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Cloudy DC, Boone EL, Kuehnert K, Smith C, Cox JO, Seashols-Williams SJ, Green TD. Statistical methods for discrimination of STR genotypes using high resolution melt curve data. Int J Legal Med 2024:10.1007/s00414-024-03289-x. [PMID: 38997516 DOI: 10.1007/s00414-024-03289-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
Despite the improvements in forensic DNA quantification methods that allow for the early detection of low template/challenged DNA samples, complicating stochastic effects are not revealed until the final stage of the DNA analysis workflow. An assay that would provide genotyping information at the earlier stage of quantification would allow examiners to make critical adjustments prior to STR amplification allowing for potentially exclusionary information to be immediately reported. Specifically, qPCR instruments often have dissociation curve and/or high-resolution melt curve (HRM) capabilities; this, coupled with statistical prediction analysis, could provide additional information regarding STR genotypes present. Thus, this study aimed to evaluate Qiagen's principal component analysis (PCA)-based ScreenClust® HRM® software and a linear discriminant analysis (LDA)-based technique for their abilities to accurately predict genotypes and similar groups of genotypes from HRM data. Melt curves from single source samples were generated from STR D5S818 and D18S51 amplicons using a Rotor-Gene® Q qPCR instrument and EvaGreen® intercalating dye. When used to predict D5S818 genotypes for unknown samples, LDA analysis outperformed the PCA-based method whether predictions were for individual genotypes (58.92% accuracy) or for geno-groups (81.00% accuracy). However, when a locus with increased heterogeneity was tested (D18S51), PCA-based prediction accuracy rates improved to rates similar to those obtained using LDA (45.10% and 63.46%, respectively). This study provides foundational data documenting the performance of prediction modeling for STR genotyping based on qPCR-HRM data. In order to expand the forensic applicability of this HRM assay, the method could be tested with a more commonly utilized qPCR platform.
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Affiliation(s)
- Darianne C Cloudy
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA
| | - Edward L Boone
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA, 23284, USA
| | - Kristi Kuehnert
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA
| | - Chastyn Smith
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA.
| | - Jordan O Cox
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA
| | - Sarah J Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA
| | - Tracey Dawson Green
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, PO Box 843079, Richmond, VA , 23284, USA
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2
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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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3
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Torres D, Smith C, Williams AL, Cox JO, Seashols-Williams SJ, Boone EL, Green TD. A quantifiler™ trio-based HRM screening assay for the accurate prediction of single source versus mixed biological samples. Int J Legal Med 2023; 137:1639-1651. [PMID: 37553510 DOI: 10.1007/s00414-023-03070-6] [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: 06/01/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
At present, the forensic DNA workflow is not capable of providing information about the contributor status (single source vs. multiple contributors) of evidentiary samples prior to end-point analysis. This exacerbates the challenges inherent to mixtures and low-template DNA samples. If additional sample information could be provided earlier in the workflow, protocols could be implemented to mitigate these challenges. An integrated Quantiplex®- high resolution melt (HRM) assay was shown to be effective in distinguishing between single source and mixture DNA samples; however, integration of the HRM assay into a more commonly used chemistry would be beneficial to the practitioner community. Thus, the assay was redesigned as an integrated Quantifiler™ Trio-HRM assay, which included the identification of a new DNA-binding dye, an increased reaction volume, and the establishment of new data analysis and standard curve metrics for all targets. This redesigned assay produced quantification values and qualitative values that were comparable to those produced when the same samples were tested using the standard Quantifiler™ Trio chemistry and settings. Further, STR profiles generated with quantification values produced from the integrated Quantifiler™ Trio-HRM assay and standard Quantifiler™ Trio chemistry were complete and fully concordant. Most importantly, the integrated Quantifiler™ Trio-HRM assay was able to accurately predict whether a sample was single source or a mixture 79.2% of the time, demonstrating the potential of this approach. With the incorporation of an expanded training set for prediction modeling, and completion of critical developmental validation studies, this assay could prove useful to the forensic DNA practitioner community.
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Affiliation(s)
- Dayanara Torres
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| | - Chastyn Smith
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA.
- Integrative Life Sciences, Virginia Commonwealth University, 1000 Cary Street, Richmond, VA, 23284, USA.
| | - Andrea L Williams
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| | - Jordan O Cox
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| | - Sarah J Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| | - Edward L Boone
- Department of Statistical Sciences & Operations Research, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
| | - Tracey Dawson Green
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, USA
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Anabalón L, Solano J, Encina-Montoya F, Bustos M, Figueroa A, Gangitano D. Cannabis Seeds Authentication by Chloroplast and Nuclear DNA Analysis Coupled with High-Resolution Melting Method for Quality Control Purposes. Cannabis Cannabinoid Res 2022; 7:548-556. [PMID: 34142864 PMCID: PMC9418366 DOI: 10.1089/can.2020.0168] [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] [Indexed: 11/13/2022] Open
Abstract
Background: Cannabis plants and their seed have been used in many cultures as a source of medicine and feeding during history. Today, there is an increasing demand for cannabis seeds for medical use. Moreover, a seed sales market with no legal regulations has also grown. This may pose some issues if a quality control is not set in place. Identification of cannabis strains is important for quality control purposes in a nonregulated growing market and in cases of illegal traffic and medical use. Owing to the high price as a pharmacological drug, commercial products of cannabis plants and seeds for medical users are often subjected to adulterations, either when packing or distributing certified seeds in the market. Materials and Methods: Cannabis commercial seeds and cannabis seeds for medical use were analyzed with high-resolution melting (HRM) analysis using barcoding markers. Humulus lupulus L. plants from a local market were used as outgroup control. DNA barcoding uses specific regions of the genome to identify differences in the genetic sequence of conserved regions such as internal transcribed spacer (ITS) and rbcL. DNA barcoding data can be generated with real-time polymerase chain reaction combined with HRM analysis to distinguish specific conserved DNA regions of closely related species. HRM analysis is the method of choice for rapid analysis of sequence variation. Results: The melting temperature (Tm) of homogeneous packages was consistent with single genotypes. However, packages containing contaminating seeds showed Tm differences of 0.2°C on average. Conclusions: An effective, rapid, and low-cost method based on ITS nuclear DNA and on chloroplast rbcL regions for screening and detection of contamination in commercial cannabis seeds was developed and applied for the analysis of different samples. This approach can be used as a quality control tool for cannabis seeds or other plant material.
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Affiliation(s)
- Leonardo Anabalón
- Departamento de Ciencias Biológicas y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Jaime Solano
- Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Francisco Encina-Montoya
- Departamento de Ciencias Ambientales, Facultad de Recursos Naturales, Núcleo de Estudios Ambientales, Universidad Católica de Temuco, Temuco, Chile
| | - Marco Bustos
- Departamento de Administración Pública, Facultad de Ciencias Sociales, Universidad Católica de Temuco, Temuco, Chile
| | - Alejandra Figueroa
- Laboratorio de Criminalística, Policía de Investigaciones de Chile, Temuco, Chile
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5
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Jedrzejczak-Silicka M, Lepczynski A, Gołębiowski F, Dolata D, Dybus A. Application of PCR-HRM method for microsatellite polymorphism genotyping in the LDHA gene of pigeons (Columba livia). PLoS One 2021; 16:e0256065. [PMID: 34411134 PMCID: PMC8376019 DOI: 10.1371/journal.pone.0256065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/01/2021] [Indexed: 11/19/2022] Open
Abstract
High-resolution melting (HRM) is a post-PCR method that allows to discriminate genotypes based on fluorescence changes during the melting phase. HRM is used to detect mutations or polymorphisms (e.g. microsatellites, SNPs, indels). Here, the (TTTAT)3-5 microsatellite polymorphism within intron 6 of the LDHA gene in pigeons was analysed using the HRM method. Individuals (123 homing pigeons) were genotyped using conventional PCR. Birds were classified into groups based on genotype type and the results were tested by qPCR-HRM and verified using sequencing. Based on the evaluated protocol, five genotypes were identified that vary in the number of TTTAT repeat units (3/3, 4/4, 3/4, 4/5, and 5/5). Sequencing have confirmed the results obtained with qPCR-HRM and verified that HRM is a suitable method for identification of three-allele microsatellite polymorphisms. It can be concluded that the high-resolution melting (HRM) method can be effectively used for rapid (one-step) discrimination of the (TTTAT)3-5 microsatellite polymorphism in the pigeon’s LDHA gene.
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Affiliation(s)
- Magdalena Jedrzejczak-Silicka
- Faculty of Biotechnology and Animal Husbandry, Laboratory of Molecular Biology, West Pomeranian University of Technology, Szczecin, Poland
- * E-mail:
| | - Adam Lepczynski
- Department of Physiology, Cytobiology and Proteomics, West Pomeranian University of Technology, Szczecin, Poland
| | | | | | - Andrzej Dybus
- Faculty of Biotechnology and Animal Husbandry, Department of Genetics, West Pomeranian University of Technology, Szczecin, Poland
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6
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Zhang X, Yu H, Wang Z, Yang Q, Xia R, Qu Y, Tao R, Shi Y, Xiang P, Zhang S, Li C. Multi-locus identification of Psilocybe cubensis by high-resolution melting (HRM). Forensic Sci Res 2021; 7:490-497. [PMID: 36353314 PMCID: PMC9639532 DOI: 10.1080/20961790.2021.1875580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Hallucinogenic mushroom is a kind of toxic strain containing psychoactive tryptamine substances such as psilocybin, psilocin and ibotenic acid, etc. The mushrooms containing hallucinogenic components are various, widely distributed and lack of standard to define, which made a great challenge to identification. Traditional identification methods, such as morphology and toxicology analysis, showed shortcomings in old or processed samples, while the DNA-based identification of hallucinogenic mushrooms would allow to identify these samples due to the stability of DNA. In this paper, four primer sets are designed to target Psilocybe cubensis DNA for increasing resolution of present identification method, and the target markers include largest subunit of RNA polymerase II (marked as PC-R1), psilocybin-related phosphotransferase gene (marked as PC-PT), glyceraldehyde 3-phosphate dehydrogenase (marked as PC-3) and translation EF1α (marked as PC-EF). Real-time PCR with high-resolution melting (HRM) assay were used for the differentiation of the fragments amplified by these primer sets, which were tested for specificity, reproducibility, sensitivity, mixture analysis and multiplex PCR. It was shown that the melting temperatures of PC-R1, PC-PT, PC-3 and PC-EF of P. cubensis were (87.93 ± 0.12) °C, (82.21 ± 0.14) °C, (79.72 ± 0.12) °C and (80.11 ± 0.19) °C in our kinds of independent experiments. Significant HRM characteristic can be shown with a low concentration of 62.5 pg/µL DNA sample, and P. cubensis could be detected in mixtures with Homo sapiens or Cannabis sativa. In summary, the method of HRM analysis can quickly and specifically distinguish P. cubensis from other species, which could be utilized for forensic science, medical diagnosis and drug trafficking cases. Supplemental data for this article are available online at https://doi.org/10.1080/20961790.2021.1875580.
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Affiliation(s)
- Xiaochun Zhang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Huan Yu
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Ziwei Wang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Qi Yang
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, China
| | - Yiling Qu
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yan Shi
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Ping Xiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Chengtao Li
- Department of Forensic Science, Medical School of Soochow University, Suzhou, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
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7
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A Forensic Detection Method for Hallucinogenic Mushrooms via High-Resolution Melting (HRM) Analysis. Genes (Basel) 2021; 12:genes12020199. [PMID: 33572950 PMCID: PMC7911181 DOI: 10.3390/genes12020199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/18/2021] [Accepted: 01/26/2021] [Indexed: 11/25/2022] Open
Abstract
In recent years, trafficking and abuse of hallucinogenic mushrooms have become a serious social problem. It is therefore imperative to identify hallucinogenic mushrooms of the genus Psilocybe for national drug control legislation. An internal transcribed spacer (ITS) is a DNA barcoding tool utilized for species identification. Many methods have been used to discriminate the ITS region, but they are often limited by having a low resolution. In this study, we sought to analyze the ITS and its fragments, ITS1 and ITS2, by using high-resolution melting (HRM) analysis, which is a rapid and sensitive method for evaluating sequence variation within PCR amplicons. The ITS HRM assay was tested for specificity, reproducibility, sensitivity, and the capacity to analyze mixture samples. It was shown that the melting temperatures of the ITS, ITS1, and ITS2 of Psilocybe cubensis were 83.72 ± 0.01, 80.98 ± 0.06, and 83.46 ± 0.08 °C, and for other species, we also obtained species-specific results. Finally, we performed ITS sequencing to validate the presumptive taxonomic identity of our samples, and the sequencing output significantly supported our HRM data. Taken together, these results indicate that the HRM method can quickly distinguish the DNA barcoding of Psilocybe cubensis and other fungi, which can be utilized for drug trafficking cases and forensic science.
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8
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Hayashi T, Aminaka R, Ishii H, Tani Y, Fujimura Y, Takihara Y, Hirayama F. Frequency of allotype "b" in human platelet antigen 1 to 29 systems among blood donors in Japan estimated using high-resolution melt analysis. Transfusion 2020; 60:2702-2713. [PMID: 32710598 DOI: 10.1111/trf.15967] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND Antibodies against human platelet antigens (HPAs) cause thrombocytopenias. It is thus important to know the frequency of "b" allotypes in each HPA system for the diagnosis and treatment of anti-HPA antibody-mediated thrombocytopenia. STUDY DESIGN AND METHODS Genomic DNA was extracted from peripheral blood cells obtained from 2170 blood donors in Japan and was subjected to high-resolution melt (HRM) analysis using polymerase chain reaction for each of the HPA genes, using 23 primer pairs. For genotyping, the resulting amplicons were classified based on their HRM curves. In some cases, direct sequence analysis was performed after HRM analysis to determine nucleotide substitutions. In cases where amino acid substitutions were predicted, protein expression levels were examined in a cell line using 293T cells. RESULTS The frequencies of each of the HPA-b genotypes were as follows: HPA-1b, 0.4%; HPA-2b, 11.8%; HPA-3b, 41.3%; HPA-4b, 0.8%; HPA-5b, 4.3%; HPA-6b, 1.9%; HPA-15b, 48.8%; HPA-21b, 0.6%; and "b" allotype in the other HPA systems, 0.0%. Twenty-eight variants were found; nine of them were predicted to cause amino acid substitution. However, expression analysis revealed that they did not affect protein expression levels on the cell surface. CONCLUSION Nine HPA systems are of primary importance in Japan in potentially triggering thrombocytopenia via the HPA antibodies. Similar studies in other countries or races, together with ours, could provide basic information for clinicians in multiethnic societies.
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Affiliation(s)
- Tomoya Hayashi
- Japanese Red Cross Kinki Block Blood Centre, Ibaraki, Osaka, Japan
| | - Ryota Aminaka
- Japanese Red Cross Kinki Block Blood Centre, Ibaraki, Osaka, Japan
| | - Hiroyuki Ishii
- Japanese Red Cross Kinki Block Blood Centre, Ibaraki, Osaka, Japan
| | | | | | | | - Fumiya Hirayama
- Japanese Red Cross Kinki Block Blood Centre, Ibaraki, Osaka, Japan
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9
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Rapid detection and genotyping of ALK fusion variants by adapter multiplex PCR and high-resolution melting analysis. J Transl Med 2020; 100:110-119. [PMID: 31641223 DOI: 10.1038/s41374-019-0330-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/08/2019] [Accepted: 09/07/2019] [Indexed: 11/08/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) fusion is a promising predictive biomarker of ALK-tyrosine kinase inhibitor (ALK-TKI) treatment. Furthermore, different fusion variants correlate to different ALK-TKIs responses. Although variant identification assists in treatment direction, most ALK detection assays do not genotype different fusion variants. We developed a high-resolution melting (HRM) assay to rapidly detect ALK fusions and automatically distinguish at least 20 fusion variants in one tube. Adapter multiplex PCR was designed to amplify ALK fusion variants and the reference gene GAPDH. After HRM, negative derivative curves showed a low temperature GAPDH peak, and if an ALK fusion was present, a high temperature peak from the ALK segment and variably a middle temperature part associated with the fusion partner. Selected regions of the second derivative curves were analyzed to extract features (∆Tm, PTS/ITS, H1/H2) that define two curve types (monotonic and non-monotonic). Synthetic samples of 20 ALK fusion variants were used to train a quadratic discriminate analysis model, and the accuracy was 97.06% (66/68) and 85.71% (144/162) for monotonic and non-monotonic variants, respectively. The limit of detection of the assay was 1%. The analytical sensitivity of genotyping was 1 and 5% for monotonic and non-monotonic variants, respectively. In a blinded study, we detected ALK fusion from formalin-fixed paraffin-embedded lung cancer samples with a 100% 47) and genotyping /47) and genotyping (7/7). Multiplex adapter HRM is a simple, fast, and sensitive way of ALK fusion detection and genotyping. Automatic genotyping with parameters extracted from second derivative curves is a promising method that may be applicable to other types of gene variants detected by HRM.
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10
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Li M, Tao R, Zhou W, Li Y, Meng M, Zhang Y, Yu L, Chen L, Bian Y, Li C. Validation studies of the ParaDNA ® Intelligence System with artificial evidence items. Forensic Sci Res 2019; 6:84-91. [PMID: 34007520 PMCID: PMC8110186 DOI: 10.1080/20961790.2019.1665159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Short tandem repeat (STR) profiling is one of the mostly used systems for forensic applications. In certain circumstances, STR profiling is time-consuming and costly, which potentially leads to delays in criminal investigations. LGC (Laboratory of the Government Chemist, UK) Forensics has developed a robust STR profiling platform called the ParaDNA® Intelligence Test System which can provide early tactical intelligence and aid investigators in making informed decisions on sample prioritization for detection. Here, we validated the ParaDNA intelligence test for its application in forensic cases using a range of mock evidence items following guidelines set by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Specifically, we tested the sensitivity and accuracy of the ParaDNA intelligence test, as well as the success rates for detecting mock samples and for use in case scenarios. Our findings demonstrate that the ParaDNA intelligence test generates useful DNA profiles, especially for samples such as blood, saliva, and semen that contain ample DNA, indicating the benefits of including ParaDNA as a prior step in forensic STR profiling pipelines.
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Affiliation(s)
- Min Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China
| | - Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China
| | - Wei Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Yanan Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China.,Department of Forensic Medical, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, China
| | - Meng Meng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China.,Department of Histology and Embryology, Harbin Medical University, Harbin, China
| | - Yilun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China.,School of Basic Medicine, Baotou Medical College, Baotou, China
| | - Linsheng Yu
- Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, China
| | - Liqin Chen
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China.,Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China
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11
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Jiang E, Zhang S, Pang H. Genotyping genetic markers from LCN and degraded DNA by HRM and their application in hair shaft. Int J Legal Med 2019; 134:31-37. [PMID: 31062081 DOI: 10.1007/s00414-019-02045-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/18/2019] [Indexed: 01/13/2023]
Abstract
Degraded and low copy number (LCN) DNA samples are common challenging materials in forensic casework because they increase the difficulty of sample processing and reduce the possibility of obtaining genetic information from DNA. High-resolution melting (HRM) curve analysis is promising for genotyping genetic markers and has been applied to the detection of LCN and degraded DNA in the field of forensic science. However, the exact assessment based on HRM at multiple genetic markers from both degraded and LCN DNA materials has not been optimized. To explore the ability of HRM to genotype LCN and degraded DNA samples, we selected three genetic markers to genotype in experimental LCN and degraded DNA and practical hair shaft materials, which are often encountered as degraded and LCN DNA in forensic medicine. The results show that DNA samples of as low as 100 pg and as short as 60 bp were successfully genotyped by the HRM assay at all three genetic markers, whereas in hair shaft DNA, two loci were accurately genotyped. The HRM assay established in this study can be applied to LCN and degraded DNA analysis in forensic casework and can act as a reference point before genotyping short tandem repeat markers. Developing the HRM strategy for genotyping DNA genetic markers enriches detectable targets in hair shaft samples and provides valuable data for further exploration.
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Affiliation(s)
- Enzhu Jiang
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, People's Republic of China
| | - Siyi Zhang
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, People's Republic of China
| | - Hao Pang
- Department of Forensic Genetics and Biology, School of Forensic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122, People's Republic of China.
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12
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Ginart S, Caputo M, Corach D, Sala A. Human DNA degradation assessment and male DNA detection by quantitative-PCR followed by high-resolution melting analysis. Forensic Sci Int 2018; 295:1-7. [PMID: 30550960 DOI: 10.1016/j.forsciint.2018.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/22/2018] [Accepted: 11/18/2018] [Indexed: 11/15/2022]
Abstract
We developed a q-PCR technique that simultaneously evaluates the extent of degradation and determines the gender of a human DNA donor. QYDEG HRM is a triplex real-time PCR whose products are analysed by high-resolution melting (HRM). The system produces three amplicons: (1) transducin (beta)-like 1, Y-linked (TBL1Y) (84bp); (2) large-target sequence (DGlt) (244bp); and (3) small-target sequence (DGst) (152bp). After HRM analysis, three melting peaks are detected in male DNA samples and two in female DNA samples. An imbalance between the DGst and DGlt melting peak heights allows for the estimation of the extent of DNA degradation. For sensitivity assessment, triplicate aliquots of 0.0032 to 50ng/μL DNA were tested, denoting good linearity and reproducibility. The results also showed the analysis to be precise and accurate in the DNA range of 0.04-5ng/μL. Diverse types of DNA samples were tested: experimentally heat-degraded DNA; crime scene samples derived from casework and highly degraded samples with partial STR profiles from corpse material and mass disaster events. The results were compared with those obtained from the Plexor® and PowerQuant® commercial kits. Additionally, the quantification results of the QYDEG HRM triplex correlate well with the STR amplification that was subsequently obtained. The method is simple, cost-effective and helpful for determining the DNA integrity and the sex of a sample donor in any field where human DNA quantification is required.
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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, Junin 956, CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-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, Junin 956, CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-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, Junin 956, CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-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, Junin 956, CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Godoy Cruz 2290, CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
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13
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Solano J, Anabalón L, Figueroa S, Lizama C, Reyes LC, Gangitano D. Psychedelic fungus (Psilocybe sp.) authentication in a case of illegal drug traffic: sporological, molecular analysis and identification of the psychoactive substance. Sci Justice 2018; 59:102-108. [PMID: 30654963 DOI: 10.1016/j.scijus.2018.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/26/2018] [Accepted: 08/10/2018] [Indexed: 11/18/2022]
Abstract
In nature, there are >200 species of fungi with hallucinogenic properties. These fungi are classified as Psilocybe, Gymnopilus, and Panaeolus which contain active principles with hallucinogenic properties such as ibotenic acid, psilocybin, psilocin, or baeocystin. In Chile, fungi seizures are mainly of mature specimens or spores. However, clandestine laboratories have been found that process fungus samples at the mycelium stage. In this transient stage of growth (mycelium), traditional taxonomic identification is not feasible, making it necessary to develop a new method of study. Currently, DNA analysis is the only reliable method that can be used as an identification tool for the purposes of supporting evidence, due to the high variability of DNA between species. One way to identify the species of a distinctive DNA fragment is to study PCR products analyzed by real time PCR and sequencing. One of the most popular sequencing methods of forensic interest at the generic and intra-generic levels in plants is internal transcribed spacer (ITS). With real time PCR it is possible to distinguish PCR products by differential analysis of their melting temperature (Tm) curves. This paper describes morphological, chemical, and genetic analysis of mycelia of psychedelic fungi collected from a clandestine laboratory. The fungus species were identified using scanning electron microscopy (SEM), mass spectrometry, HRM analysis, and ITS sequencing. The sporological studies showed a generally smooth surface and oval shape, with maximum length 10.1 μm and width 6.4 μm. The alkaloid Psilocyn was identified by mass spectrometry, while HRM analysis and ITS sequencing identified the species as Psilocybe cubensis. A genetic match was confirmed between the HRM curves obtained from the mycelia (evidence) and biological tissue extracted from the fruiting bodies. Mycelia recovered from the evidence and fruiting bodies (control) were genetically indistinguishable.
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Affiliation(s)
- Jaime Solano
- Departamento de Ciencias Agropecuarias y Acuícolas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Avenida Rudecindo Ortega 02950, Temuco, Región de La Araucanía 4813302, Chile.
| | - Leonardo Anabalón
- Departamento de Ciencias Biológicas y Químicas, Facultad de Recursos Naturales, Universidad Católica de Temuco, Avenida Rudecindo Ortega 02950, Temuco, Región de La Araucanía 4813302, Chile
| | - Sylvia Figueroa
- Laboratorio de Criminalística, Policía de Investigaciones de Chile, Chile
| | - Cristian Lizama
- Laboratorio de Criminalística, Policía de Investigaciones de Chile, Chile
| | - Luis Chávez Reyes
- Laboratorio de Criminalística, Policía de Investigaciones de Chile, Chile
| | - David Gangitano
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX 77341, USA
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14
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Cornelis S, Fauvart M, Gansemans Y, Vander Plaetsen AS, Colle F, Wiederkehr RS, Deforce D, Stakenborg T, Van Nieuwerburgh F. Multiplex STR amplification sensitivity in a silicon microchip. Sci Rep 2018; 8:9853. [PMID: 29959383 PMCID: PMC6026139 DOI: 10.1038/s41598-018-28229-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 06/18/2018] [Indexed: 11/30/2022] Open
Abstract
The demand for solutions to perform forensic DNA profiling outside of centralized laboratories is increasing. We here demonstrate highly sensitive STR amplification using a silicon micro-PCR (µPCR) chip. Exploiting industry-standard semiconductor manufacturing processes, a device was fabricated that features a small form factor thanks to an integrated heating element covering three parallel micro-reactors with a reaction volume of 0.5 µl each. Diluted reference DNA samples (1 ng–31 pg) were amplified on the µPCR chip using the forensically validated AmpFISTR Identifier Plus kit, followed by conventional capillary electrophoresis. Complete STR profiles were generated with input DNA quantities down to 62 pg. Occasional allelic dropouts were observed from 31 pg downward. On-chip STR profiles were compared with those of identical samples amplified using a conventional thermal cycler for direct comparison of amplification sensitivity in a forensic setting. The observed sensitivity was in line with kit specifications for both µPCR and conventional PCR. Finally, a rapid amplification protocol was developed. Complete STR profiles could be generated in less than 17 minutes from as little as 125 pg template DNA. Together, our results are an important step towards the development of commercial, mass-produced, relatively cheap, handheld devices for on-site testing in forensic DNA analysis.
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Affiliation(s)
- Senne Cornelis
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium.,Department of Life Sciences and Imaging, imec, 3001, Leuven, Belgium
| | - Maarten Fauvart
- Department of Life Sciences and Imaging, imec, 3001, Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
| | | | - Frederik Colle
- Department of Life Sciences and Imaging, imec, 3001, Leuven, Belgium
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium.
| | - Tim Stakenborg
- Department of Life Sciences and Imaging, imec, 3001, Leuven, Belgium
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15
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Cowan AF, Elkins KM. Detection and Identification of Psilocybe cubensis DNA Using a Real-Time Polymerase Chain Reaction High Resolution Melt Assay. J Forensic Sci 2017; 63:1500-1505. [PMID: 29194645 DOI: 10.1111/1556-4029.13714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/03/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022]
Abstract
Psilocybe cubensis, or "magic mushroom," is the most common species of fungus with psychedelic characteristics. Two primer sets were designed to target Psilocybe DNA using web-based software and NBCI gene sequences. DNA was extracted from eighteen samples, including twelve mushroom species, using the Qiagen DNeasy® Plant Mini Kit. The DNA was amplified by the polymerase chain reaction (PCR) using the primers and a master mix containing either a SYBR® Green I, Radiant™ Green, or LCGreen Plus® intercalating dye; amplicon size was determined using agarose gel electrophoresis. The PCR assays were tested for amplifiability, specificity, reproducibility, robustness, sensitivity, and multiplexing with primers that target marijuana. The observed high resolution melt (HRM) temperatures for primer sets 1 and 7 were 78.85 ± 0.31°C and 73.22 ± 0.61°C, respectively, using SYBR® Green I dye and 81.67 ± 0.06°C and 76.04 ± 0.11°C, respectively, using Radiant™ Green dye.
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Affiliation(s)
- Ashley F Cowan
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Rd, Towson, MD, 21252
| | - Kelly M Elkins
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Rd, Towson, MD, 21252
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16
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High resolution melting of Short Tandem Repeats amplicons. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.120] [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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17
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Dos Santos Rocha A, de Amorim ISS, Simão TDA, da Fonseca ADS, Garrido RG, Mencalha AL. High-Resolution Melting (HRM) of Hypervariable Mitochondrial DNA Regions for Forensic Science. J Forensic Sci 2017; 63:536-540. [PMID: 28834547 DOI: 10.1111/1556-4029.13552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 11/26/2022]
Abstract
Forensic strategies commonly are proceeding by analysis of short tandem repeats (STRs); however, new additional strategies have been proposed for forensic science. Thus, this article standardized the high-resolution melting (HRM) of DNA for forensic analyzes. For HRM, mitochondrial DNA (mtDNA) from eight individuals were extracted from mucosa swabs by DNAzol reagent, samples were amplified by PCR and submitted to HRM analysis to identify differences in hypervariable (HV) regions I and II. To confirm HRM, all PCR products were DNA sequencing. The data suggest that is possible discriminate DNA from different samples by HRM curves. Also, uncommon dual-dissociation was identified in a single PCR product, increasing HRM analyzes by evaluation of melting peaks. Thus, HRM is accurate and useful to screening small differences in HVI and HVII regions from mtDNA and increase the efficiency of laboratory routines based on forensic genetics.
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Affiliation(s)
- Alípio Dos Santos Rocha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil.,Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Isis Salviano Soares de Amorim
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
| | - Tatiana de Almeida Simão
- Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
| | - Adenilson de Souza da Fonseca
- Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Rodrigo Grazinoli Garrido
- Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
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18
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Elkins KM, Perez ACU, Quinn AA. Simultaneous Identification of Four "Legal High" Plant Species in a Multiplex PCR High-Resolution Melt Assay . J Forensic Sci 2016; 62:593-601. [PMID: 27957736 DOI: 10.1111/1556-4029.13321] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/26/2016] [Accepted: 07/31/2016] [Indexed: 11/26/2022]
Abstract
The international prevalence of "legal high" drugs necessitates the development of a method for their detection and identification. Herein, we describe the development and validation of a tetraplex multiplex real-time polymerase chain reaction (PCR) assay used to simultaneously identify morning glory, jimson weed, Hawaiian woodrose, and marijuana detected by high-resolution melt using LCGreen Plus® . The PCR assay was evaluated based on the following: (i) specificity and selectivity-primers were tested on DNA extracted from 30 species and simulated forensic samples, (ii) sensitivity-serial dilutions of the target DNA were prepared, and (iii) reproducibility and reliability-sample replicates were tested and remelted on different days. The assay is ideal for cases in which inexpensive assays are needed to quickly detect and identify trace biological material present on drug paraphernalia that is too compromised for botanical microscopic identification and for which analysts are unfamiliar with the morphology of the emerging "legal high" species.
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Affiliation(s)
- Kelly M Elkins
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Road, Towson, MD, 21252
| | - Anjelica C U Perez
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Road, Towson, MD, 21252
| | - Alicia A Quinn
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Road, Towson, MD, 21252
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19
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Schmidt U, Hulkkonen J, Naue J. Detection of a G>C single nucleotide polymorphism within a repetitive DNA sequence by high-resolution DNA melting. Int J Legal Med 2016; 130:1181-4. [PMID: 26972692 DOI: 10.1007/s00414-016-1350-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/25/2016] [Indexed: 11/26/2022]
Abstract
In standard forensic DNA analysis, single base mutations within short tandem repeats (STR) mostly escape detection. In this study, high-resolution DNA melting (HRM) is compared to minisequencing and Sanger sequencing as to determine the most suitable method for detection of a G to C mutation within a repetitive DNA sequence, the STR system DXS10161. It shows an ATG/ATC polymorphism surrounded by a variable number of (TATC) and (ATCT) motifs. Neutral base changes like G:C to C:G result in very low differences in the melting temperature (T m) of the PCR amplicons. By enhanced resolution of fluorescence vs. temperature in HRM, the technique showed to be suitable for detecting a G to C transversion in this repetitive DNA sequence context. Compared to minisequencing, HRM is more time- and cost-effective. Results were confirmed by Sanger sequencing.
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Affiliation(s)
- Ulrike Schmidt
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstr. 9, 79104, Freiburg, Germany.
| | - Johannes Hulkkonen
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstr. 9, 79104, Freiburg, Germany
- Department of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Jana Naue
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstr. 9, 79104, Freiburg, Germany
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, Netherlands
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20
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Juiz NA, Cayo NM, Burgos M, Salvo ME, Nasser JR, Búa J, Longhi SA, Schijman AG. Human Polymorphisms in Placentally Expressed Genes and Their Association With Susceptibility to Congenital Trypanosoma cruzi Infection. J Infect Dis 2015; 213:1299-306. [PMID: 26597259 DOI: 10.1093/infdis/jiv561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/12/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND It is currently unclear why only a proportion of children born to Trypanosoma cruzi-infected mothers acquire the infection. We have examined the association of 11 single-nucleotide polymorphisms (SNPs) located in genes coding for placental expression enzymes as genetic markers of susceptibility to congenital T. cruzi infection (hereafter, "congenital infection"): rs2014683 and rs1048988 in ALPP; rs11244787 and rs1871054 in ADAM12; rs243866, rs243865, rs17859821, rs243864, and rs2285053 in MMP2; and rs3918242 and rs2234681 in MMP9. METHODS Two groups of children born to mothers seropositive for T. cruzi were compared: 101 had congenital infection, and 116 were uninfected. Novel high-resolution melting and capillary electrophoresis genotyping techniques were designed and used. RESULTS Logistic regression analysis showed that mutations in rs11244787 and rs1871054 (in ADAM12) and rs243866, rs17859821, and rs2285053 (in MMP2) were associated with susceptibility to congenital infection. Multifactor dimensionality reduction revealed that genotyping results for rs11244787, rs1871054, rs243866, rs17859821 and rs243864 sites would be a good predictor of congenital infection. CONCLUSIONS Our results suggest an important role of human polymorphisms in proteins involved in extracellular matrix remodeling and the immune response during congenital infection. To our knowledge, this is the first study demonstrating the association between mutations in placentally expressed genes and susceptibility to congenital infection.
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Affiliation(s)
- Natalia A Juiz
- Grupo de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N. Torres
| | - Nelly M Cayo
- Instituto de Biología de la Altura, Universidad Nacional de Jujuy
| | - Marianela Burgos
- Servicio de Obstetricia, Departamento Materno Infantil, Hospital Nacional Profesor Alejandro Posadas
| | - Miriam E Salvo
- Servicio de Obstetricia, Departamento Materno Infantil, Hospital Nacional Profesor Alejandro Posadas
| | - Julio R Nasser
- Laboratorio de Química Biológica, Facultad de Ciencias Naturales, Universidad Nacional de Salta, Argentina
| | - Jacqueline Búa
- Instituto Nacional de Parasitología Dr Mario Fatala Chaben, ANLIS, Buenos Aires
| | - Silvia A Longhi
- Grupo de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N. Torres
| | - Alejandro G Schijman
- Grupo de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular Dr Héctor N. Torres
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21
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Blackman S, Dawnay N, Ball G, Stafford-Allen B, Tribble N, Rendell P, Neary K, Hanson EK, Ballantyne J, Kallifatidis B, Mendel J, Mills DK, Wells S. Developmental validation of the ParaDNA ® Intelligence System—A novel approach to DNA profiling. Forensic Sci Int Genet 2015; 17:137-148. [DOI: 10.1016/j.fsigen.2015.04.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/01/2015] [Accepted: 04/24/2015] [Indexed: 11/25/2022]
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22
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Pomeroy RS, Balamurugan K, Wong H, Duncan G. High-resolution melt analysis of the minisatellite D1S80: A potential forensic screening tool. Electrophoresis 2014; 35:3020-7. [DOI: 10.1002/elps.201400143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 07/24/2014] [Accepted: 08/20/2014] [Indexed: 01/11/2023]
Affiliation(s)
- Robert S. Pomeroy
- Department of Chemistry and Biochemistry; University of California; San Diego CA USA
| | | | - Helena Wong
- Department of Chemistry and Biochemistry; University of California; San Diego CA USA
| | - George Duncan
- Oceanographic Institute; Nova Southeastern University; Fort Lauderdale FL USA
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23
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Dawnay N, Stafford-Allen B, Moore D, Blackman S, Rendell P, Hanson EK, Ballantyne J, Kallifatidis B, Mendel J, Mills DK, Nagy R, Wells S. Developmental Validation of the ParaDNA® Screening System - A presumptive test for the detection of DNA on forensic evidence items. Forensic Sci Int Genet 2014; 11:73-9. [PMID: 24670380 DOI: 10.1016/j.fsigen.2014.02.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 01/07/2014] [Accepted: 02/07/2014] [Indexed: 10/25/2022]
Abstract
Current assessment of whether a forensic evidence item should be submitted for STR profiling is largely based on the personal experience of the Crime Scene Investigator (CSI) and the submissions policy of the law enforcement authority involved. While there are chemical tests that can infer the presence of DNA through the detection of biological stains, the process remains mostly subjective and leads to many samples being submitted that give no profile or not being submitted although DNA is present. The ParaDNA(®) Screening System was developed to address this issue. It consists of a sampling device, pre-loaded reaction plates and detection instrument. The test uses direct PCR with fluorescent HyBeacon™ detection of PCR amplicons to identify the presence and relative amount of DNA on an evidence item and also provides a gender identification result in approximately 75 minutes. This simple-to-use design allows objective data to be acquired by both DNA analyst and non-specialist personnel, to enable a more informed submission decision to be made. The developmental validation study described here tested the sensitivity, reproducibility, accuracy, inhibitor tolerance, and performance of the ParaDNA Screening System on a range of mock evidence items. The data collected demonstrates that the ParaDNA Screening System identifies the presence of DNA on a variety of evidence items including blood, saliva and touch DNA items.
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Affiliation(s)
- Nick Dawnay
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon, OX14 3ED.
| | - Beccy Stafford-Allen
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon, OX14 3ED
| | - Dave Moore
- Innovation & Development Team, LGC, Teddington, TW11 0LY
| | - Stephen Blackman
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon, OX14 3ED
| | - Paul Rendell
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon, OX14 3ED
| | - Erin K Hanson
- National Center for Forensic Science, PO Box 162367, Orlando, FL 32816-2367, USA
| | - Jack Ballantyne
- National Center for Forensic Science, PO Box 162367, Orlando, FL 32816-2367, USA; Department of Chemistry, University of Central Florida, PO Box 162366, Orlando, FL 32816-2366, USA
| | - Beatrice Kallifatidis
- International Forensic Research Institute, Florida International University, Miami, FL, USA
| | - Julian Mendel
- International Forensic Research Institute, Florida International University, Miami, FL, USA
| | - DeEtta K Mills
- International Forensic Research Institute, Florida International University, Miami, FL, USA; Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Randy Nagy
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon, OX14 3ED
| | - Simon Wells
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon, OX14 3ED
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