMC3265735 DOI: 10.1007/s13353-011-0068-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Revised: 09/22/2011] [Accepted: 09/23/2011] [Indexed: 12/16/2022]
Abstract
This review presents the basic problems and currently available molecular techniques used for genetic profiling in disaster victim identification (DVI). The environmental conditions of a mass disaster often result in severe fragmentation, decomposition and intermixing of the remains of victims. In such cases, traditional identification based on the anthropological and physical characteristics of the victims is frequently inconclusive. This is the reason why DNA profiling became the gold standard for victim identification in mass-casualty incidents (MCIs) or any forensic cases where human remains are highly fragmented and/or degraded beyond recognition. The review provides general information about the sources of genetic material for DNA profiling, the genetic markers routinely used during genetic profiling (STR markers, mtDNA and single-nucleotide polymorphisms [SNP]) and the basic statistical approaches used in DNA-based disaster victim identification. Automated technological platforms that allow the simultaneous analysis of a multitude of genetic markers used in genetic identification (oligonucleotide microarray techniques and next-generation sequencing) are also presented. Forensic and population databases containing information on human variability, routinely used for statistical analyses, are discussed. The final part of this review is focused on recent developments, which offer particularly promising tools for forensic applications (mRNA analysis, transcriptome variation in individuals/populations and genetic profiling of specific cells separated from mixtures).
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Vandewoestyne M, Van Nieuwerburgh F, Van Hoofstat D, Deforce D. Evaluation of three DNA extraction protocols for forensic STR typing after laser capture microdissection. Forensic Sci Int Genet 2011; 6:258-62. [PMID: 21727054 DOI: 10.1016/j.fsigen.2011.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 05/13/2011] [Accepted: 06/09/2011] [Indexed: 11/28/2022]
Abstract
In forensic sciences, short tandem repeat (STR) analysis is a valuable tool in identifying the donor(s) of biological stains. Laser capture microdissection (LCM) can be used as a cell separating technique to isolate specific cell types in mixed samples. An important challenge lies in the development of a DNA isolation method appropriate for laser microdissected cells, as these samples usually contain minute amounts of cells. In this study three different DNA isolation methods for LCM collected cells were compared. The PicoPure DNA extraction method outperformed both other methods (IQ™ system and short alkaline method). Consequently, the minimal number of LCM collected cells necessary for STR typing was determined. Using the PicoPure DNA extraction method, full DNA profiles could be obtained from as little as 10 cells. Nevertheless, despite the occurrence of allelic drop out in some of the samples, lower amounts of cells gave rise to useful DNA profiles.
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Affiliation(s)
- Mado Vandewoestyne
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium.
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13
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McAlister C. The use of fluorescence in situ hybridisation and laser microdissection to identify and isolate male cells in an azoospermic sexual assault case. Forensic Sci Int Genet 2011; 5:69-73. [DOI: 10.1016/j.fsigen.2010.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 04/01/2010] [Accepted: 04/28/2010] [Indexed: 10/19/2022]
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van Oorschot RAH, Ballantyne KN, Mitchell RJ. Forensic trace DNA: a review. INVESTIGATIVE GENETICS 2010; 1:14. [PMID: 21122102 PMCID: PMC3012025 DOI: 10.1186/2041-2223-1-14] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 12/01/2010] [Indexed: 11/10/2022]
Abstract
DNA analysis is frequently used to acquire information from biological material to aid enquiries associated with criminal offences, disaster victim identification and missing persons investigations. As the relevance and value of DNA profiling to forensic investigations has increased, so too has the desire to generate this information from smaller amounts of DNA. Trace DNA samples may be defined as any sample which falls below recommended thresholds at any stage of the analysis, from sample detection through to profile interpretation, and can not be defined by a precise picogram amount. Here we review aspects associated with the collection, DNA extraction, amplification, profiling and interpretation of trace DNA samples. Contamination and transfer issues are also briefly discussed within the context of trace DNA analysis. Whilst several methodological changes have facilitated profiling from trace samples in recent years it is also clear that many opportunities exist for further improvements.
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Affiliation(s)
- Roland AH van Oorschot
- Forensic Services Department, Victoria Police, 31 Forensic Drive, Macleod 3085, Victoria, Australia
| | - Kaye N Ballantyne
- Department of Forensic Molecular Biology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - R John Mitchell
- Department of Genetics, La Trobe University, Melbourne, Victoria 3086, Australia
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15
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Vandewoestyne M, Deforce D. Laser capture microdissection in forensic research: a review. Int J Legal Med 2010; 124:513-21. [PMID: 20680318 PMCID: PMC2952761 DOI: 10.1007/s00414-010-0499-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 07/20/2010] [Indexed: 11/30/2022]
Abstract
In forensic sciences, short tandem repeat (STR) analysis has become the prime tool for DNA-based identification of the donor(s) of biological stains and/or traces. Many traces, however, contain cells and, hence, DNA, from more than a single individual, giving rise to mixed genotypes and the subsequent difficulties in interpreting the results. An even more challenging situation occurs when cells of a victim are much more abundant than the cells of the perpetrator. Therefore, the forensic community seeks to improve cell-separation methods in order to generate single-donor cell populations from a mixed trace in order to facilitate DNA typing and identification. Laser capture microdissection (LCM) offers a valuable tool for precise separation of specific cells. This review summarises all possible forensic applications of LCM, gives an overview of the staining and detection options, including automated detection and retrieval of cells of interest, and reviews the DNA extraction protocols compatible with LCM of cells from forensic samples.
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Affiliation(s)
- Mado Vandewoestyne
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000, Ghent, Belgium
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Schulz MM, Buschner MG, Leidig R, Wehner HD, Fritz P, Häbig K, Bonin M, Schütz M, Shiozawa T, Wehner F. A New Approach to the Investigation of Sexual Offenses-Cytoskeleton Analysis Reveals the Origin of Cells Found on Forensic Swabs. J Forensic Sci 2010; 55:492-8. [DOI: 10.1111/j.1556-4029.2009.01071.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Gene expression analysis requires a sound basis of cell material to obtain realistic results. Tissue, however, consists of diverse types of cells, which often differentially express target genes, so that cell populations need to be selected. If tissue diversity is moderate and negligible, manual microdissection can be the cost-efficient method of choice. In contrast, the advantage of laser microdissection is a very exact selection down to the level of a single cell, but often with a considerable time needed to get enough material for the following analyses. The latter issue and the method of tissue preparation needed for laser microdissection are the main problems to solve if RNA, highly sensitive to degradation, shall be analyzed. This method focuses on optimized laser microdissection procedures for RNA analysis, drawing on the very heterogeneous tissue of prostatic adenocarcinoma.
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Affiliation(s)
- Anja Rabien
- Research Division, Department of Urology, Charité - UniversitätsmedizinBerlin, Campus Charité Mitte, Berlin, Germany
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Garvin AM, Bottinelli M, Gola M, Conti A, Soldati G. DNA Preparation from Sexual Assault Cases by Selective Degradation of Contaminating DNA from the Victim. J Forensic Sci 2009; 54:1297-303. [DOI: 10.1111/j.1556-4029.2009.01180.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Vandewoestyne M, Van Hoofstat D, Van Nieuwerburgh F, Deforce D. Suspension fluorescence in situ hybridization (S-FISH) combined with automatic detection and laser microdissection for STR profiling of male cells in male/female mixtures. Int J Legal Med 2009; 123:441-7. [PMID: 19319556 PMCID: PMC2754505 DOI: 10.1007/s00414-009-0341-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 03/10/2009] [Indexed: 11/25/2022]
Abstract
Laser microdissection is a valuable tool for isolating specific cells from mixtures, such as male cells in a mixture with female cells, e.g., in cases of sexual assault. These cells can be stained with Y-chromosome-specific probes. We developed an automatic screening method to detect male cells after fluorescence in situ hybridization in suspension (S-FISH). To simulate forensic casework, the method was tested on female saliva after cataglottis (a kiss involving tongue-to-tongue contact) and on licking traces (swabs of dried male saliva on female skin) even after drying. After isolation of the detected cells, short tandem repeat profiling was performed. Full DNA profiles could consistently be obtained from as little as ten buccal cells. Isolation of five cells resulted in a mean of 98% (SD of 3.4%) of the alleles detected, showing that the developed S-FISH staining had no significant negative influence on DNA recovery and can be used in forensic casework.
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Affiliation(s)
- Mado Vandewoestyne
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - David Van Hoofstat
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
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Petit C, Martel-Petit V, Hienne R, Frackowiak S. Single sperm cell isolation by micromanipulation for human identification in sexual assault. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2008. [DOI: 10.1016/j.fsigss.2007.10.186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Automatic detection of spermatozoa for laser capture microdissection. Int J Legal Med 2008; 123:169-75. [PMID: 18661142 DOI: 10.1007/s00414-008-0271-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Accepted: 06/19/2008] [Indexed: 10/21/2022]
Abstract
In sexual assault crimes, differential extraction of spermatozoa from vaginal swab smears is often ineffective, especially when only a few spermatozoa are present in an overwhelming amount of epithelial cells. Laser capture microdissection (LCM) enables the precise separation of spermatozoa and epithelial cells. However, standard sperm-staining techniques are non-specific and rely on sperm morphology for identification. Moreover, manual screening of the microscope slides is time-consuming and labor-intensive. Here, we describe an automated screening method to detect spermatozoa stained with Sperm HY-LITER. Different ratios of spermatozoa and epithelial cells were used to assess the automatic detection method. In addition, real postcoital samples were also screened. Detected spermatozoa were isolated using LCM and DNA analysis was performed. Robust DNA profiles without allelic dropout could be obtained from as little as 30 spermatozoa recovered from postcoital samples, showing that the staining had no significant influence on DNA recovery.
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22
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Sluka P, O'Donnell L, McLachlan RI, Stanton PG. Application of laser-capture microdissection to analysis of gene expression in the testis. ACTA ACUST UNITED AC 2008; 42:173-201. [PMID: 18243898 DOI: 10.1016/j.proghi.2007.10.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 10/03/2007] [Indexed: 12/13/2022]
Abstract
The isolation and molecular analysis of highly purified cell populations from complex, heterogeneous tissues has been a challenge for many years. Spermatogenesis in the testis is a particularly difficult process to study given the unique multiple cellular associations within the seminiferous epithelium, making the isolation of specific cell types difficult. Laser-capture microdissection (LCM) is a recently developed technique that enables the isolation of individual cell populations from complex tissues. This technology has enhanced our ability to directly examine gene expression in enriched testicular cell populations by routine methods of gene expression analysis, such as real-time RT-PCR, differential display, and gene microarrays. The application of LCM has however introduced methodological hurdles that have not been encountered with more conventional molecular analyses of whole tissue. In particular, tissue handling (i.e. fixation, storage, and staining), consumables (e.g. slide choice), staining reagents (conventional H&E vs. fluorescence), extraction methods, and downstream applications have all required re-optimisation to facilitate differential gene expression analysis using the small amounts of material obtained using LCM. This review will discuss three critical issues that are essential for successful procurement of cells from testicular tissue sections; tissue morphology, capture success, and maintenance of molecular integrity. The importance of these issues will be discussed with specific reference to the two most commonly used LCM systems; the Arcturus PixCell IIe and PALM systems. The rat testis will be used as a model, and emphasis will be placed on issues of tissue handling, processing, and staining methods, including the application of fluorescence techniques to assist in the identification of cells of interest for the purposes of mRNA expression analysis.
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Affiliation(s)
- Pavel Sluka
- Prince Henry's Institute of Medical Research, Monash Medical Centre, Clayton, Victoria 3168, Australia
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23
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Murray C, McAlister C, Elliott K. Identification and isolation of male cells using fluorescence in situ hybridisation and laser microdissection, for use in the investigation of sexual assault. Forensic Sci Int Genet 2007; 1:247-52. [DOI: 10.1016/j.fsigen.2007.05.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 05/07/2007] [Accepted: 05/15/2007] [Indexed: 11/25/2022]
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Anoruo B, van Oorschot R, Mitchell J, Howells D. Isolating cells from non-sperm cellular mixtures using the PALM® microlaser micro dissection system. Forensic Sci Int 2007; 173:93-6. [PMID: 17459628 DOI: 10.1016/j.forsciint.2007.01.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Accepted: 01/27/2007] [Indexed: 11/24/2022]
Abstract
Use of the Positioning Ablation Laser MicroBeam (PALM) microlaser system to isolate specific cellular components from somatic cellular mixtures (blood and saliva) prior to DNA extraction and typing is compared with routine DNA extraction and typing of the same mixture samples. Mixtures of blood and saliva at differing ratios generated complex DNA profiles that included allele peaks originating from each of the donors, or just those of the major contributor. Isolation of cells with the PALM microlaser prior to DNA extraction allowed informative, single-source, DNA profiles to be generated from a known cell type/origin.
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Affiliation(s)
- Belinda Anoruo
- Victoria Police Forensic Services Department, 31 Forensic Drive, Macleod, Vic. 3085, Australia
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25
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Affiliation(s)
- T A Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196, USA
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Montesino M, Salas A, Crespillo M, Albarrán C, Alonso A, Alvarez-Iglesias V, Cano JA, Carvalho M, Corach D, Cruz C, Di Lonardo A, Espinheira R, Farfán MJ, Filippini S, García-Hirschfeld J, Hernández A, Lima G, López-Cubría CM, López-Soto M, Pagano S, Paredes M, Pinheiro MF, Rodríguez-Monge AM, Sala A, Sóñora S, Sumita DR, Vide MC, Whittle MR, Zurita A, Prieto L. Analysis of body fluid mixtures by mtDNA sequencing: An inter-laboratory study of the GEP-ISFG working group. Forensic Sci Int 2006; 168:42-56. [PMID: 16899347 DOI: 10.1016/j.forsciint.2006.06.066] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Revised: 06/15/2006] [Accepted: 06/17/2006] [Indexed: 10/24/2022]
Abstract
The mitochondrial DNA (mtDNA) working group of the GEP-ISFG (Spanish and Portuguese Group of the International Society for Forensic Genetics) carried out an inter-laboratory exercise consisting of the analysis of mtDNA sequencing patterns in mixed stains (saliva/semen and blood/semen). Mixtures were prepared with saliva or blood from a female donor and three different semen dilutions (pure, 1:10 and 1:20) in order to simulate forensic casework. All labs extracted the DNA by preferential lysis and amplified and sequenced the first mtDNA hypervariable region (HVS-I). Autosomal and Y-STR markers were also analysed in order to compare nuclear and mitochondrial results from the same DNA extracts. A mixed stain prepared using semen from a vasectomized individual was also analysed. The results were reasonably consistent among labs for the first fractions but not for the second ones, for which some laboratories reported contamination problems. In the first fractions, both the female and male haplotypes were generally detected in those samples prepared with undiluted semen. In contrast, most of the mixtures prepared with diluted semen only yielded the female haplotype, suggesting that the mtDNA copy number per cell is smaller in semen than in saliva or blood. Although the detection level of the male component decreased in accordance with the degree of semen dilution, it was found that the loss of signal was not consistently uniform throughout each electropherogram. Moreover, differences between mixtures prepared from different donors and different body fluids were also observed. We conclude that the particular characteristics of each mixed stain can deeply influence the interpretation of the mtDNA evidence in forensic mixtures (leading in some cases to false exclusions). In this sense, the implementation of preliminary tests with the aim of identifying the fluids involved in the mixture is an essential tool. In addition, in order to prevent incorrect conclusions in the interpretation of electropherograms we strongly recommend: (i) the use of additional sequencing primers to confirm the sequencing results and (ii) interpreting the results to the light of the phylogenetic perspective.
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Laser literature watch. Photomed Laser Surg 2006; 24:424-53. [PMID: 16875454 DOI: 10.1089/pho.2006.24.424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Sato I, Barni F, Yoshiike M, Rapone C, Berti A, Nakaki S, Yamazaki K, Ishikawa F, Iwamoto T. Applicability of Nanotrap Sg as a semen detection kit before male-specific DNA profiling in sexual assaults. Int J Legal Med 2006; 121:315-9. [PMID: 16583248 DOI: 10.1007/s00414-006-0084-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Accepted: 02/13/2006] [Indexed: 11/28/2022]
Abstract
A commercially available semen detection kit, Nanotrap Sg, which employs a one-step detection test based on immunochromatographic assay for the semenogelin protein, was evaluated for profiling male-specific DNA in sexual assault casework samples. While semen diluted with phosphate-buffered saline held and kept at 4 degrees C for 1 week showed a relatively strong signal intensity with Nanotrap Sg, the signal intensity was decreased by dilution after storage at 4 degrees C or freezing and thawing repeated more than three times. The reproducibility of Nanotrap Sg was tested on a total of 174 sexual assault casework samples from three forensic laboratories using intra- and interassay and no variation was observed in the semenogelin (Sg) signal. The positive signal ratio was 12.6% higher for prostate-specific antigen immunochromatographic membrane tests than Nanotrap Sg. Although spermatozoa were not confirmed in 61 (35%) out of 174 samples, Sg-positive signals could be detected from 41 (67%) of the 61 samples. Female genetic profiles could be observed in 95% of the samples, which tested negative for Sg on the Nanotrap Sg test, but no male genetic profiles could be observed. These results suggest that Nanotrap Sg can positively identify samples containing male DNA even in the absence of detectable intact spermatozoa. Further, Sg-positive signals identified samples for which male-specific DNA profiling could be performed, even if no sperm could be detected from the sample. The potential of Nanotrap Sg for identifying forensic samples with male-specific DNA was clearly demonstrated.
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Affiliation(s)
- Itaru Sato
- Scientific Crime Laboratory, Kanagawa Prefectural Police, 155-1 Yamashita-cho, Naka-ku, Yokohama 231-0023, Japan.
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Anslinger K, Bayer B, Mack B, Eisenmenger W. Sex-specific fluorescent labelling of cells for laser microdissection and DNA profiling. Int J Legal Med 2006; 121:54-6. [PMID: 16552569 DOI: 10.1007/s00414-005-0065-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Accepted: 11/03/2005] [Indexed: 10/24/2022]
Abstract
Sex-specific isolation of cells from mixtures would greatly facilitate forensic casework. Thus, male and female cell mixtures were marked with a fluorescent X/Y-probe CEP X SpectrumOrange/Y SpectrumGreen DNA probe kit for fluorescence in situ hybridization, and single cells were isolated via laser microdissection (LMD). DNA profiling of LMD isolated, hybridized cells showed usable short tandem repeat profiles for at least 20 cells, which are comparable with results from other studies. To simulate casework samples, the method was also optimized for air-dried samples.
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Affiliation(s)
- K Anslinger
- Institute of Legal Medicine, Ludwig-Maximilians-University of Munich, Frauenlobstrasse 7a, 80337, Munich, Germany.
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