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Kelani KM, Abdel-Raoof AM, Ashmawy AM, Omran GA, Morshedy S, Wafaa Nassar AM, Talaat W, Elgazzar E. Electrochemical determination of dinitolmide in poultry product samples using a highly sensitive Mn 2O 3/MCNTs-NPs carbon paste electrode aided by greenness assessment tools. Food Chem 2022; 382:131702. [PMID: 35149471 DOI: 10.1016/j.foodchem.2021.131702] [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: 06/24/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/04/2022]
Abstract
In this paper, chemically modified carbon paste Mn2O3/MCNTs-NPs electrode for estimation of dinitolmide (DOM) utilizing square wave voltammetry method (SWV) was developed. The study investigated the electrochemical behavior of DOM, and the morphology of the modified electrode was evaluated by Scanning Electron Microscope (SEM) and Transmission Electron Microscope (TEM). The voltammetric behavior of DOM at modified electrode was recorded at a scan rate of 100 mVs-1 against Ag/AgCl reference electrode in phosphate buffer pH 4.0 within linearity range 2-12 µM, LOQ, and LOD of 1.8 and 0.594 µM, respectively, with average % recovery of (100.89 ± 0.795). GAPI and Analytical Eco-Scale tools were applied for greenness assessment. Specificity and interference study was valid for the proposed method; allowing DOM to be determined in its acidic degradation and its major interference drug. The proposed method was successfully employed to quantify DOM in bulk powder, egg, and frozen cuts-up chicken muscle samples.
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Affiliation(s)
- Khadiga M Kelani
- Analytical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St, ET-11562 Cairo, Egypt; Analytical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, Egypt
| | - Ahmed M Abdel-Raoof
- Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, 11751, Cairo, Egypt.
| | - Ashraf M Ashmawy
- Chemistry Department, Faculty of Science (boys), Al-Azhar University, 11884 Cairo, Egypt
| | - Gamal A Omran
- Department of Pharmaceutical Analytical Chemistry, Damanhour University, Damanhour, Egypt
| | - Samir Morshedy
- Department of Pharmaceutical Analytical Chemistry, Damanhour University, Damanhour, Egypt
| | - Ahmed M Wafaa Nassar
- Analytical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, Egypt
| | - Wael Talaat
- Department of Pharmaceutical Analytical Chemistry, Damanhour University, Damanhour, Egypt
| | - Elsayed Elgazzar
- Department of Physics, Faculty of Science, Suez Canal University, Ismailia, Egypt
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2
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Abdel-Raoof AM, Osman AOE, El-Desouky EA, Abdel-Fattah A, Abdul-Kareem RF, Elgazzar E. Fabrication of an (α-Mn 2O 3:Co)-decorated CNT highly sensitive screen printed electrode for the optimization and electrochemical determination of cyclobenzaprine hydrochloride using response surface methodology. RSC Adv 2020; 10:24985-24993. [PMID: 35517446 PMCID: PMC9055185 DOI: 10.1039/d0ra05106c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 11/29/2022] Open
Abstract
A new chemically optimized screen-printed electrode modified with a cobalt-doped α-Mn2O3 nanostructure on carbon nanotube paste (α-Mn2O3:Co@CNTs) has been constructed for the recognition of cyclobenzaprine hydrochloride. The prepared paste is based on the incorporation of oxide ion conductors, such as the α-Mn2O3 nanostructure with cobalt and ion pairs (tetraphenyl borate coupled with the drug), as electroactive species in the screen-printed electrode to increase the sensor surface area and decrease electrical resistance. The central composite design is a useful methodology for the estimation and modeling of the exact optimum parameters specifically designed for this process. This is a good way to graphically clarify the relationship between various experimental variables and the slope response. The proposed sensor, α-Mn2O3:Co@CNTs, possesses very good sensitivity and the ability to recognize the drug over the concentration range of 1 × 10-6 to 1 × 10-2 mol L-1 at 25 ± °C with a detection limit of 2.84 × 10-7 mol L-1. It exhibits a reproducible potential and stable linear response for six months at a Nernstian slope of 58.96 ± 0.76 mV per decade. The proposed electrode approach has been successfully applied in the direct determination of the drug in its pure and dosage forms.
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Affiliation(s)
- Ahmed M Abdel-Raoof
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University 11751, Nasr City Cairo Egypt
| | - Ayman O E Osman
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University 11751, Nasr City Cairo Egypt
| | - Ebrahim A El-Desouky
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University 11751, Nasr City Cairo Egypt
| | - Ashraf Abdel-Fattah
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University 11751, Nasr City Cairo Egypt
| | - Rady F Abdul-Kareem
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University 11751, Nasr City Cairo Egypt
| | - Elsayed Elgazzar
- Department of Physics, Faculty of Science, Suez Canal University Ismailia Egypt
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3
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Green synthesis of manganese nanoparticles: Applications and future perspective–A review. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 189:234-243. [DOI: 10.1016/j.jphotobiol.2018.10.022] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022]
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4
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Wong H, Mihalovich J. Automation of the Differential Digestion Process of Sexual Assault Evidence,. J Forensic Sci 2018; 64:539-550. [DOI: 10.1111/1556-4029.13877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/26/2018] [Accepted: 07/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Helena Wong
- Oakland Police Department Criminalistics Laboratory 455 7th Street, #608 Oakland CA 94607
| | - Jennifer Mihalovich
- Oakland Police Department Criminalistics Laboratory 455 7th Street, #608 Oakland CA 94607
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5
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Zander J, Otremba P, Nagy M. Validation of haplotype-specific extraction for separating a mitochondrial DNA model mixture and application to simulated casework. Forensic Sci Int Genet 2018; 35:57-64. [PMID: 29665468 DOI: 10.1016/j.fsigen.2018.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 01/14/2023]
Abstract
Haplotype-specific extraction (HSE) is a new field of application for the separation of mitochondrial DNA (mtDNA) mixtures and is developed to identify the mtDNA haplotypes of the contributors subsequently by sequencing. Here we show the validation of HSE with an exemplary mitochondrial DNA mixture into its individual haplotypes according to our laboratory standards. These specify several critical areas of assay performance to be tested, such as sensitivity, robustness and mixture studies comprising varying proportions of their components,degraded samples and samples of different qualities and material. Wereport the successful and unambiguous analysis of the exemplary separated mitochondrial DNA mixture under various conditions as well as simulated casework samples, which manifest as mixed nucleotide calls at single base positions previously. Here we demonstrate that the HSE assay is high sensitive, stable against degradation and applicable in a wide range of sample qualities. Based on our findings from the validation study, we believe that this assay has great potential power and may be useful for distinguishing among the mtDNA of individuals and their geographical origin in mixed DNA samples.
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Affiliation(s)
- Judith Zander
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
| | - Petra Otremba
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Forum 4/Westring 3, Germany.
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6
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Harrel M, Mayes C, Gangitano D, Hughes-Stamm S. Evaluation Of A Powder-Free DNA Extraction Method For Skeletal Remains. J Forensic Sci 2018; 63:1819-1823. [PMID: 29411392 DOI: 10.1111/1556-4029.13749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/27/2017] [Accepted: 01/15/2018] [Indexed: 11/26/2022]
Abstract
Bones are often recovered in forensic investigations, including missing persons and mass disasters. While traditional DNA extraction methods rely on grinding bone into powder prior to DNA purification, the TBone Ex buffer (DNA Chip Research Inc.) digests bone chips without powdering. In this study, six bones were extracted using the TBone Ex kit in conjunction with the PrepFiler® BTA™ DNA extraction kit (Thermo Fisher Scientific) both manually and via an automated platform. Comparable amounts of DNA were recovered from a 50 mg bone chip using the TBone Ex kit and 50 mg of powdered bone with the PrepFiler® BTA™ kit. However, automated DNA purification decreased DNA yield (p < 0.05). Nevertheless, short tandem repeat (STR) success was comparable across all methods tested. This study demonstrates that digestion of whole bone fragments is an efficient alternative to powdering bones for DNA extraction without compromising downstream STR profile quality.
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Affiliation(s)
- Michelle Harrel
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, 77340
| | - Carrie Mayes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, 77340
| | - David Gangitano
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, 77340
| | - Sheree Hughes-Stamm
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, 77340
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Zupanič Pajnič I, Zupanc T, Balažic J, Geršak ŽM, Stojković O, Skadrić I, Črešnar M. Prediction of autosomal STR typing success in ancient and Second World War bone samples. Forensic Sci Int Genet 2017; 27:17-26. [DOI: 10.1016/j.fsigen.2016.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/08/2016] [Accepted: 11/18/2016] [Indexed: 01/31/2023]
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8
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Comparison of two silica-based extraction methods for DNA isolation from bones. Leg Med (Tokyo) 2016; 22:36-41. [DOI: 10.1016/j.legalmed.2016.07.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 07/25/2016] [Accepted: 07/25/2016] [Indexed: 11/20/2022]
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9
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Frégeau CJ, Yensen C, Elliott J, Fourney RM. Optimized Configuration of Fixed-Tip Robotic Liquid-Handling Stations for the Elimination of Biological Sample Cross-Contamination. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.jala.2007.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Robotic liquid-handling stations (RLHSs) are the mainstay of high-throughput biomedical/forensic DNA sample processing facilities. These liquid-handling systems can be alternatively tooled with either disposable or fixed-tip pipetting heads. The use of disposable tips is often perceived as the best tip configuration to eliminate cross-contamination between biological samples processed on liquid-handling stations. However, this suppression can be effectively achieved on instruments equipped with fixed tips with optimally designed tip wash station (WS) configurations. Fixed-tip instruments offer many significant sample processing advantages with respect to precision, pipetting of liquids that may contain aggregates, and operational cost. This report discusses how cross-contamination suppression was achieved for the reliable processing of forensic casework samples on specially configured fixed-tip TECAN Genesis RSP/Freedom EVO RLHSs. A critical analysis of the major components involved in tip washing, as well as the specifications of a redesigned tip-washing routine that increases wash effectiveness and significantly reduces processing time and cost is also presented.
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Affiliation(s)
| | - Craig Yensen
- Royal Canadian Mounted Police, Ottawa, Ontario, Canada
| | - Jim Elliott
- Royal Canadian Mounted Police, Ottawa, Ontario, Canada
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10
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DNA recovery from a single bacterial cell using charge-reversible magnetic nanoparticles. Colloids Surf B Biointerfaces 2016; 139:117-22. [DOI: 10.1016/j.colsurfb.2015.11.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/20/2015] [Accepted: 11/27/2015] [Indexed: 11/18/2022]
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11
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Abstract
In recent years the recovery and analysis of DNA from skeletal remains has been applied to several contexts ranging from disaster victim identification to the identification of the victims of conflict. Here are described procedures for processing the bone and tooth samples including mechanical and chemical cleaning, cutting and powdering in the presence of liquid nitrogen, complete demineralization of bone and tooth powder, DNA extraction, DNA purification using magnetic beads, and the precautions and strategies implemented to avoid and detect contamination. It has proven highly successful in the analysis of bones and teeth from Second World War victims' skeletal remains that have been excavated from mass graves in Slovenia and is also suitable for genetic identification of relatively fresh human remains.
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Affiliation(s)
- Irena Zupanič Pajnič
- Laboratory of Molecular Genetics, Institute of Forensic Medicine, Vrazov trg 2, 1104, Ljubljana, Slovenia.
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12
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Zupanič Pajnič I, Debska M, Gornjak Pogorelc B, Vodopivec Mohorčič K, Balažic J, Zupanc T, Štefanič B, Geršak K. Highly efficient automated extraction of DNA from old and contemporary skeletal remains. J Forensic Leg Med 2016; 37:78-86. [DOI: 10.1016/j.jflm.2015.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022]
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13
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Maeda Y, Toyoda T, Tanaka M, Mogi T, Taguchi T, Tanaami T, Matsunaga T, Tanaka T. Reprint of: DNA recovery from a single bacterial cell based on electrostatic interaction using amine dendron-modified magnetic nanoparticles. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.04.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Purps J, Geppert M, Nagy M, Roewer L. Validation of a combined autosomal/Y-chromosomal STR approach for analyzing typical biological stains in sexual-assault cases. Forensic Sci Int Genet 2015; 19:238-242. [PMID: 26280567 DOI: 10.1016/j.fsigen.2015.08.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/23/2015] [Accepted: 08/05/2015] [Indexed: 11/26/2022]
Abstract
DNA testing is an established part of the investigation and prosecution of sexual assault. The primary purpose of DNA evidence is to identify a suspect and/or to demonstrate sexual contact. However, due to highly uneven proportions of female and male DNA in typical stains, routine autosomal analysis often fails to detect the DNA of the assailant. To evaluate the forensic efficiency of the combined application of autosomal and Y-chromosomal short tandem repeat (STR) markers, we present a large retrospective casework study of probative evidence collected in sexual-assault cases. We investigated up to 39 STR markers by testing combinations of the 16-locus NGMSElect kit with both the 23-locus PowerPlex Y23 and the 17-locus Yfiler kit. Using this dual approach we analyzed DNA extracts from 2077 biological stains collected in 287 cases over 30 months. To assess the outcome of the combined approach in comparison to stand-alone autosomal analysis we evaluated informative DNA profiles. Our investigation revealed that Y-STR analysis added up to 21% additional, highly informative (complete, single-source) profiles to the set of reportable autosomal STR profiles for typical stains collected in sexual-assault cases. Detection of multiple male contributors was approximately three times more likely with Y-chromosomal profiling than with autosomal STR profiling. In summary, 1/10 cases would have remained inconclusive (and could have been dismissed) if Y-STR analysis had been omitted from DNA profiling in sexual-assault cases.
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Affiliation(s)
- Josephine Purps
- Department Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Germany
| | - Maria Geppert
- Department Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Germany
| | - Marion Nagy
- Department Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Germany
| | - Lutz Roewer
- Department Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Germany.
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15
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Kowalczyk M, Sekuła A, Mleczko P, Olszowy Z, Kujawa A, Zubek S, Kupiec T. Practical aspects of genetic identification of hallucinogenic and other poisonous mushrooms for clinical and forensic purposes. Croat Med J 2015; 56:32-40. [PMID: 25727040 PMCID: PMC4364345 DOI: 10.3325/cmj.2015.56.32] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Aim To assess the usefulness of a DNA-based method for identifying mushroom species for application in forensic laboratory practice. Methods Two hundred twenty-one samples of clinical forensic material (dried mushrooms, food remains, stomach contents, feces, etc) were analyzed. ITS2 region of nuclear ribosomal DNA (nrDNA) was sequenced and the sequences were compared with reference sequences collected from the National Center for Biotechnology Information gene bank (GenBank). Sporological identification of mushrooms was also performed for 57 samples of clinical material. Results Of 221 samples, positive sequencing results were obtained for 152 (69%). The highest percentage of positive results was obtained for samples of dried mushrooms (96%) and food remains (91%). Comparison with GenBank sequences enabled identification of all samples at least at the genus level. Most samples (90%) were identified at the level of species or a group of closely related species. Sporological and molecular identification were consistent at the level of species or genus for 30% of analyzed samples. Conclusion Molecular analysis identified a larger number of species than sporological method. It proved to be suitable for analysis of evidential material (dried hallucinogenic mushrooms) in forensic genetic laboratories as well as to complement classical methods in the analysis of clinical material.
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Affiliation(s)
- Marek Kowalczyk
- Marek Kowalczyk, Institute of Forensic Research, Westerplatte St. 9, 31-033 Krakow, Poland,
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16
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Maeda Y, Toyoda T, Tanaka M, Mogi T, Taguchi T, Tanaami T, Matsunaga T, Tanaka T. DNA recovery from a single bacterial cell based on electrostatic interaction using amine dendron-modified magnetic nanoparticles. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.04.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Zhou R, Meng Q, Li P, Chen J, Sun Y, Li M. Improved high throughput processing of touch DNA samples. AUST J FORENSIC SCI 2015. [DOI: 10.1080/00450618.2015.1025838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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So H, Lee K, Murthy N, Pisano A. All-in-one nanowire-decorated multifunctional membrane for rapid cell lysis and direct DNA isolation. ACS APPLIED MATERIALS & INTERFACES 2014; 6:20693-9. [PMID: 25420232 PMCID: PMC4264858 DOI: 10.1021/am506153y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 11/06/2014] [Indexed: 05/20/2023]
Abstract
This paper describes a handheld device that uses an all-in-one membrane for continuous mechanical cell lysis and rapid DNA isolation without the assistance of power sources, lysis reagents, and routine centrifugation. This nanowire-decorated multifunctional membrane was fabricated to isolate DNA by selective adsorption to silica surface immediately after disruption of nucleus membranes by ultrasharp tips of nanowires for a rapid cell lysis, and it can be directly assembled with commercial syringe filter holders. The membrane was fabricated by photoelectrochemical etching to create microchannel arrays followed by hydrothermal synthesis of nanowires and deposition of silica. The proposed membrane successfully purifies high-quality DNA within 5 min, whereas a commercial purification kit needs more than an hour.
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Affiliation(s)
- Hongyun So
- Department of Mechanical
Engineering, Berkeley Sensor & Actuator
Center and Department of Bioengineering, University
of California, Berkeley, California 94720, United States
- E-mail:
| | - Kunwoo Lee
- Department of Mechanical
Engineering, Berkeley Sensor & Actuator
Center and Department of Bioengineering, University
of California, Berkeley, California 94720, United States
| | - Niren Murthy
- Department of Mechanical
Engineering, Berkeley Sensor & Actuator
Center and Department of Bioengineering, University
of California, Berkeley, California 94720, United States
| | - Albert
P. Pisano
- Department of Mechanical
Engineering, Berkeley Sensor & Actuator
Center and Department of Bioengineering, University
of California, Berkeley, California 94720, United States
- Jacobs
School of Engineering, University of California, San Diego, California 92093, United States
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19
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Hedman J, Knutsson R, Ansell R, Rådström P, Rasmusson B. Pre-PCR processing in bioterrorism preparedness: improved diagnostic capabilities for laboratory response networks. Biosecur Bioterror 2014; 11 Suppl 1:S87-101. [PMID: 23971826 DOI: 10.1089/bsp.2012.0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Diagnostic DNA analysis using polymerase chain reaction (PCR) has become a valuable tool for rapid detection of biothreat agents. However, analysis is often challenging because of the limited size, quality, and purity of the biological target. Pre-PCR processing is an integrated concept in which the issues of analytical limit of detection and simplicity for automation are addressed in all steps leading up to PCR amplification--that is, sampling, sample treatment, and the chemical composition of PCR. The sampling method should maximize target uptake and minimize uptake of extraneous substances that could impair the analysis--so-called PCR inhibitors. In sample treatment, there is a trade-off between yield and purity, as extensive purification leads to DNA loss. A cornerstone of pre-PCR processing is to apply DNA polymerase-buffer systems that are tolerant to specific sample impurities, thereby lowering the need for expensive purification steps and maximizing DNA recovery. Improved awareness among Laboratory Response Networks (LRNs) regarding pre-PCR processing is important, as ineffective sample processing leads to increased cost and possibly false-negative or ambiguous results, hindering the decision-making process in a bioterrorism crisis. This article covers the nature and mechanisms of PCR-inhibitory substances relevant for agroterrorism and bioterrorism preparedness, methods for quality control of PCR reactions, and applications of pre-PCR processing to optimize and simplify the analysis of various biothreat agents. Knowledge about pre-PCR processing will improve diagnostic capabilities of LRNs involved in the response to bioterrorism incidents.
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Affiliation(s)
- Johannes Hedman
- Johannes Hedman, PhD, is employed as a specialist at the Swedish National Laboratory of Forensic Science (SKL) and holds a research position at Applied Microbiology, Lund University. Rickard Knutsson, PhD, is Director of Security Department, National Veterinary Institute (SVA), Uppsala, Sweden . Ricky Ansell, PhD, is employed as forensic advisor and senior reporting officer at the Swedish National Laboratory of Forensic Science (SKL). Birgitta Rasmusson, PhD, is employed as research director at the Swedish National Laboratory of Forensic Science (SKL) and holds a position as adjunct professor at Applied Microbiology, Lund University. Peter Rådström, PhD, is employed as professor Applied Microbiology, Lund University
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20
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Pandeshwar P, Das R. Role of oral fluids in DNA investigations. J Forensic Leg Med 2013; 22:45-50. [PMID: 24485421 DOI: 10.1016/j.jflm.2013.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 10/22/2013] [Accepted: 12/07/2013] [Indexed: 02/04/2023]
Abstract
The assay of oral fluid (OF), a biofluid historically well-studied biochemically and physiologically, is a growing area of research with implications for basic and clinical purposes. In the last decade, it has gained considerable attention and lately, the use of OF has provided a substantial addition as an investigative tool in forensic and/or legal procedures. This article is an appraisal of various applications of OF sourced DNA in the field of forensic analysis. We have discussed the significance of different collection methods and their variations along with the application of specific analytical methods based on the condition of the sample. It is likely that the germaneness of OF assays will continue to expand thus providing a new instrument for investigation in criminal/legal proceedings.
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Affiliation(s)
- Padma Pandeshwar
- Department of Oral Medicine, Diagnosis and Radiology, Vydehi Institute of Dental Sciences, # 82, EPIP Area, Whitefield, Bangalore 560066, India.
| | - Reshma Das
- Department of Oral Medicine, Diagnosis and Radiology, Vydehi Institute of Dental Sciences, # 82, EPIP Area, Whitefield, Bangalore 560066, India
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21
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Roewer L. DNA fingerprinting in forensics: past, present, future. INVESTIGATIVE GENETICS 2013; 4:22. [PMID: 24245688 PMCID: PMC3831584 DOI: 10.1186/2041-2223-4-22] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 11/29/2022]
Abstract
DNA fingerprinting, one of the great discoveries of the late 20th century, has revolutionized forensic investigations. This review briefly recapitulates 30 years of progress in forensic DNA analysis which helps to convict criminals, exonerate the wrongly accused, and identify victims of crime, disasters, and war. Current standard methods based on short tandem repeats (STRs) as well as lineage markers (Y chromosome, mitochondrial DNA) are covered and applications are illustrated by casework examples. Benefits and risks of expanding forensic DNA databases are discussed and we ask what the future holds for forensic DNA fingerprinting.
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Affiliation(s)
- Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Berlin, Germany.
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22
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Yi L, Huang Y, Wu T, Wu J. A magnetic nanoparticles-based method for DNA extraction from the saliva of stroke patients. Neural Regen Res 2013; 8:3036-46. [PMID: 25206624 PMCID: PMC4146207 DOI: 10.3969/j.issn.1673-5374.2013.32.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/27/2013] [Indexed: 11/18/2022] Open
Abstract
C677T polymorphism in the methylenetetrahydrofolate reductase (MTHFR) gene is a risk factor for stroke, suggesting that widespread detection could help to prevent stroke. DNA from 70 stroke patients and 70 healthy controls was extracted from saliva using a magnetic nanoparticles-based method and from blood using conventional methods. Real-time PCR results revealed that the C677T polymorphism was genotyped by PCR using DNA extracted from both saliva and blood samples. The genotype results were confirmed by gene sequencing, and results for saliva and blood samples were consistent. The mutation TT genotype frequency was significantly higher in the stroke group than in controls. Homocysteine levels were significantly higher than controls in both TT genotype groups. Therefore, this noninvasive magnetic nanoparticles-based method using saliva samples could be used to screen for the MTHFR C677T polymorphism in target populations.
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Affiliation(s)
- Li Yi
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Ying Huang
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Ting Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
| | - Jun Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen 518036, Guangdong Province, China
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Rittich B, Španová A. SPE and purification of DNA using magnetic particles. J Sep Sci 2013; 36:2472-85. [DOI: 10.1002/jssc.201300331] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Bohuslav Rittich
- Faculty of Chemistry; Brno University of Technology; Brno Czech Republic
| | - Alena Španová
- Faculty of Chemistry; Brno University of Technology; Brno Czech Republic
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Langos D, Kulik L, Mundry R, Widdig A. The impact of paternity on male-infant association in a primate with low paternity certainty. Mol Ecol 2013; 22:3638-51. [PMID: 23682587 DOI: 10.1111/mec.12328] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/08/2013] [Accepted: 03/17/2013] [Indexed: 11/26/2022]
Abstract
In multimale groups where females mate promiscuously, male-infant associations have rarely been studied. However, recent studies have shown that males selectively support their offspring during agonistic conflicts with other juveniles and that father's presence accelerates offspring maturation. Furthermore, it was shown that males invest in unrelated infants to enhance future mating success with the infant's mother. Hence, infant care might provide fitness gain for males. Here, we investigate male-infant associations in rhesus macaques (Macaca mulatta), a primate with low paternity certainty as females mate with multiple partners and males ensure paternity less efficiently through mate-guarding. We combined behavioural data with genetic paternity analyses of one cohort of the semi-free-ranging population of Cayo Santiago (Puerto Rico) and recorded affiliative and aggressive interactions between focal subjects and adult males from birth to sexual maturation (0-4 years) of focal subjects. Our results revealed that 9.6% of all interactions of focal subjects involved an adult male and 94% of all male-infant interactions were affiliative, indicating the rareness of male-infant aggression. Second and most interestingly, sires were more likely to affiliate with their offspring than nonsires with unrelated infants. This preference was independent of mother's proximity and emphasized during early infancy. Male-infant affiliation rose with infant age and was pronounced between adult males and male rather than female focal subjects. Overall, our results suggest that male-infant affiliation is also an important component in structuring primate societies and affiliation directed towards own offspring presumably represent low-cost paternal care.
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Affiliation(s)
- Doreen Langos
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
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Abstract
PCR is an important and powerful tool in several fields, including clinical diagnostics, food analysis, and forensic analysis. In theory, PCR enables the detection of one single cell or DNA molecule. However, the presence of PCR inhibitors in the sample affects the amplification efficiency of PCR, thus lowering the detection limit, as well as the precision of sequence-specific nucleic acid quantification in real-time PCR. In order to overcome the problems caused by PCR inhibitors, all the steps leading up to DNA amplification must be optimized for the sample type in question. Sampling and sample treatment are key steps, but most of the methods currently in use were developed for conventional diagnostic methods and not for PCR. Therefore, there is a need for fast, simple, and robust sample preparation methods that take advantage of the accuracy of PCR. In addition, the thermostable DNA polymerases and buffer systems used in PCR are affected differently by inhibitors. During recent years, real-time PCR has developed considerably and is now widely used as a diagnostic tool. This technique has greatly improved the degree of automation and reduced the analysis time, but has also introduced a new set of PCR inhibitors, namely those affecting the fluorescence signal. The purpose of this chapter is to view the complexity of PCR inhibition from different angles, presenting both molecular explanations and practical ways of dealing with the problem. Although diagnostic PCR brings together scientists from different diagnostic fields, end-users have not fully exploited the potential of learning from each other. Here, we have collected knowledge from archeological analysis, clinical diagnostics, environmental analysis, food analysis, and forensic analysis. The concept of integrating sampling, sample treatment, and the chemistry of PCR, i.e., pre-PCR processing, will be addressed as a general approach to overcoming real-time PCR inhibition and producing samples optimal for PCR analysis.
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Affiliation(s)
- Johannes Hedman
- Swedish National Laboratory of Forensic Science, Linköping, Sweden.
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26
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Faber KL, Person EC, Hudlow WR. PCR inhibitor removal using the NucleoSpin® DNA Clean-Up XS kit. Forensic Sci Int Genet 2013; 7:209-13. [DOI: 10.1016/j.fsigen.2012.06.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 06/06/2012] [Accepted: 06/15/2012] [Indexed: 11/25/2022]
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27
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Alaeddini R. Forensic implications of PCR inhibition—A review. Forensic Sci Int Genet 2012; 6:297-305. [DOI: 10.1016/j.fsigen.2011.08.006] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 10/17/2022]
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28
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Witt S, Neumann J, Zierdt H, Gébel G, Röscheisen C. Establishing a novel automated magnetic bead-based method for the extraction of DNA from a variety of forensic samples. Forensic Sci Int Genet 2012; 6:539-47. [PMID: 22310206 DOI: 10.1016/j.fsigen.2012.01.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 12/28/2011] [Accepted: 01/04/2012] [Indexed: 10/14/2022]
Abstract
Automated systems have been increasingly utilized for DNA extraction by many forensic laboratories to handle growing numbers of forensic casework samples while minimizing the risk of human errors and assuring high reproducibility. The step towards automation however is not easy: The automated extraction method has to be very versatile to reliably prepare high yields of pure genomic DNA from a broad variety of sample types on different carrier materials. To prevent possible cross-contamination of samples or the loss of DNA, the components of the kit have to be designed in a way that allows for the automated handling of the samples with no manual intervention necessary. DNA extraction using paramagnetic particles coated with a DNA-binding surface is predestined for an automated approach. For this study, we tested different DNA extraction kits using DNA-binding paramagnetic particles with regard to DNA yield and handling by a Freedom EVO(®)150 extraction robot (Tecan) equipped with a Te-MagS magnetic separator. Among others, the extraction kits tested were the ChargeSwitch(®)Forensic DNA Purification Kit (Invitrogen), the PrepFiler™Automated Forensic DNA Extraction Kit (Applied Biosystems) and NucleoMag™96 Trace (Macherey-Nagel). After an extensive test phase, we established a novel magnetic bead extraction method based upon the NucleoMag™ extraction kit (Macherey-Nagel). The new method is readily automatable and produces high yields of DNA from different sample types (blood, saliva, sperm, contact stains) on various substrates (filter paper, swabs, cigarette butts) with no evidence of a loss of magnetic beads or sample cross-contamination.
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Affiliation(s)
- Sebastian Witt
- LKA35 (DNA-Analytik), Landeskriminalamt Hamburg, Bruno-Georges-Platz 1, 22297 Hamburg, Germany.
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Frégeau CJ, De Moors A. Competition for DNA binding sites using Promega DNA IQ™ paramagnetic beads. Forensic Sci Int Genet 2012; 6:511-22. [PMID: 22264505 DOI: 10.1016/j.fsigen.2011.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 10/21/2011] [Accepted: 12/14/2011] [Indexed: 11/25/2022]
Abstract
The Promega DNA IQ™ system is easily amenable to automation and has been an integral part of standard operating procedures for many forensic laboratories including those of the Royal Canadian Mounted Police (RCMP) since 2004. Due to some failure to extract DNA from samples that should have produced DNA using our validated automated DNA IQ™-based protocol, the competition for binding sites on the DNA IQ™ magnetic beads was more closely examined. Heme from heavily blooded samples interfered slightly with DNA binding. Increasing the concentration of Proteinase K during lysis of these samples did not enhance DNA recovery. However, diluting the sample lysate following lysis prior to DNA extraction overcame the reduction in DNA yield and preserved portions of the lysates for subsequent manual or automated extraction. Dye/chemicals from black denim lysates competed for binding sites on the DNA IQ™ beads and significantly reduced DNA recovery. Increasing the size or number of black denim cuttings during lysis had a direct adverse effect on DNA yield from various blood volumes. The dilution approach was successful on these samples and permitted the extraction of high DNA yields. Alternatively, shortening the incubation time for cell lysis to 30 min instead of the usual overnight at 56 °C prevented competition from black denim dye/chemicals and increased DNA yields.
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Affiliation(s)
- Chantal J Frégeau
- Royal Canadian Mounted Police, National Services and Research, 1200 Vanier Parkway, Ottawa, Ontario K1G 3M8, Canada.
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30
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Hudlow WR, Buoncristiani MR. Development of a rapid, 96-well alkaline based differential DNA extraction method for sexual assault evidence. Forensic Sci Int Genet 2012; 6:1-16. [DOI: 10.1016/j.fsigen.2010.12.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 12/15/2010] [Accepted: 12/20/2010] [Indexed: 10/18/2022]
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31
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Brownlow RJ, Dagnall KE, Ames CE. A Comparison of DNA Collection and Retrieval from Two Swab Types (Cotton and Nylon Flocked Swab) when Processed Using Three QIAGEN Extraction Methods. J Forensic Sci 2011; 57:713-7. [DOI: 10.1111/j.1556-4029.2011.02022.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Current genetic methodologies in the identification of disaster victims and in forensic analysis. J Appl Genet 2011; 53:41-60. [PMID: 22002120 PMCID: PMC3265735 DOI: 10.1007/s13353-011-0068-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Revised: 09/22/2011] [Accepted: 09/23/2011] [Indexed: 12/16/2022]
Abstract
This review presents the basic problems and currently available molecular techniques used for genetic profiling in disaster victim identification (DVI). The environmental conditions of a mass disaster often result in severe fragmentation, decomposition and intermixing of the remains of victims. In such cases, traditional identification based on the anthropological and physical characteristics of the victims is frequently inconclusive. This is the reason why DNA profiling became the gold standard for victim identification in mass-casualty incidents (MCIs) or any forensic cases where human remains are highly fragmented and/or degraded beyond recognition. The review provides general information about the sources of genetic material for DNA profiling, the genetic markers routinely used during genetic profiling (STR markers, mtDNA and single-nucleotide polymorphisms [SNP]) and the basic statistical approaches used in DNA-based disaster victim identification. Automated technological platforms that allow the simultaneous analysis of a multitude of genetic markers used in genetic identification (oligonucleotide microarray techniques and next-generation sequencing) are also presented. Forensic and population databases containing information on human variability, routinely used for statistical analyses, are discussed. The final part of this review is focused on recent developments, which offer particularly promising tools for forensic applications (mRNA analysis, transcriptome variation in individuals/populations and genetic profiling of specific cells separated from mixtures).
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Hudlow WR, Krieger R, Meusel M, Sehhat JC, Timken MD, Buoncristiani MR. The NucleoSpin® DNA Clean-up XS kit for the concentration and purification of genomic DNA extracts: An alternative to microdialysis filtration. Forensic Sci Int Genet 2011; 5:226-30. [DOI: 10.1016/j.fsigen.2010.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 02/23/2010] [Accepted: 03/12/2010] [Indexed: 11/29/2022]
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34
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Stangegaard M, Frøslev TG, Frank-Hansen R, Hansen AJ, Morling N. Automated Extraction of DNA from Blood and PCR Setup using a Tecan Freedom EVO Liquid Handler for Forensic Genetic STR Typing of Reference Samples. ACTA ACUST UNITED AC 2011; 16:134-40. [DOI: 10.1016/j.jala.2010.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Indexed: 10/18/2022]
Abstract
We have implemented and validated automated protocols for DNA extraction and PCR setup using a Tecan Freedom EVO liquid handler mounted with the Te-MagS magnetic separation device (Tecan, Mannedorf, Switzerland). The protocols were validated for accredited forensic genetic work according to ISO 17025 using the Qiagen MagAttract DNA Mini M48 kit (Qiagen GmbH, Hilden, Germany) from fresh whole blood and blood from deceased individuals. The workflow was simplified by returning the DNA extracts to the original tubes minimizing the risk of misplacing samples. The tubes that originally contained the samples were washed with MilliQ water before the return of the DNA extracts. The PCR was setup in 96-well microtiter plates. The methods were validated for the kits: AmpFSTR Identifier, SGM Plus and Yfiler (Applied Biosystems, Foster City, CA), GenePrint FFFL and PowerPlex Y (Promega, Madison, Wl). The automated protocols allowed for extraction and addition of PCR master mix of 96 samples within 3.5 h. In conclusion, we demonstrated that (1) DNA extraction with magnetic beads and (2) PCR setup for accredited, forensic genetic short tandem repeat typing can be implemented on a simple automated liquid handler leading to the reduction of manual work, and increased quality and throughput.
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Affiliation(s)
- Michael Stangegaard
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tobias G. Frøslev
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rune Frank-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders J. Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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35
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Roeber F, Jex AR, Campbell AJD, Campbell BE, Anderson GA, Gasser RB. Evaluation and application of a molecular method to assess the composition of strongylid nematode populations in sheep with naturally acquired infections. INFECTION GENETICS AND EVOLUTION 2011; 11:849-54. [PMID: 21256979 DOI: 10.1016/j.meegid.2011.01.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Revised: 01/13/2011] [Accepted: 01/14/2011] [Indexed: 11/30/2022]
Abstract
We evaluated the performance of a PCR method for the diagnosis of naturally acquired strongylid nematode infections in sheep (n = 470; in a temperate climatic zone of south-eastern Australia), using a panel of 100 'negative control' samples from sheep known not to harbour parasitic helminths. We compared the diagnostic sensitivity (98%) and specificity (100%) of this assay against a conventional faecal flotation method and also established a system to rank the contribution of particular strongylid nematodes to the faecal egg counts (FECs) from 'mixed infections' in individual sheep. The testing of faecal samples herein revealed that Teladorsagia circumcincta (80%) and Trichostrongylus spp. (66%) were most prevalent, followed by Chabertia ovina (33%), Oesophagostomum venulosum (28%) and Haemonchus contortus (1%). For the majority of sheep in this study, T. circumcincta and Trichostrongylus spp. represented the largest proportion of strongylid eggs in faecal samples from individual sheep. This is the first large-scale prevalence survey of gastrointestinal nematodes in live sheep using a molecular tool. The ability to rapidly rank strongylid nematodes according to their contribution to mixed infections represents a major advantage over routine coprological methods. This PCR tool has the potential to replace the conventional technique of larval culture. Future efforts will focus on enhancing and adapting this molecular method for high throughput application in routine, diagnostic settings.
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Affiliation(s)
- Florian Roeber
- Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria 3030, Australia
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36
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Validation of a DNA IQ™-based extraction method for TECAN robotic liquid handling workstations for processing casework. Forensic Sci Int Genet 2010; 4:292-304. [DOI: 10.1016/j.fsigen.2009.11.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 11/02/2009] [Accepted: 11/03/2009] [Indexed: 11/19/2022]
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Holland MM, Parson W. GeneMarker® HID: A reliable software tool for the analysis of forensic STR data. J Forensic Sci 2010; 56:29-35. [PMID: 20887353 DOI: 10.1111/j.1556-4029.2010.01565.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
GeneMarker(®) HID was assessed as a software tool for the analysis of forensic short tandem repeat (STR) data and as a resource for analysis of custom STR multiplexes. The software is easy to learn and use, and includes design features that have the potential to reduce user fatigue. To illustrate reliability and accuracy, STR data from both single-source and mixture profiles were analyzed and compared to profiles interpreted with another software package. A total of 1898 STR profiles representing 28,470 loci and more than 42,000 alleles were analyzed with 100% concordance. GeneMarker HID was also used to successfully analyze data generated from a custom STR multiplex, with simplified and rapid implementation. Finally, the impact of the user-friendly design features of the software was assessed through a time scale study. The results suggest that laboratories can reduce the time required for data analysis by at least 25% when using GeneMarker HID.
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Affiliation(s)
- Mitchell M Holland
- The Pennsylvania State University, 107 Whitmore Laboratory, University Park, PA 16802, USA.
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38
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Molecular genetic identification of skeletal remains from the Second World War Konfin I mass grave in Slovenia. Int J Legal Med 2010; 124:307-17. [PMID: 20217112 PMCID: PMC2887502 DOI: 10.1007/s00414-010-0431-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 02/10/2010] [Indexed: 11/06/2022]
Abstract
This paper describes molecular genetic identification of one third of the skeletal remains of 88 victims of postwar (June 1945) killings found in the Konfin I mass grave in Slovenia. Living relatives were traced for 36 victims. We analyzed 84 right femurs and compared their genetic profiles to the genetic material of living relatives. We cleaned the bones, removed surface contamination, and ground the bones into powder. Prior to DNA isolation using Biorobot EZ1 (Qiagen), the powder was decalcified. The nuclear DNA of the samples was quantified using the real-time polymerase chain reaction method. We extracted 0.8 to 100 ng DNA/g of bone powder from 82 bones. Autosomal genetic profiles and Y-chromosome haplotypes were obtained from 98% of the bones, and mitochondrial DNA (mtDNA) haplotypes from 95% of the bones for the HVI region and from 98% of the bones for the HVII region. Genetic profiles of the nuclear and mtDNA were determined for reference persons. For traceability in the event of contamination, we created an elimination database including genetic profiles of the nuclear and mtDNA of all persons that had been in contact with the skeletal remains. When comparing genetic profiles, we matched 28 of the 84 bones analyzed with living relatives (brothers, sisters, sons, daughters, nephews, or cousins). The statistical analyses showed a high confidence of correct identification for all 28 victims in the Konfin I mass grave (posterior probability ranged from 99.9% to more than 99.999999%).
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39
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Stangegaard M, Frøslev TG, Frank-Hansen R, Laursen SS, Jørgensen M, Hansen AJ, Morling N. Automated extraction of DNA and PCR setup using a Tecan Freedom EVO® liquid handler. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Roewer L. Y chromosome STR typing in crime casework. Forensic Sci Med Pathol 2009; 5:77-84. [DOI: 10.1007/s12024-009-9089-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 04/20/2009] [Indexed: 10/20/2022]
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41
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Application of BioRobot M48 to forensic DNA extraction. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2008. [DOI: 10.1016/j.fsigss.2007.10.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Saiyed ZM, Ramchand CN, Telang SD. Isolation of genomic DNA using magnetic nanoparticles as a solid-phase support. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2008; 20:204153. [PMID: 21694281 DOI: 10.1088/0953-8984/20/20/204153] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In recent years, techniques employing magnetizable solid-phase supports (MSPS) have found application in numerous biological fields. This magnetic separation procedure offers several advantages in terms of subjecting the analyte to very little mechanical stress compared to other methods. Secondly, these methods are non-laborious, cheap, and often highly scalable. The current paper details a genomic DNA isolation method optimized in our laboratory using magnetic nanoparticles as a solid-phase support. The quality and yields of the isolated DNA from all the samples using magnetic nanoparticles were higher or equivalent to the traditional DNA extraction procedures. Additionally, the magnetic method takes less than 15 min to extract polymerase chain reaction (PCR) ready genomic DNA as against several hours taken by traditional phenol-chloroform extraction protocols. Moreover, the isolated DNA was found to be compatible in PCR amplification and restriction endonuclease digestion. The developed procedure is quick, inexpensive, robust, and it does not require the use of organic solvents or sophisticated instruments, which makes it more amenable to automation and miniaturization.
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Affiliation(s)
- Z M Saiyed
- Kemin Nutritional Technologies (India) Pvt Ltd, The Trapezium, Nelson Manickam Road, Chennai 600 029, India. Department of Biochemistry, Faculty of Science, The M S University of Baroda, Sayajigunj, Vadodara 390 002, India
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43
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Frégeau CJ, Marc Lett C, Elliott J, Yensen C, Fourney RM. Automated Processing of Forensic Casework Samples Using Robotic Workstations Equipped with Nondisposable Tips: Contamination Prevention. J Forensic Sci 2008; 53:632-51. [DOI: 10.1111/j.1556-4029.2008.00697.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Kohler S, Pascher A, Junge G, Sauer IM, Nagy M, Schönemann C, Koch M, Neumann U, Pratschke J, Neuhaus P. Graft versus host disease after liver transplantation - a single center experience and review of literature. Transpl Int 2008; 21:441-51. [PMID: 18266778 DOI: 10.1111/j.1432-2277.2007.00625.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Graft versus host disease (GvHD) after liver transplantation has an incidence of 0.1-1%. It is an infrequent but severe and mostly lethal complication. Approximately, 80 cases have been reported in literature so far. A single center experience is reported retrospectively. We performed a retrospective analysis of 1815 liver transplants in our center, transplanted over a period of 17 years. Five patients (5/1815 = 0.28%) with histologically diagnosed GvHD were included in the analysis. Onset of GvHD was between postoperative day (POD) 20 and 60. All patients developed skin rash, being the first symptom in four cases; one patient had joint pain as initial symptom. Macrochimerism was confirmed in all patients. Treatment consisted of augmentation of baseline immunosuppression (n = 4), methylprednisolone (n = 4), and T-cell depleting antibodies (n = 3). One patient received no specific therapy because of her deleterious condition. All patients died because of either haemorrhage or uncontrollable infections. In our experience, GvHD has been an extremely rare, albeit deleterious clinical condition, which was resistant to classical immunosuppressive rescue regimens.
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Affiliation(s)
- Sven Kohler
- Department of Visceral and Transplant Surgery, Charité-Universitaetsmedizin Berlin, Berlin, Germany.
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45
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Riemann K, Adamzik M, Frauenrath S, Egensperger R, Schmid KW, Brockmeyer NH, Siffert W. Comparison of manual and automated nucleic acid extraction from whole-blood samples. J Clin Lab Anal 2007; 21:244-8. [PMID: 17621359 PMCID: PMC6649159 DOI: 10.1002/jcla.20174] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Nucleic acid extraction and purification from whole blood is a routine application in many laboratories. Automation of this procedure promises standardized sample treatment, a low error rate, and avoidance of contamination. The performance of the BioRobot M48 (Qiagen) and the manual QIAmp DNA Blood Mini Kit (Qiagen) was compared for the extraction of DNA from whole blood. The concentration and purity of the extracted DNAs were determined by spectrophotometry. Analytical sensitivity was assessed by common PCR and genotyping techniques. The quantity and quality of the generated DNAs were slightly higher using the manual extraction method. The results of downstream applications were comparable to each other. Amplification of high-molecular-weight PCR fragments, genotyping by restriction digest, and pyrosequencing were successful for all samples. No cross-contamination could be detected. While automated DNA extraction requires significantly less hands-on time, it is slightly more expensive than the manual extraction method.
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Affiliation(s)
- Kathrin Riemann
- Institute of Pharmacogenetics, University Hospital Essen, Essen, Germany.
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Affiliation(s)
- T A Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196, USA
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47
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Saiyed ZM, Parasramka M, Telang SD, Ramchand CN. Extraction of DNA from agarose gel using magnetic nanoparticles (magnetite or Fe3O4). Anal Biochem 2007; 363:288-90. [PMID: 17316542 DOI: 10.1016/j.ab.2007.01.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 12/27/2006] [Accepted: 01/08/2007] [Indexed: 11/30/2022]
Affiliation(s)
- Z M Saiyed
- Department of Biochemistry, Faculty of Science, Maharaja Sayajirao University of Baroda, Sayajigunj, 390 002 Vadodara, India
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Gomes I, Prinz M, Pereira R, Meyers C, Mikulasovich RS, Amorim A, Carracedo A, Gusmão L. Genetic analysis of three US population groups using an X-chromosomal STR decaplex. Int J Legal Med 2007; 121:198-203. [PMID: 17237948 DOI: 10.1007/s00414-006-0146-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 11/27/2006] [Indexed: 11/29/2022]
Abstract
An X-chromosomal multiplex amplifying ten short tandem repeats (STRs) in one single PCR reaction was developed and optimized in this work. The X-STRs included were DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101, and DXS6789. Decaplex performance was tested on 377 male samples from three United States population groups, namely, 130 African Americans, 104 Asians, and 143 Hispanics. DXS8377 was the most polymorphic locus across all three populations, whereas DXS7423 was the least informative marker. Genetic distance analysis (R (ST) and F (ST)) performed for the three populations residing in New York showed significant genetic distances between population groups for most pairwise comparisons, except for HPRTB, DXS6809, and DXS7132. When testing linkage disequilibrium for all pairs of loci in the three groups, no significant association was found between any pair of the loci studied, after applying Bonferroni correction. The high values for the average probability of excluding a random man obtained in all three populations when both mother and daughter are tested or when father/daughter relationships are evaluated support the potential of this decaplex system in kinship analysis. Also, the overall high power of discrimination values for samples of female and male origin, confirms the usefulness of this decaplex system in identification analysis. As expected, results also support the use of independent databases comprising these ten X-linked loci for the three US populations evaluated.
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Affiliation(s)
- Iva Gomes
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.
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Kishore R, Reef Hardy W, Anderson VJ, Sanchez NA, Buoncristiani MR. Optimization of DNA Extraction from Low-Yield and Degraded Samples Using the BioRobot�EZ1 and BioRobot�M48. J Forensic Sci 2006; 51:1055-61. [PMID: 17018081 DOI: 10.1111/j.1556-4029.2006.00204.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Robotic extraction of DNA from dilutions of blood and semen using either the BioRobots EZ1 or BioRobots M48 consistently produced lower recoveries than standard organic extractions of the same samples. In an effort to increase the efficiency of robotically extracted DNA, glycogen and carrier RNA were added following cell lysis. The addition of glycogen, postlysis, resulted in no improvement in DNA recovery with the BioRobot EZ1. However, when carrier RNA was added to the cell lysate of limited and degraded samples extracted on the EZ1 or the M48, DNA recoveries dramatically increased four- to 20-fold. DNA yields obtained by robotic extraction in the presence of carrier RNA were as high, or higher, as those obtained by organic extraction lacking carrier RNA, while experiments that utilized carrier RNA in both types of extractions showed increased sensitivity for both methods. Furthermore, carrier RNA substantially increased the recovery of fragmented DNA with the EZ1.
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Affiliation(s)
- Ram Kishore
- Jan Bashinski DNA Laboratory, California Department of Justice, 1001W. Cutting Blvd., Suite 110, Richmond, CA 94804, USA
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50
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Nagy M, Rascon J, Massenkeil G, Ebell W, Roewer L. Evaluation of whole-genome amplification of low-copy-number DNA in chimerism analysis after allogeneic stem cell transplantation using STR marker typing. Electrophoresis 2006; 27:3028-37. [PMID: 16807933 DOI: 10.1002/elps.200500813] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Whole-genome DNA amplification (WGA) is a promising method that generates large amounts of DNA from samples of limited quantity. We investigated the accuracy of a multiplex PCR approach to WGA over STR loci. The amplification bias within a locus and over all analyzed loci was investigated in relation to the amount of template in the WGA reaction, the specific STR locus, and allele length. We observed reproducible error-free STR profiles with 10 ng down to 1 ng of DNA template. The amplification deviation at a locus and between loci was within the intra-method reproducibility. WGA is the method of choice for amplifying nanogram amounts of genomic DNA for different applications. We detected unbalanced STR amplifications at one locus and between loci, allelic drop-outs, and additional alleles after WGA of low-copy-number DNA. We found that the high number of drop-outs and drop-ins could be eradicated using pooled DNA from separate WGA reactions even with as little as 100 pg of starting template. Nevertheless, the quality of the results was still not sufficient for use in routine chimerism analysis of limited specific cell populations after allogeneic stem cell transplantation.
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Affiliation(s)
- Marion Nagy
- Institute of Legal Medicine, Charité, University Medicine Berlin, Hannoversche Strasse 6, D-10115 Berlin, Germany.
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