1
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Dash HR. Advancements in differentiation between sperm cells and epithelial cells for efficient forensic DNA analysis in sexual assault cases. Int J Legal Med 2024:10.1007/s00414-024-03285-1. [PMID: 38995400 DOI: 10.1007/s00414-024-03285-1] [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: 04/11/2024] [Accepted: 06/30/2024] [Indexed: 07/13/2024]
Abstract
Most of the sexual assault casework samples are of mixed sources. Forensic DNA laboratories are always in the requirement of a precise technique for the efficient separation of sperm and non-sperm DNA from mixed samples. Since the introduction of the differential extraction technique in 1985, it has seen significant advancements in the form of either chemicals used or modification of incubation times. Several automated and semi-automated techniques have also adopted the fundamentals of conventional differential extraction techniques. However, lengthy incubation, several manual steps, and carryover over non-sperm material in sperm fraction are some of the major limitations of this technique. Advanced cell separation techniques have shown huge promise in separating sperm cells from a mixture based on their size, shape, composition, and membrane structure and antigens present on sperm membranes. Such advanced techniques such as DEParray, ADE, FACS, LCM, HOT and their respective pros and cons have been discussed in this article. As current-day forensic techniques should be as per the line of Olympic slogan i.e., faster, higher, stronger, the advanced cell separation techniques show a huge potential to be implemented in the casework samples.
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Affiliation(s)
- Hirak Ranjan Dash
- National Forensic Sciences University, Delhi Campus, Sector-3, 110085, Rohini, New Delhi, India.
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2
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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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3
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Costanzo H, Gooch J, Tungsirisurp S, Frascione N. The Development and Characterisation of ssDNA Aptamers via a Modified Cell-SELEX Methodology for the Detection of Human Red Blood Cells. Int J Mol Sci 2024; 25:1814. [PMID: 38339091 PMCID: PMC10855528 DOI: 10.3390/ijms25031814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Blood is one of the most commonly found biological fluids at crime scenes, with the detection and identification of blood holding a high degree of evidential value. It can provide not only information about the nature of the crime but can also lead to identification via DNA profiling. Presumptive tests for blood are usually sensitive but not specific, so small amounts of the substrate can be detected, but false-positive results are often encountered, which can be misleading. Novel methods for the detection of red blood cells based on aptamer-target interactions may be able to overcome these issues. Aptamers are single-stranded DNA or RNA sequences capable of undergoing selective antigen association due to three-dimensional structure formation. The use of aptamers as a target-specific moiety poses several advantages and has the potential to replace antibodies within immunoassays. Aptamers are cheaper to produce, display no batch-to-batch variation and can allow for a wide range of chemical modifications. They can help limit cross-reactivity, which is a hindrance to current forensic testing methods. Within this study, a modified Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process was used to generate aptamers against whole red blood cells. Obtained aptamer pools were analysed via massively parallel sequencing to identify viable sequences that demonstrate a high affinity for the target. Using bioinformatics platforms, aptamer candidates were identified via their enrichment profiles. Binding characterisation was also conducted on two selected aptamer candidates via fluorescent microscopy and qPCR to visualise and quantify aptamer binding. The potential for these aptamers is broad as they can be utilised within a range of bioassays for not only forensic applications but also other analytical science and medical applications. Potential future work includes the incorporation of developed aptamers into a biosensing platform that can be used at crime scenes for the real-time detection of human blood.
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Affiliation(s)
| | | | | | - Nunzianda Frascione
- Department of Analytical, Environmental & Forensic Sciences, Faculty of Life Sciences & Medicine, King’s College London, London SE1 9NH, UK; (H.C.); (J.G.); (S.T.)
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4
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Dawnay N, Sheppard K. From crime scene to courtroom: A review of the current bioanalytical evidence workflows used in rape and sexual assault investigations in the United Kingdom. Sci Justice 2023; 63:206-228. [PMID: 36870701 DOI: 10.1016/j.scijus.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Sexual assault casework requires the collaboration of multiple agency staff to formalise an investigative pipeline running from crime scene to court. While the same could be said of many other forensic investigations, few require the additional support of health care staff and the combined forensic involvement of body-fluid examiners, DNA experts and analytical chemists. The sheer amount of collaborative effort between agencies is laid out through a detailed examination of the investigative workflow from crime scene to courtroom with each step in the pipelines detailed and discussed. Beginning with a review of sexual assault legislation in the United Kingdom this article details how sexual assault investigations are initiated by police and supported by sexual assault referral centre (SARC) staff who are often the first responders providing primary healthcare and patient support to victims while simultaneously collecting and assessing forensic evidence. Detailing the myriad of evidential material that can be documented and collected at the SARC, the review identifies and categorises key forensic tests to first detect and identify body-fluids recovered from evidence through to the secondary analysis of DNA to help identify the suspect. This review also focusses on the collection and analysis of biological material used to support the allegation that the sexual activity was non-consensual and provides a breakdown of common marks and trauma as well as a review of common analytical methods used to infer Drug Facilitated Sexual Assault (DFSA). The culmination of the investigative pipeline is discussed by reviewing the Rape and Serious Sexual Assault (RASSO) workflow used by the Crown Prosecution Service before providing our thoughts on the future of forensic analysis and possible changes to the described workflows.
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Affiliation(s)
- Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom.
| | - Kayleigh Sheppard
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom
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5
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Grosjean F, Favre M, Castella V. Comparison between MACSprep™ forensic sperm microbead kit and Erase Sperm Isolation kit for the enrichment of sperm fractions recovered from sexual assault samples. Int J Legal Med 2023; 137:267-278. [PMID: 35773355 PMCID: PMC9816209 DOI: 10.1007/s00414-022-02861-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/21/2022] [Indexed: 01/11/2023]
Abstract
Sexual assault samples often contain mixtures of cells coming from at least two donors. Ideally, one would need to separate the cells into two cellular fractions: one consisting of the alleged aggressor's spermatozoa (the sperm fraction) and the other containing the victim's epithelial cells (the non-sperm fraction). This separation increases the probability of obtaining the alleged offender's autosomal DNA profile. However, spermatozoa are often collected along with an excess of biological material originating from the victim, and with unfavorable male:female biological material ratios, the absence of separation could result in the PCR amplification of the victim's DNA profile only. Several approaches are available to enrich/purify the spermatozoa present on sexual assault samples. In this paper, we compare a new method, the MACSprep™ Forensic Sperm MicroBead Kit (MACSprep, based on microbeads conjugated with antibodies bound to spermatozoa and their retention within a magnetic column) with the Erase Sperm Isolation Kit (Erase, a standard differential lysis separation procedure combined with a specific removal of free DNA) routinely used in our lab. The performance of both kits was tested using sets of vaginal and buccal swabs loaded with different dilutions of sperm, or azoospermic semen, representing a total of 120 independent samples. For the samples containing undiluted sperm, an average recovery of 58% was observed for the MACSprep's sperm fractions and 43% for Erase's. Significantly better recovery of azoospermic semen was observed in MACSprep's non-sperm fractions (~ 85%) compared to Erase (~ 28%). Erase performed significantly better than MACSprep in terms of recovery for diluted sperm samples (1:10 to 1:800 sperm dilutions) in the presence of vaginal cells, while the purities of the achieved sperm fractions were in favor of MACSprep for the highest sperm dilutions tested. Similar trends were observed with buccal swabs loaded with 1:200 sperm dilutions. Increased sperm dilutions on vaginal swabs resulted in higher variability in the male material recovered, whatever the separation method used. Both methods were easy to perform and resulted in male DNA extracts ready to use in less than 2 h. Both kits showed their specificities in terms of recovery efficiency and purity of the sperm fractions. Ideally, additional experiments should be performed in different laboratories, using workflow and chemistries different than ours, to better define the peculiarities observed with MACSprep for high dilutions. Improving the recovery of MACSprep for diluted samples, in addition to its better purity observed in the experiments performed, could make it a method of choice for laboratory workflow, despite MACSprep's current price per sample being about twice the price of Erase's.
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Affiliation(s)
- Frederic Grosjean
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
| | - Marylou Favre
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
| | - Vincent Castella
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
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6
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Sinha SK, Brown H, Holt H, Khan MR, Brown R, Sgueglia JB, Loftus A, Murphy G, Montgomery A. Development and validation of a novel method "SpermX™" for high throughput differential extraction processing of sexual assault kits (SAKs) for DNA analysis. Forensic Sci Int Genet 2022; 59:102690. [PMID: 35338894 DOI: 10.1016/j.fsigen.2022.102690] [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: 10/16/2021] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Abstract
The Sperm X method uses a nanotechnology derived polymer membrane that functions as a separation medium to effectively trap sperm cells while enabling efficient flow through of the digested epithelial cell DNA. This specialized membrane enabled development of a method that could significantly increase a forensic laboratory's ability to obtain male sperm fraction DNA profiles. The SpermX device provides a rapid, reproducible procedure that is easy to implement in a single-tube format as well as high-throughput truly automated hands-free workflows. Validation studies, performed using the manual SpermX method, include sensitivity, stability, precision (reproducibility and repeatability), mixtures, and a method comparison to the traditional differential extraction. Sensitivity and method comparison studies demonstrated a wide range of sperm cells, from a high of over 2.78 million cells (9158 ng) to a low of 25 cells (83 pg), can be trapped by the SpermX membrane. Stability studies on various substrates (i.e., carpet, cotton, denim, polyester, and silk) and degraded semen gave the expected male DNA profiles. Data from the same operator and a different operator were consistent with low variance. Mixtures, with ratios ranging from approximately 10:1-18182:1, created to simulate real casework type samples including buccal/semen, vaginal epithelial/semen, and post coital swabs at different time intervals, were tested. A comparison of the SpermX method to the conventional differential extraction method resulted in comparable probative male profile allelic data and associated statistical probabilities. For low level sperm samples, down to 25 sperm cells (83 pg), the SpermX method outperformed the conventional differential extraction with more genotypic information and associated probabilities.
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Affiliation(s)
- Sudhir K Sinha
- InnoGenomics Technologies, LLC. 2000 Lakeshore Dr #5016, New Orleans, LA 70148, USA.
| | - Hiromi Brown
- InnoGenomics Technologies, LLC. 2000 Lakeshore Dr #5016, New Orleans, LA 70148, USA
| | - Hailey Holt
- InnoGenomics Technologies, LLC. 2000 Lakeshore Dr #5016, New Orleans, LA 70148, USA
| | - Mah-Ro Khan
- InnoGenomics Technologies, LLC. 2000 Lakeshore Dr #5016, New Orleans, LA 70148, USA
| | - Ryan Brown
- InnoGenomics Technologies, LLC. 2000 Lakeshore Dr #5016, New Orleans, LA 70148, USA
| | - Joanne B Sgueglia
- InnoGenomics Technologies, LLC. 2000 Lakeshore Dr #5016, New Orleans, LA 70148, USA
| | - Andrew Loftus
- InnoGenomics Technologies, LLC. 2000 Lakeshore Dr #5016, New Orleans, LA 70148, USA
| | - Gina Murphy
- InnoGenomics Technologies, LLC. 2000 Lakeshore Dr #5016, New Orleans, LA 70148, USA
| | - Anne Montgomery
- InnoGenomics Technologies, LLC. 2000 Lakeshore Dr #5016, New Orleans, LA 70148, USA
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7
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Schellhammer SK, Hudson BC, Cox JO, Dawson Green T. Alternative direct‐to‐amplification sperm cell lysis techniques for sexual assault sample processing. J Forensic Sci 2022; 67:1668-1678. [PMID: 35285573 PMCID: PMC9314082 DOI: 10.1111/1556-4029.15027] [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: 01/07/2022] [Revised: 02/13/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Abstract
The prevalence of sexual assault cases and increasingly sensitive DNA analysis methods have resulted in sexual assault kit backlogs in the United States. Although traditional DNA extraction and purification utilizing detergents, proteinase K, and DTT have been the primary technique for lysing sperm cell fractions from these samples, it is labor‐intensive and inefficient regarding time and sperm DNA recovery – hindering the ability of forensic analysts to keep pace with evidence submissions. Thus, this study examined seven alternative sperm cell lysis techniques to develop a method that could efficiently lyse sperm and consistently generate high‐quality profiles while also reducing time, labor, and cost requirements. Microscopic examination of lysates indicated only Casework Direct and alkaline techniques could lyse all spermatozoa within samples, while quantification results demonstrated all methods performed comparably to the control method of forensicGEM™ Sperm (p > 0.06). Amplification with 0.25 ng DNA revealed that unpurified lysates from Casework Direct, alkaline, and NP‐40 techniques produced DNA profiles with acceptable mean STR peak heights and interlocus balance, both of which were similar to or better than the control. Overall, this study demonstrated the ability of Casework Direct, alkaline, and NP‐40 methods to efficiently lyse spermatozoa and provide high‐quality STR profiles despite the absence of a purification step. Ultimately, based on the data reported herein, alkaline lysis is the recommended alternative sperm lysis approach given its ability to generate high‐quality profiles, save time, and decrease the cost per reaction when compared to traditional sperm cell lysis methods.
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Affiliation(s)
- Sarah K. Schellhammer
- Department of Forensic Science Virginia Commonwealth University Richmond Virginia USA
| | - Brittany C. Hudson
- Department of Forensic Science Virginia Commonwealth University Richmond Virginia USA
- Integrative Life Sciences Virginia Commonwealth University Richmond Virginia USA
| | - Jordan O. Cox
- Department of Forensic Science Virginia Commonwealth University Richmond Virginia USA
| | - Tracey Dawson Green
- Department of Forensic Science Virginia Commonwealth University Richmond Virginia USA
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8
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Basset P, Blandin P, Grini A, Delemont S, Samie L, Castella V. A simplified protocol for the detection of blood, saliva, and semen from a single biological trace using immunochromatographic tests. Forensic Sci Med Pathol 2022; 18:141-148. [PMID: 35171453 PMCID: PMC9106612 DOI: 10.1007/s12024-021-00453-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 11/29/2022]
Abstract
The detection of body fluids (e.g., blood, saliva or semen) provides information that is important both for the investigation and for the choice of the analytical protocols. Because of their sensitivity, specificity, as well as their simplicity of use, immunochromatographic tests are widely applied. These tests target different body fluids and generally require specific buffer solutions. If one needs to investigate whether the material is of a specific nature (e.g., blood), this is fine. However, if the material can also contain other material (e.g., saliva or semen) then the use of different tests can be problematic. Indeed, if the different tests require different buffers, it will not be possible to perform all tests on the exact same specimen. In this study, we assess the use of the RSID™-universal buffer to perform three immunochromatographic tests (HEXAGON OBTI, RSID-saliva, and PSA Semiquant) as well as spermatozoa detection. We use the same eluate for the detection of all three body fluids. The proposed protocol provides similar results to those obtained when each test is conducted independently. Furthermore, it does not affect the quality of the DNA profiles. The main advantage of this protocol is that the results of the presumptive test(s) and of the DNA analyses are representative of the exact same specimen.
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Affiliation(s)
- Patrick Basset
- Forensic Genetics Unit, University Centre of Legal Medicine Lausanne-Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, Lausanne 25, CH-1000, Switzerland.
| | - Prisca Blandin
- Forensic Genetics Unit, University Centre of Legal Medicine Lausanne-Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, Lausanne 25, CH-1000, Switzerland
| | - Annalisa Grini
- Forensic Genetics Unit, University Centre of Legal Medicine Lausanne-Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, Lausanne 25, CH-1000, Switzerland
| | - Séverine Delemont
- Forensic Genetics Unit, University Centre of Legal Medicine Lausanne-Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, Lausanne 25, CH-1000, Switzerland
| | - Lydie Samie
- Forensic Genetics Unit, University Centre of Legal Medicine Lausanne-Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, Lausanne 25, CH-1000, Switzerland
| | - Vincent Castella
- Forensic Genetics Unit, University Centre of Legal Medicine Lausanne-Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, Lausanne 25, CH-1000, Switzerland
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Nakagawa T, Doi M, Nishi K, Sugahara T. Advantages of filtration method for sperm-DNA genotyping in sexual assault cases. Leg Med (Tokyo) 2022; 54:101988. [PMID: 34915337 DOI: 10.1016/j.legalmed.2021.101988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 01/12/2023]
Abstract
Differential extraction (DE) is a conventional method to isolate sperms from forensic semen samples (e.g. vaginal swab containing semen) for sperm-DNA genotyping. Subsequent to selective digestion of somatic cells in a mixture sample, sperms are collected and purified as a pellet by repetitive centrifugation based on the specific gravity of sperm heads. However, the centrifugation operation requires a technical proficiency and an extensive time to prevent a loss of sperms from the pellet as much as possible. Therefore, we devised a "filtration method (FM)", in which a vacuum filtration operation based on the size of sperm heads is adapted, instead of DE, for isolation of sperms without any loss in principle. Sperms are collected and purified on a polycarbonate membrane filter. In this study, we have compared results of forensic assays by DE and FM for sperm-DNA genotyping from forensic semen samples. Consequently, FM had advantages of easy operation, timesaving, and high yield of sperms from semen samples compared with DE, although FM had a comparable ability to DE for a purification of sperms from mixture samples. Thus, we present that FM could simply lead to success of sperm-DNA genotyping and has a possibility to supersede DE as a gold-standard method.
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Affiliation(s)
- Toshifumi Nakagawa
- Forensic Science Laboratory, Ehime Prefectural Police Headquarters, 2-2 Minamihoribatacho, Matsuyama, Ehime 790-8573, Japan.
| | - Masanori Doi
- Forensic Science Laboratory, Ehime Prefectural Police Headquarters, 2-2 Minamihoribatacho, Matsuyama, Ehime 790-8573, Japan
| | - Kosuke Nishi
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan; Food and Health Sciences Research Center, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Takuya Sugahara
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan; Food and Health Sciences Research Center, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
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10
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Development of a combined differential DNA/RNA co-extraction protocol and its application in forensic casework. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Wisner M, Erlich H, Shih S, Calloway C. Resolution of mitochondrial DNA mixtures using a probe capture next generation sequencing system and phylogenetic-based software. Forensic Sci Int Genet 2021; 53:102531. [PMID: 34052577 DOI: 10.1016/j.fsigen.2021.102531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/27/2021] [Accepted: 05/07/2021] [Indexed: 11/24/2022]
Abstract
Interpreting mixtures with nuclear genetic markers remains one of the persisting challenges in forensic DNA analysis, particularly when the DNA is degraded or present in trace amounts. In these scenarios, analyzing mitochondrial (mt) DNA can be useful due to the higher copy number per cell compared to nuclear DNA. However, until the emergence of Next-Generation Sequencing (NGS) with its clonal sequencing capability, analysis of mtDNA mixtures was very challenging. A mitochondrial genome probe capture Next-Generation Sequencing (NGS) system was used to sequence complex mtDNA mixtures and two different software programs to analyze the sequence data. Analysis of contrived mixtures of two contributors in 50:50 and 95:5 ratios as well as three-person mixtures ranging from near equal proportions (~33:33:33 ratio) to low amounts of the minor contributors (e.g., a 90:5:5 ratio) is reported. This system was also applied to the analysis of mtDNA mixtures from forensically relevant samples. For data analysis, both the variant frequency-based software program GeneMarker®HTS and the phylogenetic-based software program Mixemt was used to de-convolute the mixtures. Using the massively parallel, clonal features of NGS, one can bioinformatically separate and count the individual sequence reads to calculate the proportions of individual contributors using phylogenetically informative polymorphisms. GeneMarker®HTS allows us to detect all mutations, including "private" mutations (non-phylogenetically informative polymorphisms) and assign them to individual contributors based on the frequency of the sequence reads, provided that the proportions of the various contributors are sufficiently different. Using a probe capture NGS system and both GeneMarker®HTS and Mixemt software programs, the interpretation of complex mixtures of equal proportion contributors, trace amount contributors, and more than two contributors in contrived mixtures, as well as interpretation of challenging forensic specimens is demonstrated.
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Affiliation(s)
- Mary Wisner
- Forensic Science Graduate Program, University of California-Davis, 1909 Galileo Ct. Ste. B, Davis, CA, USA
| | - Henry Erlich
- Children's Hospital Oakland Research Institute (CHORI), 5700 M.L.K. Jr. Way, Oakland, CA, USA
| | - Shelly Shih
- Children's Hospital Oakland Research Institute (CHORI), 5700 M.L.K. Jr. Way, Oakland, CA, USA
| | - Cassandra Calloway
- Children's Hospital Oakland Research Institute (CHORI), 5700 M.L.K. Jr. Way, Oakland, CA, USA.
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12
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BIO-INSPIRED MAGNETIC BEADS FOR ISOLATION OF SPERM FROM HETEROGENOUS SAMPLES IN FORENSIC APPLICATIONS. Forensic Sci Int Genet 2020; 52:102451. [PMID: 33556896 DOI: 10.1016/j.fsigen.2020.102451] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/26/2020] [Accepted: 12/02/2020] [Indexed: 12/23/2022]
Abstract
Rapid and efficient processing of sexual assault evidence will accelerate forensic investigation and decrease casework backlogs. The standardized protocols currently used in forensic laboratories require the continued innovation to handle the increasing number and complexity of samples being submitted to forensic labs. Here, we present a new technique leveraging the integration of a bio-inspired oligosaccharide (i.e., Sialyl-LewisX) with magnetic beads that provides a rapid, inexpensive, and easy-to-use strategy that can potentially be adapted with current differential extraction practice in forensics labs. This platform (i) selectively captures sperm; (ii) is sensitive within the forensic cut-off; (iii) provides a cost effective solution that can be automated with existing laboratory platforms; and (iv) handles small volumes of sample (∼200 μL). This strategy can rapidly isolate sperm within 25 minutes of total processing that will prepare the extracted sample for downstream forensic analysis and ultimately help accelerate forensic investigation and reduce casework backlogs.
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13
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Buonasera T, Eerkens J, de Flamingh A, Engbring L, Yip J, Li H, Haas R, DiGiuseppe D, Grant D, Salemi M, Nijmeh C, Arellano M, Leventhal A, Phinney B, Byrd BF, Malhi RS, Parker G. A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation. Sci Rep 2020; 10:11897. [PMID: 32681049 PMCID: PMC7368048 DOI: 10.1038/s41598-020-68550-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/19/2020] [Indexed: 11/09/2022] Open
Abstract
Sex estimation of skeletons is fundamental to many archaeological studies. Currently, three approaches are available to estimate sex-osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. We present matching osteological, shotgun-genomic, and proteomic data to estimate the sex of 55 individuals, each with an independent radiocarbon date between 2,440 and 100 cal BP, from two ancestral Ohlone sites in Central California. Sex estimation was possible in 100% of this burial sample using proteomics, in 91% using genomics, and in 51% using osteology. Agreement between the methods was high, however conflicts did occur. Genomic sex estimates were 100% consistent with proteomic and osteological estimates when DNA reads were above 100,000 total sequences. However, more than half the samples had DNA read numbers below this threshold, producing high rates of conflict with osteological and proteomic data where nine out of twenty conditional DNA sex estimates conflicted with proteomics. While the DNA signal decreased by an order of magnitude in the older burial samples, there was no decrease in proteomic signal. We conclude that proteomics provides an important complement to osteological and shotgun-genomic sex estimation.
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Affiliation(s)
- Tammy Buonasera
- Department of Environmental Toxicology, University of California, Rm 5241B Meyer Hall, 1 Shields Ave, Davis, CA, 95616, USA. .,Department of Anthropology, University of California, Davis, USA.
| | - Jelmer Eerkens
- Department of Anthropology, University of California, Davis, USA
| | - Alida de Flamingh
- Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana-Champaign, USA
| | - Laurel Engbring
- Far Western Anthropological Research Group, Inc, Davis, CA, USA
| | - Julia Yip
- Department of Environmental Toxicology, University of California, Rm 5241B Meyer Hall, 1 Shields Ave, Davis, CA, 95616, USA
| | - Hongjie Li
- Department of Anthropology, University of Illinois, Urbana-Champaign, USA
| | - Randall Haas
- Department of Anthropology, University of California, Davis, USA
| | | | - Dave Grant
- D&D Osteological Services, LLC, San Jose, CA, USA
| | - Michelle Salemi
- Proteomic Core Facility, Genome Center, University of California, Davis, CA, USA
| | - Charlene Nijmeh
- Muwekma Ohlone Tribe of the San Francisco Bay Area, Milpitas, CA, USA
| | - Monica Arellano
- Muwekma Ohlone Tribe of the San Francisco Bay Area, Milpitas, CA, USA
| | - Alan Leventhal
- Muwekma Ohlone Tribe of the San Francisco Bay Area, Milpitas, CA, USA.,Department of Anthropology, San Jose State University, San Jose, CA, USA
| | - Brett Phinney
- Proteomic Core Facility, Genome Center, University of California, Davis, CA, USA
| | - Brian F Byrd
- Far Western Anthropological Research Group, Inc, Davis, CA, USA
| | - Ripan S Malhi
- Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana-Champaign, USA.,Department of Anthropology, University of Illinois, Urbana-Champaign, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, USA
| | - Glendon Parker
- Department of Environmental Toxicology, University of California, Rm 5241B Meyer Hall, 1 Shields Ave, Davis, CA, 95616, USA.
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14
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Wright SN, Huge BJ, Dovichi NJ. Capillary zone electrophoresis separation and collection of spermatozoa for the forensic analysis of sexual assault evidence. Electrophoresis 2020; 41:1344-1353. [PMID: 32453860 DOI: 10.1002/elps.201900455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/29/2020] [Accepted: 05/21/2020] [Indexed: 01/23/2023]
Abstract
The processing of sexual assault kits (SAKs) relies on the genetic analysis of material extracted from swabs collected from the assault victim. A vital step in producing an identifiable DNA profile of the perpetrator is the effective separation of perpetrator (sperm) and victim (epithelial) DNA that have been isolated from the collected evidence. We report the use of capillary zone electrophoresis for the separation of intact sperm from whole and lysed epithelial cells in SAKs. The separated components are deposited into wells of a microtiter plate using a computer-controlled fraction collector, and quantitative PCR is used to verify the collection of sperm cells by targeted amplification of male DNA. We present results from simulated sexual assault samples that have been aged for up to 18 months, as well as vaginal swabs from authentic forensic kits. Components extracted from the vaginal swabs from the SAK comigrated with an aged semen sample at 6.25 ± 0.25 min. Epithelial cells migrated from 10-12 min, producing baseline resolution of the components. Sperm cells were collected in a microtiter plate for downstream analysis.
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15
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Abstract
Semen is crucial evidence for some sex crimes, with its sole confirmation being sperm detection. The success of sperm detection is dependent on all levels of preanalytic and analytic procedures. Specimen collection must be performed by well-trained and competent forensic physicians as well as forensic nurses, with preservation done properly before laboratory transfer. Laboratory procedures should consider archival sperm identification, by visualization, with adequate amounts separated from other cells to obtain male DNA profiles. Differential extraction is robust and accepted as the forensic standard but is time consuming and may result in male DNA loss. Thus, alternative methods and microdevices have been developed. Challenges in sperm isolation from vaginal or buccal epithelium mixes and discrimination in multiperpetrator cases have been overcome by single-cell profiling; however, problems inherent in identical twin discrimination and azoospermia have yet to be solved. Epigenetics and future molecular biomarkers may hold the key; therefore, all laboratory processes must consider DNA and RNA protection. Long-term specimen preservation should be done when possible in light of future confirmatory tests.
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Rodriguez JJRB, Calacal GC, Laude RP, De Ungria MCA. Integrating presumptive and confirmatory semen tests into DNA profiling of sexual assault evidence: a Philippine example. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2019. [DOI: 10.1186/s41935-019-0149-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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17
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Inci F, Ozen MO, Saylan Y, Miansari M, Cimen D, Dhara R, Chinnasamy T, Yuksekkaya M, Filippini C, Kumar DK, Calamak S, Yesil Y, Durmus NG, Duncan G, Klevan L, Demirci U. A Novel On-Chip Method for Differential Extraction of Sperm in Forensic Cases. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1800121. [PMID: 30250782 PMCID: PMC6145299 DOI: 10.1002/advs.201800121] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/13/2018] [Indexed: 05/20/2023]
Abstract
One out of every six American women has been the victim of a sexual assault in their lifetime. However, the DNA casework backlog continues to increase outpacing the nation's capacity since DNA evidence processing in sexual assault casework remains a bottleneck due to laborious and time-consuming differential extraction of victim's and perpetrator's cells. Additionally, a significant amount (60-90%) of male DNA evidence may be lost with existing procedures. Here, a microfluidic method is developed that selectively captures sperm using a unique oligosaccharide sequence (Sialyl-LewisX), a major carbohydrate ligand for sperm-egg binding. This method is validated with forensic mock samples dating back to 2003, resulting in 70-92% sperm capture efficiency and a 60-92% reduction in epithelial fraction. Captured sperm are then lysed on-chip and sperm DNA is isolated. This method reduces assay-time from 8 h to 80 min, providing an inexpensive alternative to current differential extraction techniques, accelerating identification of suspects and advancing public safety.
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Affiliation(s)
- Fatih Inci
- Bio‐Acoustic MEMS in Medicine (BAMM) LaboratoryCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford School of MedicineStanford UniversityPalo AltoCA94304USA
| | - Mehmet O. Ozen
- Bio‐Acoustic MEMS in Medicine (BAMM) LaboratoryCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford School of MedicineStanford UniversityPalo AltoCA94304USA
| | - Yeseren Saylan
- Bio‐Acoustic MEMS in Medicine (BAMM) LaboratoryCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford School of MedicineStanford UniversityPalo AltoCA94304USA
| | - Morteza Miansari
- Bio‐Acoustic MEMS in Medicine (BAMM) LaboratoryCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford School of MedicineStanford UniversityPalo AltoCA94304USA
| | - Duygu Cimen
- Bio‐Acoustic MEMS in Medicine (BAMM) LaboratoryCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford School of MedicineStanford UniversityPalo AltoCA94304USA
| | - Raghu Dhara
- Bio‐Acoustic MEMS in Medicine (BAMM) LaboratoryCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford School of MedicineStanford UniversityPalo AltoCA94304USA
| | - Thiruppathiraja Chinnasamy
- Bio‐Acoustic MEMS in Medicine (BAMM) LaboratoryCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford School of MedicineStanford UniversityPalo AltoCA94304USA
| | - Mehmet Yuksekkaya
- Department of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Chiara Filippini
- Department of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Deepan Kishore Kumar
- Department of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Semih Calamak
- Bio‐Acoustic MEMS in Medicine (BAMM) LaboratoryCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford School of MedicineStanford UniversityPalo AltoCA94304USA
| | - Yusuf Yesil
- Bio‐Acoustic MEMS in Medicine (BAMM) LaboratoryCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford School of MedicineStanford UniversityPalo AltoCA94304USA
| | - Naside Gozde Durmus
- Department of BiochemistryStanford UniversityStanford Genome Technology CenterPalo AltoCA94304USA
| | - George Duncan
- Crime LaboratoryBroward County Sheriff's OfficeFort LauderdaleFL33301USA
| | | | - Utkan Demirci
- Bio‐Acoustic MEMS in Medicine (BAMM) LaboratoryCanary Center at Stanford for Cancer Early DetectionDepartment of RadiologyStanford School of MedicineStanford UniversityPalo AltoCA94304USA
- Department of Electrical Engineering (by courtesy)Stanford UniversityStanfordCA94305USA
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18
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Sperm cell purification from mock forensic swabs using SOMAmer™ affinity reagents. Forensic Sci Int Genet 2018; 35:9-13. [DOI: 10.1016/j.fsigen.2018.03.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 03/01/2018] [Accepted: 03/26/2018] [Indexed: 11/18/2022]
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19
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Yousuff CM, Ho ETW, Hussain K. I, Hamid NHB. Microfluidic Platform for Cell Isolation and Manipulation Based on Cell Properties. MICROMACHINES 2017. [PMCID: PMC6189901 DOI: 10.3390/mi8010015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Caffiyar Mohamed Yousuff
- Correspondence: (C.M.Y.); (E.T.W.H.); (N.H.B.H.); Tel.: +60-1678-50269 (C.M.Y.); +60-1238-17752 (E.T.W.H.); +60-1927-87127 (N.H.B.H.)
| | - Eric Tatt Wei Ho
- Correspondence: (C.M.Y.); (E.T.W.H.); (N.H.B.H.); Tel.: +60-1678-50269 (C.M.Y.); +60-1238-17752 (E.T.W.H.); +60-1927-87127 (N.H.B.H.)
| | | | - Nor Hisham B. Hamid
- Correspondence: (C.M.Y.); (E.T.W.H.); (N.H.B.H.); Tel.: +60-1678-50269 (C.M.Y.); +60-1238-17752 (E.T.W.H.); +60-1927-87127 (N.H.B.H.)
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20
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Campbell R, Pierce SJ, Sharma DB, Shaw J, Feeney H, Nye J, Schelling K, Fehler-Cabral G. Comparing Standard and Selective Degradation DNA Extraction Methods: Results from a Field Experiment with Sexual Assault Kits,. J Forensic Sci 2016; 62:213-222. [DOI: 10.1111/1556-4029.13251] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 04/18/2016] [Accepted: 04/24/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Rebecca Campbell
- Department of Psychology; Michigan State University; East Lansing MI
| | - Steven J. Pierce
- Center for Statistical Training & Consultation; Michigan State University; East Lansing MI
| | - Dhruv B. Sharma
- Center for Statistical Training & Consultation; Michigan State University; East Lansing MI
| | - Jessica Shaw
- Department of Social Work; Boston College; Chestnut Hill MA
| | - Hannah Feeney
- Department of Psychology; Michigan State University; East Lansing MI
| | - Jeffrey Nye
- Michigan State Police; Forensic Science Division; Lansing MI
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21
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Cotton RW, Fisher MB. Review: Properties of sperm and seminal fluid, informed by research on reproduction and contraception. Forensic Sci Int Genet 2015; 18:66-77. [DOI: 10.1016/j.fsigen.2015.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/10/2015] [Accepted: 03/12/2015] [Indexed: 12/12/2022]
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