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Jansson L, Aili Fagerholm S, Börkén E, Hedén Gynnå A, Sidstedt M, Forsberg C, Ansell R, Hedman J, Tillmar A. Assessment of DNA quality for whole genome library preparation. Anal Biochem 2024; 695:115636. [PMID: 39111682 DOI: 10.1016/j.ab.2024.115636] [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: 03/11/2024] [Revised: 07/26/2024] [Accepted: 08/03/2024] [Indexed: 08/22/2024]
Abstract
In recent years, more sophisticated DNA technologies for genotyping have enabled considerable progress in various fields such as clinical genetics, archaeogenetics and forensic genetics. DNA samples previously rejected as too challenging to analyze due to low amounts of degraded DNA can now provide useful information. To increase the chances of success with the new methodologies, it is crucial to know the fragment size of the template DNA molecules, and whether the DNA in a sample is mostly single or double stranded. With this knowledge, an appropriate library preparation method can be chosen, and the DNA shearing parameters of the protocol can be adjusted to the DNA fragment size in the sample. In this study, we first developed and evaluated a user-friendly fluorometry-based protocol for estimation of DNA strandedness. We also evaluated different capillary electrophoresis methods for estimation of DNA fragmentation levels. Next, we applied the developed methodologies to a broad variety of DNA samples processed with different DNA extraction protocols. Our findings show that both the applied DNA extraction method and the sample type affect the DNA strandedness and fragmentation. The established protocols and the gained knowledge will be applicable for future sequencing-based high-density SNP genotyping in various fields.
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Affiliation(s)
- Linda Jansson
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | | | - Emelie Börkén
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Arvid Hedén Gynnå
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden
| | - Maja Sidstedt
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden
| | | | - Ricky Ansell
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden; Department of Physics, Chemistry and Biology, IFM, Linköping University, Linköping, Sweden
| | - Johannes Hedman
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
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2
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Hudson BC, Dawson Green T. Modified differential lysis for sexual assault samples using a combined enzymatic and alkaline approach. Forensic Sci Res 2024; 9:owae022. [PMID: 38831792 PMCID: PMC11146638 DOI: 10.1093/fsr/owae022] [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: 10/14/2023] [Accepted: 03/28/2024] [Indexed: 06/05/2024] Open
Abstract
Sexual assault sample processing, despite recent funding and research efforts, remains time-consuming, labourious, and inefficient. These limitations, combined with the prevalence of sexual assaults, have prompted the need to develop a cheaper, quicker, and more robust method for separating victim and perpetrator contributions within sexual assault evidence so that analysts can keep pace with submissions and cases can be resolved in a timely manner. Thus, this study examined the use of a combined enzymatic and alkaline approach for differential cell lysis-with the goal of developing a quick, cheap, and more efficient DNA isolation method. Quantification results for this assay revealed that (72.0 ± 18.3)%, (15.8 ± 14.2)%, and (29.5 ± 23.7)% of total DNA were retained in sperm fractions for neat semen, neat vaginal, and semen-vaginal mixture eluates, respectively. Short tandem repeat (STR) analysis of mixture samples processed with this technique exhibited sperm fraction DNA profiles with mean male-to-female ratios of 1.74:1, which was a 3.01 ± 2.30-fold improvement in male-to-female ratios and led to the recovery of 5.90 ± 7.80 unshared male contributor alleles in sperm fractions that were otherwise undetected in unseparated controls. Overall, this study presented a modified differential lysis approach using prepGEM™ and sodium hydroxide treatments that can accomplish cell elution and fractional lysis within 25 min. Future studies should investigate alternative "non-sperm" cell lysis methods to enhance lysis efficiency and minimize the potential for inhibition, as well as the optimization and automation of this technique. Key points Traditional sexual assault sample processing methods are time-consuming and inefficient.This modified differential lysis method produces lysates with sufficient DNA yield and quality.A combined technique using enzymatic and alkaline lysis can accomplish fractional separation.Lysis with prepGEM and NaOH absent purification is compatible with downstream processes.
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Affiliation(s)
- Brittany C Hudson
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
- Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - Tracey Dawson Green
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
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3
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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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Ginart S, Garrigos Calivares L, Caputo M, Corach D, Sala A. Improving the efficiency of Y-chromosome detection and the quality of STR typing in forensic casework with an in-house made qPCR and HRM system based on SYTO™ 9 chemistry. Forensic Sci Int 2024; 354:111893. [PMID: 38064775 DOI: 10.1016/j.forsciint.2023.111893] [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: 06/09/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
Abstract
DNA quantification prior to STR amplification is a crucial step in forensic casework. Obtaining good-quality genetic STR profiles depends mainly on the amount and integrity of the DNA input in the PCR. In addition, the detection of male trace DNA provides key information for forensic investigation. AIM To evaluate the correlation between the quantification results obtained with the previously developed Amel-Y system, and its ability to detect Y-chromosome DNA by HRM, with the resulting STR profiles, and to ultimately show that Amel-Y can be routinely used in forensic casework to improve STR and Y-STR results. MATERIAL & METHODS Biological samples derived from forensic casework (85 reference and 391 evidence samples) were quantified by the Amel-Y system (a duplex qPCR/HRM based on SYTO™ 9 chemistry) using Rotor-Gene 6000. STRs were amplified and analyzed with GeneAmp™ PCR System 9700 or Veriti™ Thermal Cyclers and ABI 3500 Genetic Analyzer, respectively. RESULTS After DNA normalization, a total of 386 STR profiles were obtained (305 full and 81 partial). Sex typing by HRM was 100% successful in reference samples. Male DNA was detected by HRM in 210 evidence samples. 80/201 were mixed with an excess of female DNA. In addition, Amel-Y was able to detect Y-chromosome DNA in mixed samples that did not amplify the Y-variant of Amelogenin marker with commercial STR kits. The reproducibility and precision of the Amel-Y system were demonstrated (CVCt% ≤ 9.55) within the dynamic range analyzed (0.016-50 ng/µL; 41 independent runs). Amel-Y also proved to be compatible with other real-time PCR platforms. CONCLUSION We demonstrated that Amel-Y is a robust quantification system that can be routinely used in forensic casework to obtain reliable autosomal STR profiles and can be suitable as a predictor for Y-STR typing success when male DNA is detected. HRM can be used as a rapid screening tool for male DNA detection in mixed samples. Alternative designs like Amel-Y offer independence from commercial quantification kits in forensic labs.
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Affiliation(s)
- S Ginart
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina.
| | - L Garrigos Calivares
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - M Caputo
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - D Corach
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - A Sala
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
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Haarkötter C, Saiz M, Gálvez X, Vinueza-Espinosa DC, Medina-Lozano MI, Lorente JA, Álvarez JC. Performance comparison of four qPCR and three autosomal STR commercial kits from degraded skeletal remains. Forensic Sci Int 2023; 353:111856. [PMID: 37863006 DOI: 10.1016/j.forsciint.2023.111856] [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: 05/22/2023] [Revised: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023]
Abstract
This research evaluates the current DNA quantification (Quantifiler™ Trio, PowerQuant®, Investigator® Quantiplex® Pro and InnoQuant® HY Fast) and autosomal STRs amplification kits (GlobalFiler™, PowerPlex® Fusion 6 C, Investigator® 24Plex QS) using 62 degraded skeletal remains from armed conflicts (petrous bone, femur, tibia, and tooth) with several parameters (autosomal small, large, and male target, degradation index, probability of degradation, number of alleles above analytical threshold, number of alleles above stochastic threshold, RFU, peak height ratio, number of reportable loci). The best qPCR/autosomal STRs amplification tandem was determined by comparing quantification results by a DNA quantity estimation based on sample average RFU. InnoQuant® HY Fast was the most sensitive kit, and no significative differences were observed among amplification kits; however, Investigator® 24 Plex QS was found to be the most sensitive in our samples. That is why InnoQuant™ and Investigator® 24Plex QS were determined to be the best tandem.
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Affiliation(s)
- Christian Haarkötter
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - María Saiz
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain.
| | - Xiomara Gálvez
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - Diana C Vinueza-Espinosa
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - María Isabel Medina-Lozano
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - José Antonio Lorente
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - Juan Carlos Álvarez
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
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Bonsu DNO, Higgins D, Austin JJ. From clean spaces to crime scenes: Exploring trace DNA recovery from titania-coated self-cleaning substrates. Sci Justice 2023; 63:588-597. [PMID: 37718006 DOI: 10.1016/j.scijus.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/28/2023] [Accepted: 07/16/2023] [Indexed: 09/19/2023]
Abstract
Titanium dioxide (titania, TiO2) is frequently used as a coating for a variety of self-cleaning products, such as antifogging vehicle mirrors, ceramic tiles, and glass windows because of its distinct physiochemical features. When exposed to light TiO2 causes photocatalytic decomposition of organic contaminants, potentially compromising DNA integrity. The impact of TiO2-coated commercial glasses, Bioclean® and SaniTise™, on trace DNA persistence, recovery, and profiling was investigated. DNA in saliva and touch samples deposited on self-cleaning glass slides exposed to indoor fluorescent light for up to seven days was more degraded than control samples indicating some degree of fluorescent light-induced photocatalytic activity of the self-cleaning surfaces. When exposed to sunlight, DNA yields from saliva and touch samples deposited on the titania-coated substrates decreased rapidly, with a corresponding increase in DNA degradation. After three days no DNA samples applied to self-cleaning glass and exposed to natural sunlight yielded STR profiles. These results suggest that the photocatalytic activation of TiO2 is the likely mechanism of action underlying the extreme DNA degradation on the Bioclean® and SaniTise™ glasses. Consequently, rapid sample collection and use may be warranted in casework scenarios involving TiO2-coated materials.
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Affiliation(s)
- Dan Nana Osei Bonsu
- Chemistry and Forensic Sciences, Griffith University, Nathan, Queensland, Australia; Forensics Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, South Australia, Australia; Forensic Science Queensland, 39 Kessels Rd, Coopers Plains, Queensland, Australia.
| | - Denice Higgins
- Forensics Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, South Australia, Australia; School of Dentistry, Health and Medical Sciences, The University of Adelaide, South Australia, Australia.
| | - Jeremy J Austin
- Forensics Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, South Australia, Australia.
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7
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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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8
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Yao Y, Ko Y, Grasman G, Raymond JE, Lahann J. The steep road to nonviral nanomedicines: Frequent challenges and culprits in designing nanoparticles for gene therapy. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2023; 14:351-361. [PMID: 36959977 PMCID: PMC10028570 DOI: 10.3762/bjnano.14.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The potential of therapeutically loaded nanoparticles (NPs) has been successfully demonstrated during the last decade, with NP-mediated nonviral gene delivery gathering significant attention as highlighted by the broad clinical acceptance of mRNA-based COVID-19 vaccines. A significant barrier to progress in this emerging area is the wild variability of approaches reported in published literature regarding nanoparticle characterizations. Here, we provide a brief overview of the current status and outline important concerns regarding the need for standardized protocols to evaluate NP uptake, NP transfection efficacy, drug dose determination, and variability of nonviral gene delivery systems. Based on these concerns, we propose wide adherence to multimodal, multiparameter, and multistudy analysis of NP systems. Adoption of these proposed approaches will ensure improved transparency, provide a better basis for interlaboratory comparisons, and will simplify judging the significance of new findings in a broader context, all critical requirements for advancing the field of nonviral gene delivery.
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Affiliation(s)
- Yao Yao
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yeongun Ko
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- School of Polymer Science and Engineering, Chonnam National University, Buk-gu, Gwangju 61186, South Korea
| | - Grant Grasman
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffery E Raymond
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joerg Lahann
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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Schulze Johann K, Bauer H, Wiegand P, Pfeiffer H, Vennemann M. Detecting DNA damage in stored blood samples. Forensic Sci Med Pathol 2023; 19:50-59. [PMID: 36355320 PMCID: PMC10014702 DOI: 10.1007/s12024-022-00549-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2022] [Indexed: 11/11/2022]
Abstract
Several commercially available quantitative real-time PCR (qPCR) systems enable highly sensitive detection of human DNA and provide a degradation index (DI) to assess DNA quality. From routine casework in forensic genetics, it was observed that DNA degradation in forensic samples such as blood samples stored under sub-optimal conditions leads to visible effects in multiplex analyses of short tandem repeat markers (STRs) due to decreased amplification efficiencies in longer amplicons. It was further noticed that degradation indices often remain below the value that is considered to be critical. Thus, the aim of this work was to systematically analyze this effect and to compare conventional qPCR assays with a modified qPCR approach using uracil DNA glycosylase (UNG) and DNA quality assessment methods based on electrophoresis. Blood samples were stored at three different storage temperatures for up to 316 days. Significantly increased DNA recovery was observed from samples stored at high temperatures (37 °C) compared samples stored at room temperature and 4 °C. We observed typical effects of degradation in STR analyses but no correlation between DI and storage time in any of the storage conditions. Adding UNG slightly increased the sensitivity of detecting DNA degradation in one of the qPCR kits used in this study. This observation was not confirmed when using a second qPCR system. Electrophoretic systems did also not reveal significant correlations between integrity values and time. Methods for detecting DNA degradation are usually limited to the detection of DNA fragmentation, and we conclude that degradation affecting forensic STR typing is more complex.
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Affiliation(s)
- Kristina Schulze Johann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany.
| | - Hannah Bauer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
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Development and validation of a SYBR green-based mitochondrial DNA quantification method by following the MIQE and other guidelines. Leg Med (Tokyo) 2022; 58:102096. [PMID: 35689884 DOI: 10.1016/j.legalmed.2022.102096] [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: 01/30/2022] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 01/28/2023]
Abstract
In forensic mitochondrial DNA (mtDNA) analysis, quantitative PCR (qPCR) is usually performed to obtain high-quality sequence data for subsequent Sanger or massively parallel sequencing. Unlike methods for nuclear DNA quantification using qPCR, a calibrator is necessary to obtain mtDNA concentrations (i.e., copies/µL). Herein, we developed and validated a mtDNA quantification method based on a SYBR Green assay by following MIQE [Bustin et al., Clin. Chem. 55 (2009) 611-22] and other guidelines. Primers were designed to amplify nucleotide positions 16,190-16,420 in hypervariable region 1 for qPCR using PowerUp SYBR Green and QuantStudio 5. The optimized conditions were 0.3 µM each primer and an annealing temperature of 60 °C under a 2-step cycling protocol. K562 DNA at 100 pg/µL was converted into a mtDNA concentration of 16,400 copies/µL using linearized plasmid DNA. This mtDNA calibrator was obtained by cloning the synthesized DNA fragments of mtDNA (positions 16,140-16,470) containing a 100-bp inversion. The linear dynamic range of the K562 standard curve was 10,000-0.1 pg/µL (r2 ≥ 0.999). The accuracy was examined using NIST SRM 2372a, and its components A, B, and C were quantified with differences of -29.4%, -35.0%, and -22.0%, respectively, against the mtDNA concentrations calculated from published NIST data. We also examined the specificity of the primers, stability of the reaction mix, precision, tolerance against PCR inhibitors, and cross-reactivity against DNA from various animal taxa. Our newly developed mtDNA quantification method is expected to be useful for forensic mtDNA analysis.
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11
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Doniec A, Januła M, Grzmil P, Kupiec T. Assessing the utility of quantitative and qualitative metrics in the DNA quantification process of skeletal remains for autosomal and Y-chromosome STR amplification purposes. Forensic Sci Int Genet 2022; 60:102751. [PMID: 35914369 DOI: 10.1016/j.fsigen.2022.102751] [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: 02/15/2022] [Revised: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022]
Abstract
In historical cases, ancient DNA investigations and missing persons identification, teeth or bone samples are often the only and almost always the best biological material available for DNA typing. On the other hand, DNA obtained from bone material may be characterized by a high degradation index (DI) or its low content, or DNA tests cannot be repeated due to bone piece size limitation. That is often the effect of the environment in which the material was placed and the time during which exposure to unfavorable environmental factors took place. Therefore, it is very important to use appropriate procedures related to STR analysis. For our study, we selected 80 challenging bone samples. The amount of DNA was compared in qPCR using Quantifiler™ Trio DNA Quantification Kit and Investigator® Quantiplex® Pro RGQ. All qPCR results were confirmed by PCR-CE. The results of DNA concentrations and the assigned degradation index (DI) differed significantly within analyzed samples (~10%). Additionally, the Y-chromosome DI also differed from the autosomal DI in the samples. The difference in degradation indexes could explain the lower Y-chromosome amplification success rate compared to autosomal e.g. during human identification process. The results indicate that performing two DNA quantifications with the use of two different kits (primers sets) allows for a much more precise evaluation of the DNA quality and quantity in the isolate. We suggest that at least one of two suggested DNA concentration measurements should be based on an additional determination of the Y chromosome degradation index. Altogether, it allows for rational isolate management, especially when the volume is limited and the sample is unique.
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Affiliation(s)
- Andrzej Doniec
- Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland; Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland.
| | - Miłosz Januła
- Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland
| | - Paweł Grzmil
- Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Tomasz Kupiec
- Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland.
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12
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Phua CH, Kitpipit T, Pradutkanchana J, Duangsuwan P, Samai W, Thanakiatkrai P. Direct STR typing from human bones. Forensic Sci Int 2021; 330:111099. [PMID: 34794063 DOI: 10.1016/j.forsciint.2021.111099] [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: 08/28/2021] [Revised: 10/12/2021] [Accepted: 11/04/2021] [Indexed: 11/26/2022]
Abstract
Identification by STR analysis of bones is time-consuming, mainly due to the lengthy decalcification required and complex DNA extraction process. To streamline this process, we developed a direct STR typing protocol from bone samples. We optimized bone sample amounts using femur and tibia and two commercial PCR kits (Identifiler™ Plus and IDplex Plus kits). Optimally, 100 mg of bone powder in 300 µL PBS buffer was heated at 98 °C for three minutes to produce a supernatant for DNA amplification. IDplex Plus performed better than Identifiler™ Plus in terms of allele recovery and peak height. Fifteen samples of each of seven bone elements (1st distal phalange of hand, capitate, femur, metacarpal 4, patella, talus, and tibia; N = 105) were then subjected to direct STR typing with the optimized protocol, and 94.3% were high partial to full profiles. The performance of the developed protocol was similar for all bone elements. Median peak heights were significantly better in profiles of cancellous bone than compact bone (p = 0.033) and significantly different across the bone elements (p < 0.001). Ten casework samples from various conditions and up to 7-year-PMI were subjected to both direct STR and conventional STR typing. No significant difference in the number of alleles was seen (95% HDI of -13.5 to 5.15). As well as being rapid, convenient, and safe, the protocol could help improve STR typing from bones.
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Affiliation(s)
- Cheng Ho Phua
- Forensic Science Program, Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Thitika Kitpipit
- Forensic Science Program, Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand; Forensic Science Innovation and Service Center, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Jintana Pradutkanchana
- Division of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Pornsawan Duangsuwan
- Anatomy Program, Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Wirachai Samai
- Division of Pathology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Phuvadol Thanakiatkrai
- Forensic Science Program, Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand; Forensic Science Innovation and Service Center, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
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13
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Manzella AM, Carte KM, King SL, Moreno LI. Assessment of the ANDE 6C Rapid DNA system and investigative biochip for the processing of calcified and muscle tissue. Forensic Sci Int Genet 2021; 53:102526. [PMID: 33991866 DOI: 10.1016/j.fsigen.2021.102526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022]
Abstract
The ANDE 6C Rapid DNA system could offer a potential alternative for the processing of calcified and soft tissue samples, often encountered in mass disaster scenarios. While originally designed for single source buccal swabs, interest in the performance of these instruments when using other types of single source samples continues to grow. To enhance the recovery of otherwise lesser quality samples, the manufacturer developed the investigative biochip, an alternative to the NDIS approved Arrestee biochip for reference sample buccal swabs. This study explores the viability of using the ANDE 6C system and the investigative biochip to process soft and calcified tissue, and uses conventional sample processing to contrast the results. Though the success rate obtained using the instrument's expert system was lower than expected - 0% muscle, 11% ribs, and 50% teeth -, the ANDE 6C offers an advantage over conventional calcified tissue processing in terms of turn-around time and processing complexity. If robust analysis parameters can be established to allow the evaluation of the generated data by a qualified analyst on a third party software platform, the use of the ANDE 6C and investigative biochip could be a suitable alternative for currently employed procedures. However, as is the case with conventional DNA typing, the quantity, age, type of biological material and quality of the exemplars could all play a role in the success of the ANDE 6C typing process. In addition, it appears as if the calcified tissue pre-processing protocol that provides the better opportunity for the ANDE 6C success is not appropriate to be carried out in the field or by non-trained personnel as special equipment as well as a certain level of exe expertise and technique is necessary. Nevertheless, disaster victim and unidentified human remain samples could be processed in a laboratory setting using the Rapid DNA ANDE 6C platform provided sufficient material is available to conduct a second, 'rescue' sample processing if necessary.
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Affiliation(s)
- April M Manzella
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA; EnProVera, 410 Ware Blvd, Tampa, FL 33619, USA
| | - Kathryn M Carte
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA; EnProVera, 410 Ware Blvd, Tampa, FL 33619, USA
| | - Sheria L King
- Scientific Support Services, Royal Bahamas Police Force, East St, Nassau, Bahamas
| | - Lilliana I Moreno
- DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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14
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Heß SA, Trapani S, Boronat MDM, Theunissen GMG, Rolf B, Jäger R. Ribosomal DNA as target for the assessment of DNA degradation of human and canine DNA. Leg Med (Tokyo) 2020; 48:101819. [PMID: 33248354 DOI: 10.1016/j.legalmed.2020.101819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022]
Abstract
The assessment of DNA amount and DNA integrity can support forensic DNA analysis, in particular of problematic traces such as single telogen hairs where STR typing success is often hampered by low amounts and strong degradation of nuclear DNA. Common strategies consist of quantitative polymerase chain reaction (qPCR)-based analysis of the abundance of a short versus a long nuclear amplicon, the latter prone to DNA degradation. To increase sensitivity, commercial qPCR solutions rest on amplification of multi-copy DNA sequences. Here we show that ribosomal DNA (rDNA) sequences are well suited for the same purpose. Because rDNA sequences are present in high copy number in most eukaryotic species, qPCR strategies can easily be adapted to non-human species. In this paper, we establish qPCR-based assays for human or dog DNA, respectively, which allow for sensitive analysis of DNA amounts and DNA degradation. We show that the human system can be applied to DNA of single telogen hairs, where STR typing success correlates with measured amounts and integrity of the DNA. By adapting the system to dog rDNA sequences we found that single telogen dog hairs often displayed less DNA degradation than human telogen hairs, in most cases allowing for successful STR typing. Thus, qPCR-based analysis of rDNA represents a cost-effective, highly sensitive strategy to assess DNA amount and integrity that can be adapted to hairs or other traces from various animal species.
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Affiliation(s)
- Sarah Aurora Heß
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany; Institute of Safety and Security Research, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Salvatore Trapani
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany; Università degli Studi di Palermo, University of Palermo, 90133 Palermo, PA, Italy
| | - Maria Del Mar Boronat
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany
| | - Glenn M G Theunissen
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany; Institute of Safety and Security Research, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Burkhard Rolf
- Eurofins Medigenomix Forensik GmbH, Anzinger Str. 7a, 85560 Ebersberg, Germany
| | - Richard Jäger
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany; Institute of Safety and Security Research, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany; Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757, Sankt Augustin, Germany.
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15
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Simoes Dutra Correa H, Brescia G, Cortellini V, Cerri N, Verzeletti A. DNA quantitation and degradation assessment: a quantitative PCR protocol designed for small forensic genetics laboratories. Electrophoresis 2020; 41:714-719. [DOI: 10.1002/elps.201900360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/16/2020] [Accepted: 02/11/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Heitor Simoes Dutra Correa
- Forensic Medicine UnitDepartment of Medical and Surgical SpecialtiesRadiological Sciences and Public HealthUniversity of Brescia Brescia Italy
| | - Gloria Brescia
- Forensic Medicine UnitDepartment of Medical and Surgical SpecialtiesRadiological Sciences and Public HealthUniversity of Brescia Brescia Italy
| | - Venusia Cortellini
- Forensic Medicine UnitDepartment of Medical and Surgical SpecialtiesRadiological Sciences and Public HealthUniversity of Brescia Brescia Italy
| | - Nicoletta Cerri
- Forensic Medicine UnitDepartment of Medical and Surgical SpecialtiesRadiological Sciences and Public HealthUniversity of Brescia Brescia Italy
| | - Andrea Verzeletti
- Forensic Medicine UnitDepartment of Medical and Surgical SpecialtiesRadiological Sciences and Public HealthUniversity of Brescia Brescia Italy
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16
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Development and forensic validation of human genomic DNA quantification kit. Int J Legal Med 2020; 134:963-975. [DOI: 10.1007/s00414-019-02131-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/26/2019] [Indexed: 10/26/2022]
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17
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Hakim HM, Khan HO, Ismail SA, Ayob S, Lalung J, Kofi EA, Chambers GK, Edinur HA. Assessment of autosomal and male DNA extracted from casework samples using Casework Direct Kit, Custom and Maxwell 16 System DNA IQ Casework Pro Kit for autosomal-STR and Y-STR profiling. Sci Rep 2019; 9:14558. [PMID: 31601905 PMCID: PMC6787247 DOI: 10.1038/s41598-019-51154-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/25/2019] [Indexed: 11/26/2022] Open
Abstract
Short repetitive regions in autosomal and Y chromosomes known as short tandem repeats (STRs) are currently used for DNA profiling in crime investigations. However, DNA profiling requires a sufficient quality and quantity of DNA template, which is often not obtained from trace evidence or degraded biological samples collected at the scene of a crime. Here, we assessed autosomal and male DNA components extracted from crime scene and mock casework samples using the Casework Direct Kit, Custom and compared the results against those obtained by extraction of matching samples using well-established Maxwell 16 System DNA IQ Casework Pro Kit. The quantity and quality of extracted DNA obtained using both Casework Direct Kit, Custom and Maxwell 16 System DNA IQ Casework Pro Kit were analyzed using PowerQuant Systems followed by autosomal and Y-chromosome STR profiling using GlobalFiler Express PCR Amplification Kit and PowerPlex Y23 System, respectively. Our results showed that the Casework Direct Kit and Maxwell 16 DNA IQ Casework Pro Kit have more or less equal capacity to extract inhibitor free DNA, but that the latter produces slightly better quality and more DNA template and subsequently higher numbers of STR allele calls for autosomal and Y-STR analyses. Nonetheless, the Casework Direct Kit, Custom is the quicker and cheaper option for extraction of good, clean DNA from high content material and might best be used for extraction of reference samples. Such reference DNA samples typically come from buccal swabs or freshly drawn blood. So, in general, they can confidently be expected to have a high nucleic acid content and to be inhibitor-free.
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Affiliation(s)
- Hashom Mohd Hakim
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia. .,School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia.
| | - Hussein Omar Khan
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Siti Afifah Ismail
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Shahrizad Ayob
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Japareng Lalung
- School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | - Edward Abban Kofi
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.,Forensic Science Laboratory, Criminal Investigation Department, Ghana Police Service, P.O. Box 505, Accra, Ghana
| | - Geoffrey Keith Chambers
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Hisham Atan Edinur
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia. .,Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia. .,Environmental Futures Research Institute, Griffith University, Nathan, Queensland, 4111, Australia.
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18
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The importance of forensic storage support: DNA quality from 11-year-old saliva on FTA cards. Int J Legal Med 2019; 133:1743-1750. [PMID: 31463575 DOI: 10.1007/s00414-019-02146-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
Storage conditions influence the integrity of the recoverable DNA from forensic evidence in terms of yield and quality. FTA cards are widely used in the forensic practice as their chemically treated matrix provides protection from the moment of collection to the point of analysis with current STR typing technology. In this study, we assess the recoverability and the integrity of DNA from 11-year-old saliva on FTA cards using a forensic quantitative real-time polymerase chain reaction (qPCR) commercial assay. The quality after long-term storage was investigated in order to evaluate if the FTA device could assure enough stability over time, applying some internally validated quality criteria of the STR profile. Furthermore, we used a 3D interpolation model to combine the quantitative and qualitative data from qPCR to calculate the minimum optimal DNA input (MODI) to add to the downstream PCR reaction based on the quantitative and qualitative data of a sample. According to our results, when saliva sample is properly transferred onto FTA cards and then correctly stored according to the manufacturer's instructions, it is possible to recover sufficient amounts of DNA for human identification even after more than a decade of storage at ambient temperature. Degradation affected the quality of results especially when the Degradation Index exceeds the value of 2.12, requiring modifications of the standard internal workflow to improve the genotyping quality. Above this value, the application of a "corrective factor" to the PCR normalization process was necessary in order to adjust the recommended manufacturer's PCR DNA input taking into account the degradation level. Our results demonstrated the importance to consider in predictive terms the parameters obtained with the real-time quantification assay, both in terms of quantity (DNA concentration) and of quality (DI, inhibition). Informatics predictive tools including qPCR data together with the variables of storage duration and conditions should be developed in order to optimize the DNA analysis process.
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19
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Caputo M, Corach D. Reply to comment “A DNA extraction method of small quantities of bone for high-quality genotyping”. Forensic Sci Int Genet 2019; 41:e18-e19. [DOI: 10.1016/j.fsigen.2019.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 11/26/2022]
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