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Czado N, Houston R, Hughes S. Evaluation of metal ions and DNA recovery from the surface of fired and unfired brass ammunition to improve STR profiling. Int J Legal Med 2024; 138:1265-1272. [PMID: 38433135 DOI: 10.1007/s00414-024-03200-8] [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: 10/17/2023] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
Interest in recovering DNA from the surface of ammunition evidence for genotyping has increased over the past few years. Numerous studies have examined a variety of methods to maximize DNA recovery from these types of challenging samples, but successful DNA profiling has been inconsistent. Low amounts of DNA and PCR inhibition due to metal ions have been suggested as the leading causes of poor results; however, no study quantitatively examined the presence of metal ions at various stages of the DNA analysis workflow from DNA collection through to amplification. In this study, the effectiveness of six different DNA collection and purification methods commonly used by forensic laboratories to process brass ammunition for DNA evidence was investigated. The amount of copper, zinc, and other metals co-recovered from fired and unfired brass casings during DNA collection (using numerous soaking, swabbing, and direct PCR protocols) was quantified via Inductively Coupled Plasma - Optical Emission Spectrometry (ICP-OES). This same panel of metals was subsequently quantified after DNA lysis and purification steps. Results demonstrated that low amounts of DNA, DNA damage, and degradation are more detrimental to STR typing results than PCR inhibition, as metal ions were successfully removed by all DNA purification methods tested. Furthermore, the use of metal ion chelators increased the amount of DNA recovered and number of reportable STR alleles. This research informs the forensic community on the most effective way to collect and process trace amounts of biological material from brass ammunition and similar evidence.
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Affiliation(s)
- Natalia Czado
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, USA
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, USA
| | - Sheree Hughes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, USA.
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2
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Bonsu DNO, Higgins D, Simon C, Henry JM, Austin JJ. Metal-DNA interactions: Exploring the impact of metal ions on key stages of forensic DNA analysis. Electrophoresis 2024; 45:779-793. [PMID: 37638716 DOI: 10.1002/elps.202300070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/15/2023] [Accepted: 08/18/2023] [Indexed: 08/29/2023]
Abstract
Forensic DNA analysis continues to be hampered by the complex interactions between metals and DNA. Metal ions may cause direct DNA damage, inhibit DNA extraction and polymerase chain reaction (PCR) amplification or both. This study evaluated the impact of metal ions on DNA extraction, quantitation, and short tandem repeat profiling using cell-free and cellular (saliva) DNA. Of the 11 metals assessed, brass exhibited the strongest PCR inhibitory effects, for both custom and Quantifiler Trio quantitation assays. Metal ion inhibition varied across the two quantitative PCR assays and the amount of DNA template used. The Quantifiler Trio internal PCR control (IPC) only revealed evidence of PCR inhibition at higher metal ion concentrations, limiting the applicability of IPC as an indicator of the presence of metal inhibitor in a sample. Notably, ferrous ions were found to significantly decrease the extraction efficiency of the DNA-IQ DNA extraction system. The amount of DNA degradation and inhibition in saliva samples caused by metal ions increased with a dilution of the sample, suggesting that the saliva matrix provides protection from metal ion effects.
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Affiliation(s)
- Dan Nana Osei Bonsu
- Chemistry and Forensic Science, School of Environment and Science, Griffith University, Nathan, Queensland, Australia
- Forensic Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Denice Higgins
- Forensic Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- School of Dentistry, Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Claire Simon
- Forensic Science SA, Attorney-General's Department, Adelaide, South Australia, Australia
| | - Julianne M Henry
- Forensic Science SA, Attorney-General's Department, Adelaide, South Australia, Australia
| | - Jeremy J Austin
- Forensic Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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3
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Bonsu DNO, Higgins D, Simon C, Goodwin CS, Henry JM, Austin JJ. Quantitative PCR overestimation of DNA in samples contaminated with tin. J Forensic Sci 2023. [PMID: 37326229 DOI: 10.1111/1556-4029.15312] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023]
Abstract
Metals can pose challenges while conducting forensic DNA analysis. The presence of metal ions in evidence-related DNA extracts can degrade DNA or inhibit PCR as applied to DNA quantification (real-time PCR or qPCR) and/or STR amplification, leading to low success in STR profiling. Different metal ions were spiked into 0.2 and 0.5 ng of human genomic DNA in an "inhibition study" and the impact was evaluated by qPCR using the Quantifiler™ Trio DNA Quantification Kit (Thermo Fisher Scientific) and an in-house SYBR Green assay. This study reports on a contradictory finding specific to tin (Sn) ions, which caused at least a 38,000-fold overestimation of DNA concentration when utilizing Quantifiler Trio. This was explained by the raw and multicomponent spectral plots, which indicated that Sn suppresses the Quantifiler Trio passive reference dye (Mustang Purple™, MP) at ion concentrations above 0.1 mM. This effect was not observed when DNA was quantified using SYBR Green with ROX™ as the passive reference, nor when DNA was extracted and purified prior to Quantifiler Trio. The results show that metal contaminants can interfere with qPCR-based DNA quantification in unexpected ways and may be assay dependent. The results also highlight the importance of qPCR as a quality check to determine steps for sample cleanup prior to STR amplification that may be similarly impacted by metal ions. Forensic workflows should recognize the risk of inaccurate DNA quantification of samples that are collected from substrates containing tin.
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Affiliation(s)
- Dan Nana Osei Bonsu
- Chemistry and Forensic Sciences, Griffith University, Nathan, Brisbane, Queensland, Australia
- Forensic Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Denice Higgins
- Forensic Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- School of Dentistry, Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Claire Simon
- Forensic Science SA, Attorney-General's Department, Adelaide, South Australia, Australia
| | | | - Julianne M Henry
- Forensic Science SA, Attorney-General's Department, Adelaide, South Australia, Australia
| | - Jeremy J Austin
- Forensic Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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4
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McElhoe J, Mandracchia T, Bille T, Holland M. Impact of storage conditions and time on DNA yield from ammunition cartridges. Int J Legal Med 2023:10.1007/s00414-023-03018-w. [PMID: 37237149 DOI: 10.1007/s00414-023-03018-w] [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: 01/03/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023]
Abstract
Recovery of suitable amounts of DNA from ammunition cartridges for short tandem repeat (STR) or mitochondrial (mt) DNA analysis has been a challenge for crime laboratories. The metal composition of cartridge cases and projectiles exposes the DNA to harmful ions that damage and ultimately degrade the DNA such that it cannot be effectively amplified. The current study assessed the impact of time and storage conditions on touch DNA deposited on cartridge components of varying metal content: aluminum, nickel, brass, and copper. Elevated humidity levels facilitated greater DNA degradation and loss compared to low humidity (or "dry") conditions, indicating that recovered cartridge component evidence should be stored in a low-humidity environment immediately after collection, preferably with a desiccant. As expected, a relationship was observed between the amount of time elapsed since the cartridge components were handled and the associated DNA yield. Interestingly, while yields dropped considerably in the first 48-96 h post-handling, regardless of the storage conditions, a layering effect was observed that helps maintain a relatively constant level of surface DNA over extended periods of time. An apparent layering effect was also observed on cartridge components following multiple surface depositions, where yields were two times higher than single deposition samples at similar timepoints. Overall, these findings suggest that storage conditions and a layering affect play an important role in the preservation of DNA on ammunition components.
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Affiliation(s)
- Jennifer McElhoe
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA.
| | - Therese Mandracchia
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA
| | - Todd Bille
- United States Bureau of Alcohol, Tobacco, Firearms, and Explosives, National Laboratory Center, 6000 Ammendale Road, Beltsville, MD, 20705, USA
| | - Mitchell Holland
- Forensic Science Program, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA
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Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.
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6
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Canale LC, McElhoe JA, Dimick G, DeHeer KM, Beckert J, Holland MM. Routine Mitogenome MPS Analysis from 1 and 5 mm of Rootless Human Hair. Genes (Basel) 2022; 13:2144. [PMID: 36421819 PMCID: PMC9690917 DOI: 10.3390/genes13112144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 08/16/2023] Open
Abstract
While hair shafts are a common evidence type in forensic cases, they are often excluded from DNA analysis due to their limited DNA quantity and quality. Mitochondrial (mt) DNA sequencing is the method of choice when working with rootless hair shaft fragments due to the elevated copy number of mtDNA and the highly degraded nature of nuclear (n) DNA. Using massively parallel sequencing (MPS) of the mitochondrial (mito) genome, we studied the impact of hair age (time since collection) and physical characteristics (hair diameter, medullary structure, and length of hair tested) on mtDNA recovery and MPS data quality. Hair shaft cuttings of 1 and 5 mm from hairs less than five years to 46 years of age from 60 donors were characterized microscopically. Mitogenome sequences were generated using the Promega PowerSeqTM Whole Mito System prototype kit and the Illumina MiSeq instrument. Reportable mitogenome sequences were obtained from all hairs up to 27 years of age (37 donors), with at least 98% of the mitogenome reported for more than 94% of the 74 hair samples analyzed; the minimum reported sequence was 88%. Furthermore, data from the 1 and 5 mm replicates gave concordant haplotypes. As expected, mtDNA yield decreased, mtDNA degradation increased, and mitogenome MPS data quality declined as the age of the hair increased. Hair diameter and medullary structure had minimal impact on yield and data quality. Our findings support that MPS is a robust and reliable method for routinely generating mitogenome sequences from 1 and 5 mm hair shaft samples up to 27 years of age, which is of interest to the forensic community, biological anthropologists, and medical geneticists.
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Affiliation(s)
- Lauren C. Canale
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Jennifer A. McElhoe
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Gloria Dimick
- Mitotyping Technologies, 2565 Park Center Blvd., Suite 200, State College, PA 16801, USA
| | | | - Jason Beckert
- Microtrace 790 Fletcher Drive, Suite 106, Elgin, IL 60123, USA
| | - Mitchell M. Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA 16802, USA
- Mitotyping Technologies, 2565 Park Center Blvd., Suite 200, State College, PA 16801, USA
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7
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Genetic profiling from 9 mm fired cartridge cases over 30 days. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Czado N, Houston R, Hughes S. Comparison of metal ions recovered during DNA analysis of brass ammunition and effects of copper and zinc ions on DNA profiling. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Elwick K, Gauthier Q, Rink S, Cropper E, Kavlick MF. Recovery of DNA from fired and unfired cartridge casings: comparison of two DNA collection methods. Forensic Sci Int Genet 2022; 59:102726. [PMID: 35660851 DOI: 10.1016/j.fsigen.2022.102726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/22/2022] [Accepted: 05/17/2022] [Indexed: 01/14/2023]
Abstract
For over 10 years, various studies have attempted to increase the recovery of DNA from ammunition by modifying the DNA collection, extraction, purification, and amplification procedures, with varying levels of success. This study focused on the "soaking" method of Montpetit & O'Donnell [1] and the "rinse-and-swab" method of Bille et al. [2]. First, testing for the presence of exogenous DNA, 210 boxed cartridges (brass, steel, and nickel-plated) from nine manufacturers were swabbed and DNA was extracted, concentrated, and quantified. Extracts that quantified > 0 ng/µL (44 of 210) were amplified and genotyped with GlobalFiler™. Of those, only one extract yielded two alleles indicating that the manufacturing and packaging of ammunition was virtually DNA free. Next, to obtain a baseline comparison of two DNA collection methods on a non-metallic substrate and identify a suitable number of cells to spot on cartridges, different DNA input amounts of primary human adult epidermal keratinocytes (HEKa) were tested. Thereafter, 300 brass and 300 nickel-plated, cartridges were spotted with HEKa cells containing ~5 ng of DNA, fired or unfired, and processed with either method. Finally, five methods representing hybrids of the soaking and rinse-and-swab methods were tested to determine if variations of those methods could be used to increase DNA yield and recovery. The results show that the soaking method consistently yielded more DNA than the rinse-and-swab method from a non-metallic substrate. However, the comparison study demonstrated that both methods performed comparably for cartridges. On average, the soaking method recovered 0.25 ng of DNA (5.1% recovery) and the rinse-and-swab method recovered 0.28 ng (5.8% recovery). However, average recoveries were significantly different among three analysts and considerable variation in yields were observed, possibly due to storage time. Furthermore, consistent with prior reports, the DNA recovered from brass casings was only 16% of that recovered from nickel-plated casings and the average yield of DNA from fired casings was reduced to 67% of unfired casings. Moreover, DNA extracts from brass or nickel-plated casings did not appear to contain amplification inhibitors and only 30/596 appeared severely degraded. Finally, both the published rinse-and-swab and soaking methods yielded more DNA than all modifications of the two methods. Overall, both methods yielded equivalent DNA quantities. Additionally, recovery of DNA from any given cartridge casing may be dependent on storage time as well as the skill, proficiency, and experience of the analyst and may reflect stochastic effects, particularly for casings containing low copy and/or degraded DNA.
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Affiliation(s)
- Kyleen Elwick
- Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Research and Support Unit, 2501 Investigation Parkway, Quantico, VA 22135, USA
| | - Quentin Gauthier
- Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Research and Support Unit, 2501 Investigation Parkway, Quantico, VA 22135, USA
| | - Stephanie Rink
- Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Research and Support Unit, 2501 Investigation Parkway, Quantico, VA 22135, USA
| | - Emily Cropper
- Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Research and Support Unit, 2501 Investigation Parkway, Quantico, VA 22135, USA
| | - Mark F Kavlick
- Federal Bureau of Investigation Laboratory Division, Research and Support Unit, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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10
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van Oorschot RAH, Meakin GE, Kokshoorn B, Goray M, Szkuta B. DNA Transfer in Forensic Science: Recent Progress towards Meeting Challenges. Genes (Basel) 2021; 12:genes12111766. [PMID: 34828372 PMCID: PMC8618004 DOI: 10.3390/genes12111766] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 01/16/2023] Open
Abstract
Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to DNA quantities and profile types being obtained given particular scenarios and circumstances, is paramount when performing, and giving guidance on, evaluations of DNA findings given activity level propositions (activity level evaluations). In late 2018 and early 2019, three major reviews were published on aspects of DNA-TPPR, with each advocating the need for further research and other actions to support the conduct of DNA-related activity level evaluations. Here, we look at how challenges are being met, primarily by providing a synopsis of DNA-TPPR-related articles published since the conduct of these reviews and briefly exploring some of the actions taken by industry stakeholders towards addressing identified gaps. Much has been carried out in recent years, and efforts continue, to meet the challenges to continually improve the capacity of forensic experts to provide the guidance sought by the judiciary with respect to the transfer of DNA.
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Affiliation(s)
- Roland A. H. van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, VIC 3085, Australia
- School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia
- Correspondence:
| | - Georgina E. Meakin
- Centre for Forensic Science, University of Technology Sydney, Ultimo, NSW 2007, Australia;
- Centre for the Forensic Sciences, Department of Security and Crime Science, University College London, London WC1H 9EZ, UK
| | - Bas Kokshoorn
- Netherlands Forensic Institute, 2497 GB The Hague, The Netherlands;
- Faculty of Technology, Amsterdam University of Applied Sciences, 1097 DZ Amsterdam, The Netherlands
| | - Mariya Goray
- College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia;
| | - Bianca Szkuta
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220, Australia;
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11
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Patterson C, Gray S, Wendt FR, Roy R. Inhibition of DNA amplification caused by metal in extracted bloodstains and in direct amplification. Forensic Sci Int Genet 2021; 55:102598. [DOI: 10.1016/j.fsigen.2021.102598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022]
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12
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Comparison of Isohelix™ and Rayon swabbing systems for touch DNA recovery from metal surfaces. Forensic Sci Med Pathol 2021; 17:577-584. [PMID: 34674113 PMCID: PMC8528942 DOI: 10.1007/s12024-021-00423-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2021] [Indexed: 01/11/2023]
Abstract
A previous study evaluating two swabbing systems found that DNA was best recovered from sterile metal substrates using an Isohelix™ swab wetted with isopropyl alcohol rather than a Rayon swab with water as the wetting agent. We tested the same swabbing systems on metal (aluminum, brass, and stainless steel) and plastic substrates in a regularly touched environment to simulate the non-deliberate transfer of touch evidence likely seen in a casework scenario, to ascertain the performance of these swabs in an uncontrolled situation. Higher amounts of touch DNA were recovered with Isohelix™ swabs (0.5 – 3.3 ng) compared to Rayon swabs (0.13 – 1.2 ng). The Isohelix™ swabbing system was found to significantly recover more touch DNA (p = 0.04) from the metal substrates than the Rayon swabbing system, consistent with the findings of our previous work. The results contribute to our understanding of the impact of sample collection techniques on touch DNA recovery from problematic metal surfaces and suggest that supplemental cleaning of substrates as a precautionary step against the spread of infections may affect touch DNA persistence and the recovery efficiency of swabs.
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Moore D, Beaumont D, Brown M, Clayton T, Coleman K, Subhani Z, Thomson J. An investigation of two methods of DNA recovery from fired and unfired 9 mm ammunition. Sci Justice 2021; 61:160-169. [PMID: 33736848 DOI: 10.1016/j.scijus.2020.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/01/2020] [Accepted: 11/07/2020] [Indexed: 01/12/2023]
Abstract
Cartridge cases are often recovered from crime scenes involving firearms and, in the United Kingdom (where gun possession is strictly controlled), these are commonly from 9 mm calibre ammunition. The ability to obtain informative DNA profiles from touch DNA on recovered cartridges could have a significant impact on the investigation of that type of offence. However, this avenue may not be routinely considered as investigators in the UK have historically had a low expectation of obtaining useful DNA profiles. This stance may not be unreasonable given that (a) only trace amounts of DNA are likely to have been transferred onto the cartridge cases through handling; and (b) when the cartridge is spent, the potential deterioration of that DNA caused by the act of discharging the weapon. We introduce a novel semi-automatable method using direct lysis for the recovery of DNA from ammunition and compare it with a traditional double-swabbing method (using wet and dry swabs). DNA profiling of the DNA recovered using both methods was carried out using the ESI17 FAST STR system (Promega). This demonstrated a significant increase in DNA recovery using the direct lysis approach, and correspondingly improved STR results. We also investigated the effect on the recovery and profiling of DNA from fired, and unfired, 9 mm cartridges using the direct lysis technique. These results demonstrate that DNA suitable for STR analysis can still be recovered from fired ammunition with only slightly reduced yields compared to unfired ammunition. In these experiments, the handler of the ammunition was most commonly either the sole contributor or the major contributor to the recovered DNA profile.
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Affiliation(s)
| | | | - Melanie Brown
- School of Science, Engineering & Design, Teesside University, Middlesbrough, UK
| | | | - Kiera Coleman
- School of Science, Engineering & Design, Teesside University, Middlesbrough, UK
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14
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Marshall C, Parson W. Interpreting NUMTs in forensic genetics: Seeing the forest for the trees. Forensic Sci Int Genet 2021; 53:102497. [PMID: 33740708 DOI: 10.1016/j.fsigen.2021.102497] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/29/2023]
Abstract
Nuclear mitochondrial DNA (mtDNA) segments (NUMTs) were discovered shortly after sequencing the first human mitochondrial genome. They have earlier been considered to represent archaic elements of ancient insertion events, but modern sequencing technologies and growing databases of mtDNA and NUMT sequences confirm that they are abundant and some of them phylogenetically young. Here, we build upon mtDNA/NUMT review articles published in the mid 2010 s and focus on the distinction of NUMTs and other artefacts that can be observed in aligned sequence reads, such as mixtures (contamination), point heteroplasmy, sequencing error and cytosine deamination. We show practical examples of the effect of the mtDNA enrichment method on the representation of NUMTs in the mapped sequence data and discuss methods to bioinformatically filter NUMTs from mtDNA reads.
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Affiliation(s)
- Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19902, USA; SNA International, Contractor Supporting the AFMES-AFDIL, Alexandria, VA 22314, USA; Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Walther Parson
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA; Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria.
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15
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Bonsu DOM, Higgins D, Henry J, Austin JJ. Evaluation of the efficiency of Isohelix™ and Rayon swabs for recovery of DNA from metal surfaces. Forensic Sci Med Pathol 2020; 17:199-207. [PMID: 33180274 DOI: 10.1007/s12024-020-00329-x] [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] [Accepted: 10/08/2020] [Indexed: 11/28/2022]
Abstract
PURPOSE We investigated the recovery and extraction efficiency of DNA from three metal surfaces (brass, copper, steel) relevant to forensic casework, and plastic (control) using two different swabbing systems; Rayon and Isohelix™ swabs, with sterile water and isopropyl alcohol respectively, as the wetting solutions. METHODS Twenty nanograms of human genomic DNA were applied directly to Isohelix™ and Rayon swabs; and to the metal and plastic substrates. All substrates were left to dry for 24 h, followed by single wet swabbing and extraction with the DNA IQ™ System. DNA extracts were quantified using real time quantitative PCR assays with SYBR green chemistry. RESULTS DNA was extracted from directly seeded Isohelix™ swabs with a high efficiency of 98%, indicating effective DNA-release from the swab into the extraction buffer. In contrast, only 58% of input DNA was recovered from seeded Rayon swabs, indicating higher DNA retention by these swabs. Isohelix™ swabs recovered 32 - 53% of DNA from metal surfaces, whilst the Rayon swabs recovered 11-29%. DNA recovery was lowest from copper and highest from brass. Interestingly, Rayon swabs appeared to collect more DNA from the plastic surface than Isohelix™ swabs, however, due to the lower release of DNA from Rayon swabs they returned less DNA overall following extraction than Isohelix™ swabs. CONCLUSION These results demonstrate that DNA samples deposited on metal surfaces can be more efficiently recovered using Isohelix™ swabs wetted with isopropyl alcohol than Rayon swabs wetted with sterile water, although recovery is affected by the substrate type.
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Affiliation(s)
- Dan O M Bonsu
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia. .,Department of Forensic Sciences, University of Cape Coast, Cape Coast, Ghana.
| | - Denice Higgins
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.,School of Dentistry, Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Julianne Henry
- Forensic Science SA (FSSA), Adelaide, South Australia, Australia.,College of Science and Engineering, Flinders University of South Australia, Adelaide, South Australia, Australia
| | - Jeremy J Austin
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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16
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Melchionda F, Stanciu F, Buscemi L, Pesaresi M, Tagliabracci A, Turchi C. Searching the undetected mtDNA variants in forensic MPS data. Forensic Sci Int Genet 2020; 49:102399. [PMID: 33038616 DOI: 10.1016/j.fsigen.2020.102399] [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: 06/12/2020] [Revised: 08/27/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
The efficiency of MPS in forensic mtDNA analysis has been thoroughly proven, although a reliable and well established data evaluation still remains a critical point. Numerous bioinformatics tools have been developed, but most of them require specific operating systems and high costs, while free open-source programs with user-friendly interfaces are few. In this study, 43 full mtGenomes were sequenced using the Ion Personal Genome Machine™ (PGM™) System and analyzed utilizing the plug-in Variant Caller (TVC) of the Ion Torrent Software Suite and the mtDNA-Server (mDS), a free web-based mitochondrial analysis tool for MPS data. The outcomes of these two different analysis tools were compared to variants noted after manual inspection of the aligned reads performed using Integrative Genomics Viewer (IGV). The comparison highlighted the presence of thirty-nine discordant variant calls, which were resolved by Sanger sequencing that confirmed the presence of all variants, except for 7 deletions. The combined adoption of IGV and Sanger type sequencing confirmatory steps, in addition of TVC and mDS analysis, resulted in a more accurate variants assignment with the detection of 32 additional true polymorphisms, which were noted in the final dataset. Regarding the heteroplasmy issue, out of a total of thirty heteroplasmic variants, twenty-eight were detected by the TVC, while the mDS detected twenty-two. Overall, none of the used bioinformatics tools were the perfect choice and a secondary analysis with an expert's opinion in complete mtGenome MPS data evaluation is still required in forensic genetic analysis.
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Affiliation(s)
- Filomena Melchionda
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Florin Stanciu
- Romanian National DNA Database, National Forensic Science Institute, General Inspectorate of Romanian Police, Bucharest, Romania.
| | - Loredana Buscemi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Mauro Pesaresi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Adriano Tagliabracci
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Chiara Turchi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
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Holland CA, McElhoe JA, Gaston-Sanchez S, Holland MM. Damage patterns observed in mtDNA control region MPS data for a range of template concentrations and when using different amplification approaches. Int J Legal Med 2020; 135:91-106. [PMID: 32940843 DOI: 10.1007/s00414-020-02410-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/21/2020] [Indexed: 12/15/2022]
Abstract
Massively parallel sequencing (MPS) of mitochondrial (mt) DNA allows practitioners the ability to fully resolve heteroplasmic sites. In forensic DNA analysis, identifying heteroplasmy (a naturally occurring mixture of two mtDNA profiles) can provide additional mtDNA profile information which can lead to an increase in the discrimination potential of an mtDNA match between an evidentiary sample and reference source. Forensic samples such as hair and skeletal remains, especially older, more compromised samples, can often exhibit DNA damage. Because both damage and heteroplasmy can manifest as a mixture of two nucleotides, it is important to differentiate between the two conditions when interpreting mtDNA MPS data. In this study, DNA damage was applied under controlled conditions to samples containing a range of template concentrations, including some with identified heteroplasmy. Damage was applied via storage in water at room temperature on samples diluted before or after storage to mimic low template scenarios. Damage was assessed with respect to the following areas: mtDNA quantification and degradation ratios, MPS read depth, MPS profile results, overall damage rates, and the interpretation of heteroplasmy. Datasets were generated to assess and compare two different amplification and library preparation strategies: the Promega PowerSeq™ CRM Nested System kit and a 1.16 kb target amplicon of the entire mtDNA control region followed by a Nextera® XT library preparation. The results of this study provide an evaluation of the Promega 10-plex MPS procedure as an improved process to mitigate the impact of mtDNA damage on low template samples. Some of the negative effects of damage observed in this study were a decrease in mtDNA yield by 20-30% and lower quality MPS sequencing results. These effects were observed more frequently when samples were diluted prior to inducing damage, illustrating that low template samples are more susceptible to damage. The findings of this study will assist forensic laboratories in differentiating between damage and heteroplasmy, which is essential when developing robust mtDNA MPS interpretation guidelines such as setting appropriate reporting thresholds.
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Affiliation(s)
- Charity A Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA
| | - Jennifer A McElhoe
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA
| | - Sidney Gaston-Sanchez
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA.,Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, USA
| | - Mitchell M Holland
- Forensic Science Program, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, 014 Thomas Building, University Park, PA, 16802, USA.
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18
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Forensic touch DNA recovery from metal surfaces – A review. Sci Justice 2020; 60:206-215. [DOI: 10.1016/j.scijus.2020.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/20/2020] [Accepted: 01/26/2020] [Indexed: 12/23/2022]
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19
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McElhoe JA, Holland MM. Characterization of background noise in MiSeq MPS data when sequencing human mitochondrial DNA from various sample sources and library preparation methods. Mitochondrion 2020; 52:40-55. [PMID: 32068127 DOI: 10.1016/j.mito.2020.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 12/18/2019] [Accepted: 02/12/2020] [Indexed: 12/20/2022]
Abstract
Improved resolution of massively parallel sequencing (MPS) allows for the characterization of mitochondrial (mt) DNA heteroplasmy to levels previously unattainable with traditional sequencing approaches. An essential criterion for the reporting of heteroplasmy is the ability of the MPS method to distinguish minor sequence variants (MSVs) from system noise, or error. Therefore, an assessment of the background noise in the MPS method is desirable to identify the point at which reliable data can be reported. Substitution and sequence specific error (SSE) was evaluated for a variety of sample types and two library preparations. Substitution error rates ranged from 0.18 to 0.49 per 100 nucleotides with C positions generally having the highest rate of misincorporation. Comparison of error rates across sample types indicated a significant increase for samples with damaged DNA. The positions of error were varied across datasets (pairwise concordance 0-68%), but had greater consistency within the damaged samples (80-96%). The most commonly observed motif preceding error in forward reads was CCG, while GGT was most common in reverse reads, both consistent with previous findings. The findings illustrate that for datasets containing samples with damaged DNA, reporting thresholds for heteroplasmy may have to be modified and individual sites with error levels exceeding thresholds should be scrutinized. Collectively, the shifting error profiles observed across the various sample types and library preparation methods demonstrates the need for an assessment of error under these varying circumstances. Characterization of the applicable background noise will help to ensure that thresholds are reliably set for detection of true MSVs.
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Affiliation(s)
- Jennifer A McElhoe
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
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20
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Bille TW, Fahrig G, Weitz SM, Peiffer GA. An improved process for the collection and DNA analysis of fired cartridge cases. Forensic Sci Int Genet 2020; 46:102238. [PMID: 32028222 DOI: 10.1016/j.fsigen.2020.102238] [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: 10/11/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 01/14/2023]
Abstract
Improvements to the DNA analysis of fired cartridge cases have been made in recent years, yet successful analysis of this important evidence type remains difficult. In this study, we describe both a novel device for the collection and transport of fired cartridge cases and a new DNA recovery method that incorporates a rinse-and-swab technique. This technique combines two different types of swabs and a rinse solution with additives that reduce the degradative effects that copper has on DNA. The new recovery method yielded approximately threefold more DNA than the traditional double swab method and reduced the evidence of degradation. After validation, we estimated the real-world success rate of obtaining DNA profiles suitable for comparison with the rinse-and-swab method by testing over 100 cartridge cases collected from crime scenes. Approximately 67 % of the time (8 of 12), at least one DNA profile suitable for comparison was obtained from fired cartridge cases assumed to be associated with a single firearm using the collection device and the rinse-and-swab method when the fired cartridge cases were collected within 24 h.
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Affiliation(s)
- Todd W Bille
- United States Bureau of Alcohol, Tobacco, Firearms, and Explosives, National Laboratory Center, 6000 Ammendale Road, Beltsville, MD, 20705, United States.
| | - Glenn Fahrig
- United States Bureau of Alcohol, Tobacco, Firearms, and Explosives, National Laboratory Center, 6000 Ammendale Road, Beltsville, MD, 20705, United States
| | - Steven M Weitz
- United States Bureau of Alcohol, Tobacco, Firearms, and Explosives, National Laboratory Center, 6000 Ammendale Road, Beltsville, MD, 20705, United States
| | - Greg A Peiffer
- United States Bureau of Alcohol, Tobacco, Firearms, and Explosives, National Laboratory Center, 6000 Ammendale Road, Beltsville, MD, 20705, United States
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21
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High throughput sequencing data analysis workflow: mtDNA variant detection and identification of STR/Y-STR alleles and iso-alleles. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.121] [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]
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22
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Strobl C, Churchill Cihlar J, Lagacé R, Wootton S, Roth C, Huber N, Schnaller L, Zimmermann B, Huber G, Lay Hong S, Moura-Neto R, Silva R, Alshamali F, Souto L, Anslinger K, Egyed B, Jankova-Ajanovska R, Casas-Vargas A, Usaquén W, Silva D, Barletta-Carrillo C, Tineo DH, Vullo C, Würzner R, Xavier C, Gusmão L, Niederstätter H, Bodner M, Budowle B, Parson W. Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel. Forensic Sci Int Genet 2019; 42:244-251. [PMID: 31382159 DOI: 10.1016/j.fsigen.2019.07.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/09/2019] [Accepted: 07/21/2019] [Indexed: 12/24/2022]
Abstract
The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.
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Affiliation(s)
- Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Robert Lagacé
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Sharon Wootton
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Chantal Roth
- Human Identification Group, ThermoFisher Scientific, San Francisco, CA, USA
| | - Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Lisa Schnaller
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Seah Lay Hong
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Rodrigo Moura-Neto
- Laboratório de Biologia Molecular Forense, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rosane Silva
- Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Farida Alshamali
- Dubai Police, Gen. Dept. Forensic Science & Criminology, Dubai, United Arab Emirates
| | - Luis Souto
- Laboratorio de Genética Aplicada, Departamento de Biologia, Universidade de Aveiro, Portugal
| | | | - Balazs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Renata Jankova-Ajanovska
- Institute of Forensic Medicine, Criminalistic and Medical Deontology, Medical Faculty, University "St. Cyril and Methodius", Skopje, Macedonia
| | - Andrea Casas-Vargas
- Group of Population Genetics and Identification, Genetics Institute, National University of Colombia, Bogotá, Colombia
| | - Wiliam Usaquén
- Group of Population Genetics and Identification, Genetics Institute, National University of Colombia, Bogotá, Colombia
| | - Dayse Silva
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | | | - Dean Herman Tineo
- Universidad Nacional Mayor de San Marcos, Instituto de Medicina Legal del Perú, Lima, Peru
| | - Carlos Vullo
- DNA Forensic Laboratory, Argentinean Forensic Anthropology team (EAAF), Córdoba, Argentina
| | - Reinhard Würzner
- Division of Hygiene & Med. Microbiology, Medical University of Innsbruck, Austria
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, TX, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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