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An evaluation of the RapidHIT® system for reliably genotyping reference samples. Forensic Sci Int Genet 2014; 13:104-11. [DOI: 10.1016/j.fsigen.2014.06.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/23/2014] [Accepted: 06/16/2014] [Indexed: 11/21/2022]
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2
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Schumm JW, Gutierrez-Mateo C, Tan E, Selden R. A 27-locus STR assay to meet all United States and European law enforcement agency standards. J Forensic Sci 2013; 58:1584-92. [PMID: 23822765 DOI: 10.1111/1556-4029.12214] [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: 03/04/2012] [Revised: 08/15/2012] [Accepted: 08/19/2012] [Indexed: 11/27/2022]
Abstract
Different national and international agencies have selected specific STR sets for forensic database use. To enhance database comparison across national and international borders, a 27-locus multiplex system was developed comprising all 15 STR loci of the European standard set, the current 13 STR loci of the CODIS core, the proposed 22 STR loci of the expanded CODIS core, 4 additional commonly used STR loci, and the amelogenin locus. Development required iterative primer design to resolve primer-related artifacts, amplicon sizing, and locus-to-locus balance issues. The 19.5-min assay incorporated newly developed six-dye chemistry analyzed using a novel microfluidic electrophoresis instrument capable of simultaneous detection and discrimination of 8 or more fluorescent dyes. The 27-locus multiplex offers the potential for a new international STR standard permitting laboratories in any jurisdiction to use a single reaction to determine profiles for loci they typically generate plus an expanded common STR profiling set of global interest.
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3
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Sim JE, Park SJ, Lee HC, Kim SY, Kim JY, Lee SH. High-Throughput STR Analysis for DNA Database Using Direct PCR,. J Forensic Sci 2013; 58:989-92. [DOI: 10.1111/1556-4029.12166] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 06/22/2012] [Accepted: 06/30/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Jeong Eun Sim
- DNA Analysis Laboratory; Division of Forensic DNA; Supreme Prosecutors' Office; Seoul; 137-730; Korea
| | - Su Jeong Park
- DNA Analysis Laboratory; Division of Forensic DNA; Supreme Prosecutors' Office; Seoul; 137-730; Korea
| | - Han Chul Lee
- DNA Analysis Laboratory; Division of Forensic DNA; Supreme Prosecutors' Office; Seoul; 137-730; Korea
| | - Se-Yong Kim
- DNA Analysis Laboratory; Division of Forensic DNA; Supreme Prosecutors' Office; Seoul; 137-730; Korea
| | | | - Seung Hwan Lee
- DNA Analysis Laboratory; Division of Forensic DNA; Supreme Prosecutors' Office; Seoul; 137-730; Korea
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4
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A dedicated automated system for extraction, quantification and STR amplification of forensic evidence samples. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2009. [DOI: 10.1016/j.fsigss.2009.08.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Brevnov M, Mundt J, Benfield J, Treat-Clemons L, Kalusche G, Meredith J, Porter G, Furtado MR, Shewale JG. Automated Extraction of DNA from Forensic Sample Types Using the PrepFiler Automated Forensic DNA Extraction Kit. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.jala.2009.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The HID EVOlution—Extraction System (Tecan Group Ltd., Mannedorf, Switzerland) was developed to automate DNA extraction from biological samples using the PrepFiler Automated Forensic DNA Extraction Kit (Applied Biosystems, Foster City, CA). The system consists of a Tecan Freedom EVO 150 robot (Tecan Group Ltd., Mannedorf, Switzerland), a graphical user interface designed for use with Freedom EVOware software v 2.1 SPI (Tecan Group Ltd., Mannedorf, Switerland) as well as instrument hardware and plastic to support the PrepFiler reagents and protocol. The DNA quality and quantity obtained were comparable to that observed with the corresponding manual extraction protocol. Purified DNA was free of inhibitors and ready for downstream applications, such as real-time quantitative PCR and PCR for short tandem repeat (STR) analysis. The DNA quantity and quality obtained were consistent as demonstrated by the quantification and STR results. Our studies indicate that the HID EVOlution—Extraction System can easily be adopted in forensic laboratories to alleviate some of the bottlenecks of sample preparation in forensic laboratories.
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Affiliation(s)
| | - Janna Mundt
- Life Technologies Corporation, Foster City, CA
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6
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Extracting evidence from forensic DNA analyses: future molecular biology directions. Biotechniques 2009; 46:339-40, 342-50. [PMID: 19480629 DOI: 10.2144/000113136] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Molecular biology tools have enhanced the capability of the forensic scientist to characterize biological evidence to the point where it is feasible to analyze minute samples and achieve high levels of individualization. Even with the forensic DNA field's maturity, there still are a number of areas where improvements can be made. These include: enabling the typing of samples of limited quantity and quality; using genetic information and novel markers to provide investigative leads; enhancing automation with robotics, different chemistries, and better software tools; employing alternate platforms for typing DNA samples; developing integrated microfluidic/microfabrication devices to process DNA samples with higher throughput, faster turnaround times, lower risk of contamination, reduced labor, and less consumption of evidentiary samples; and exploiting high-throughput sequencing, particularly for attribution in microbial forensics cases. Knowledge gaps and new directions have been identified where molecular biology will likely guide the field of forensics. This review aims to provide a roadmap to guide those interested in contributing to the further development of forensic genetics.
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Hedman J, Albinsson L, Ansell C, Tapper H, Hansson O, Holgersson S, Ansell R. A fast analysis system for forensic DNA reference samples. Forensic Sci Int Genet 2008; 2:184-9. [DOI: 10.1016/j.fsigen.2007.12.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 11/27/2007] [Accepted: 12/17/2007] [Indexed: 10/22/2022]
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Parson W, Dür A. EMPOP--a forensic mtDNA database. Forensic Sci Int Genet 2007; 1:88-92. [PMID: 19083735 DOI: 10.1016/j.fsigen.2007.01.018] [Citation(s) in RCA: 259] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 01/27/2007] [Indexed: 10/23/2022]
Abstract
Mitochondrial DNA databases stand as the basis for frequency estimations of mtDNA sequences that became relevant in a case. The establishment of mtDNA databases sounds trivial; however, it has been shown in the past that this undertaking is prone to error for several reasons, particularly human error. We have established a concept for mtDNA data generation, analysis, transfer and quality control that meets forensic standards. Due to the complexity of mtDNA population data tables it is often difficult if not impossible to detect errors, especially for the untrained eye. We developed software based on quasi-median network analysis that visualizes mtDNA data tables and thus signposts sequencing, interpretation and transcription errors. The mtDNA data (N=5173; release 1) are stored and made publicly available via the Internet in the form of the EDNAP mtDNA Population Database, short EMPOP. This website also facilitates quasi-median network analysis and provides results that can be used to check the quality of mtDNA sequence data. EMPOP has been launched on 16 October 2006 and is since then available at http://www.empop.org.
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Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University Müllerstreet 44, 6020 Innsbruck, Austria.
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10
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Grubwieser P, Mühlmann R, Berger B, Niederstätter H, Pavlic M, Parson W. A new "miniSTR-multiplex" displaying reduced amplicon lengths for the analysis of degraded DNA. Int J Legal Med 2005; 120:115-20. [PMID: 16012830 DOI: 10.1007/s00414-005-0013-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Accepted: 06/14/2005] [Indexed: 10/25/2022]
Abstract
A multiplex PCR was designed for the loci D2S1338, D16S539, D18S51, TH01 and FGA using redesigned primers in order to reduce the lengths of the amplification products compared to the designs used in commercially available multiplex PCR kits, also including amelogenin. The new PCR primers were used to amplify highly degraded DNA from casework samples, which had shown no or only poor results for these loci in previous analyses with standard primer sets. The application of the new miniSTR-multiplex resulted in an increased overall typing success rate for degraded DNA samples. In a concordance study between the conventional and the newly designed primers, no genotype differences were revealed in 124 randomly selected individuals.
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Affiliation(s)
- P Grubwieser
- Institute of Legal Medicine, Innsbruck Medical University, Müllerstrasse 44, 6020 Innsbruck, Austria
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11
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Parson W, Brandstätter A, Alonso A, Brandt N, Brinkmann B, Carracedo A, Corach D, Froment O, Furac I, Grzybowski T, Hedberg K, Keyser-Tracqui C, Kupiec T, Lutz-Bonengel S, Mevag B, Ploski R, Schmitter H, Schneider P, Syndercombe-Court D, Sørensen E, Thew H, Tully G, Scheithauer R. The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives. Forensic Sci Int 2004; 139:215-26. [PMID: 15040920 DOI: 10.1016/j.forsciint.2003.11.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2003] [Revised: 10/27/2003] [Accepted: 11/07/2003] [Indexed: 10/26/2022]
Abstract
This paper presents an overview of the organisation and the results of the collaborative exercises (CE) of the European DNA Profiling (EDNAP) Group's mitochondrial DNA population database project (EMPOP). The aim of the collaborative exercises was to determine whether uniformity of mtDNA sequencing results could be achieved among different laboratories. These were asked to sequence either the complete mtDNA control region or the two hypervariable regions HVI (16024-16365) and HVII (73-340) from DNA extracts, buccal swabs or bloodstains, proceeding in accordance with the protocol and strategies used in each individual laboratory. The results of the collaborative exercises were employed to identify possible sources of errors that could arise during the analysis and interpretation of mtDNA profiles. These findings were taken as a basis to tentatively make suitable arrangements for the construction of a high quality mtDNA database. One hundred fifty mtDNA profiles were submitted to the evaluating laboratory, and disaccording profiles were classified into four groups corresponding to the source of error: clerical errors, sample mix-ups, contaminations and discrepancies with respect to the mtDNA nomenclature. Overall, 14 disaccording haplotypes (16 individual errors) were observed. The errors included 10 clerical errors, 3 interpretation problems, 2 cases of sample mix-up and 1 case of point heteroplasmic mixture, where the 2 sequencing reactions brought inconsistent base calls. This corresponds to an error rate of 10.7% in a virtual mtDNA database consisting of the collaborative exercise results. However, this estimate is still conservative compared to conclusions drawn by authors of meanwhile numerous publications critically reviewing published mtDNA population databases. Our results and earlier published concerns strongly emphasize the need for appropriate safety regulations when mtDNA profiles are compiled for database purposes in order to accomplish the high standard required for mtDNA databases that are used in the forensic context.
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Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, Innsbruck 6020, Austria.
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12
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Komonski D, Marignani A, Richard M, Frappier J, Newman J. Validation of the DNA IQ™ System for use in the DNA Extraction of High Volume Forensic Casework. CANADIAN SOCIETY OF FORENSIC SCIENCE JOURNAL 2004. [DOI: 10.1080/00085030.2004.10757568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Grubwieser P, Mühlmann R, Parson W. New sensitive amplification primers for the STR locus D2S1338 for degraded casework DNA. Int J Legal Med 2003; 117:185-8. [PMID: 12799739 DOI: 10.1007/s00414-002-0359-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2002] [Accepted: 12/10/2002] [Indexed: 10/25/2022]
Abstract
PCR primers for the locus D2S1338 were redesigned in order to reduce the length of the amplification product compared with the conventional design. The new amplification primers were applied to highly degraded casework samples, which gave no or only weak results for D2 in previous analyses. The application of the new primers resulted in an increased overall typing success rate. In a concordance study between the conventional and the newly designed primers, no genotype differences were revealed in 503 randomly selected individuals. This suggests robust amplification conditions with respect to mutation-based allele drop-out.
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Affiliation(s)
- P Grubwieser
- Institute of Legal Medicine, University of Innsbruck, Müllerstrasse 44, 6020 Innsbruck, Austria
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Walsh SJ, Moss DS, Kliem C, Vintiner GM. The collation of forensic DNA case data into a multi-dimensional intelligence database. Sci Justice 2002; 42:205-14. [PMID: 12632936 DOI: 10.1016/s1355-0306(02)71830-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primary aim of any DNA Database is to link individuals to unsolved offenses and unsolved offenses to each other via DNA profiling. This aim has been successfully realised during the operation of the New Zealand (NZ) DNA Databank over the past five years. The DNA Intelligence Project (DIP), a collaborative project involving NZ forensic and law enforcement agencies, interrogated the forensic case data held on the NZ DNA databank and collated it into a functional intelligence database. This database has been used to identify significant trends which direct Police and forensic personnel towards the most appropriate use of DNA technology. Intelligence is being provided in areas such as the level of usage of DNA techniques in criminal investigation, the relative success of crime scene samples and the geographical distribution of crimes. The DIP has broadened the dimensions of the information offered through the NZ DNA Databank and has furthered the understanding and investigative capability of both Police and forensic scientists. The outcomes of this research fit soundly with the current policies of 'intelligence led policing', which are being adopted by Police jurisdictions locally and overseas.
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Affiliation(s)
- S J Walsh
- Institute of Environmental Science and Research Ltd., Private Bag 92 021, Auckland, New Zealand
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Steinlechner M, Berger B, Niederstätter H, Parson W. Rare failures in the amelogenin sex test. Int J Legal Med 2002; 116:117-20. [PMID: 12056519 DOI: 10.1007/s00414-001-0264-9] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Determination of sex using the amelogenin sex test is well established in the forensic field especially for casework and DNA databasing purposes. The sex test is part of commercially available PCR kits. Among 29,432 phenotypic male individuals stored in the Austrian National DNA database, 6 individuals were found to lack the amelogenin Y-specific PCR product which was confirmed using alternative amelogenin primers. The amplification of eight Y-chromosomal STR markers resulted in full profiles in five out of the six samples, one sample failed to amplify Y-STRs at all. The amplification of a fragment of the SRY gene gave positive results in all six samples, confirming the male phenotype of the individuals. The observed failure rate of the amelogenin sex test was 0.018% in this study.
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