101
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Dong H, Wang J, Zhang T, Ge JY, Dong YQ, Sun QF, Liu C, Li CX. Comparison of preprocessing methods and storage times for touch DNA samples. Croat Med J 2017; 58:4-13. [PMID: 28252870 PMCID: PMC5346895 DOI: 10.3325/cmj.2017.58.4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Aim To select appropriate preprocessing methods for different substrates by comparing the effects of four different preprocessing methods on touch DNA samples and to determine the effect of various storage times on the results of touch DNA sample analysis. Method Hand touch DNA samples were used to investigate the detection and inspection results of DNA on different substrates. Four preprocessing methods, including the direct cutting method, stubbing procedure, double swab technique, and vacuum cleaner method, were used in this study. DNA was extracted from mock samples with four different preprocessing methods. The best preprocess protocol determined from the study was further used to compare performance after various storage times. DNA extracted from all samples was quantified and amplified using standard procedures. Results The amounts of DNA and the number of alleles detected on the porous substrates were greater than those on the non-porous substrates. The performances of the four preprocessing methods varied with different substrates. The direct cutting method displayed advantages for porous substrates, and the vacuum cleaner method was advantageous for non-porous substrates. No significant degradation trend was observed as the storage times increased. Conclusion Different substrates require the use of different preprocessing method in order to obtain the highest DNA amount and allele number from touch DNA samples. This study provides a theoretical basis for explorations of touch DNA samples and may be used as a reference when dealing with touch DNA samples in case work.
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Affiliation(s)
| | | | | | | | | | | | | | - Cai-Xia Li
- Cai-xia Li, Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing100038, China,
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102
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Oldoni F, Castella V, Grosjean F, Hall D. Sensitive DIP-STR markers for the analysis of unbalanced mixtures from “touch” DNA samples. Forensic Sci Int Genet 2017; 28:111-117. [DOI: 10.1016/j.fsigen.2017.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/27/2017] [Accepted: 02/09/2017] [Indexed: 01/31/2023]
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103
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Szkuta B, Ballantyne KN, van Oorschot RA. Transfer and persistence of DNA on the hands and the influence of activities performed. Forensic Sci Int Genet 2017; 28:10-20. [DOI: 10.1016/j.fsigen.2017.01.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 12/16/2016] [Accepted: 01/09/2017] [Indexed: 11/26/2022]
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104
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Helping to distinguish primary from secondary transfer events for trace DNA. Forensic Sci Int Genet 2017; 28:155-177. [DOI: 10.1016/j.fsigen.2017.02.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/17/2017] [Accepted: 02/16/2017] [Indexed: 11/21/2022]
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105
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Samlal-Soedhoe R, Willemstein LM, Baiker M, van der Weerd J. Combined recovery of biological and fibre traces. Sci Justice 2017; 57:174-180. [PMID: 28454626 DOI: 10.1016/j.scijus.2017.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/17/2017] [Accepted: 02/05/2017] [Indexed: 11/24/2022]
Abstract
We present a method in which DNA and fibre traces are jointly recovered by taping. The DNA traces are isolated by standard laboratory procedures. Fibre traces are isolated afterwards in order to improve efficiency. Two tests have been carried out to evaluate the suitability of the presented method. In the first test, possible changes in appearance of fibres due to the DNA isolation procedures are investigated. In the second test, the recovery of fibres from a contaminated surface and their possible loss due to the DNA isolation procedure are investigated. It is concluded that polyester fibres are hardly affected by the DNA isolation procedure. In contrast, a relatively large number of the investigated cotton fibres were altered. The observed differences do not indicate a structural damage to the fibre or the dyes, but rather the washing-out of some components. The observed changes may require that fibres from a known source are also exposed to the DNA isolation procedures to assess the induced changes, but do not prevent a meaningful comparison. The recovery of fibres is slightly lower than the routine procedures for fibre recovery. Therefore, it was decided to perform extra taping of the recipient in cases where fibre investigation is requested. During DNA-isolation, some of the fibres present are released from the tapes. These fibres are not lost however, as they can be found on the filter in the used DNA isolation vials.
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Affiliation(s)
- Radha Samlal-Soedhoe
- Netherlands Forensic Institute, Division of Chemical and Physical Traces, P.O.Box 24044, 2490AA The Hague, The Netherlands.
| | - Laura M Willemstein
- Netherlands Forensic Institute, Division of Biological Traces, P.O.Box 24044, 2490AA The Hague, The Netherlands.
| | - Martin Baiker
- Netherlands Forensic Institute, Division of Chemical and Physical Traces, P.O.Box 24044, 2490AA The Hague, The Netherlands.
| | - Jaap van der Weerd
- Netherlands Forensic Institute, Division of Chemical and Physical Traces, P.O.Box 24044, 2490AA The Hague, The Netherlands.
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106
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Kirgiz IA, Calloway C. Increased recovery of touch DNA evidence using FTA paper compared to conventional collection methods. J Forensic Leg Med 2017; 47:9-15. [DOI: 10.1016/j.jflm.2017.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/08/2016] [Accepted: 01/30/2017] [Indexed: 10/20/2022]
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107
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Jäger AC, Alvarez ML, Davis CP, Guzmán E, Han Y, Way L, Walichiewicz P, Silva D, Pham N, Caves G, Bruand J, Schlesinger F, Pond SJK, Varlaro J, Stephens KM, Holt CL. Developmental validation of the MiSeq FGx Forensic Genomics System for Targeted Next Generation Sequencing in Forensic DNA Casework and Database Laboratories. Forensic Sci Int Genet 2017; 28:52-70. [PMID: 28171784 DOI: 10.1016/j.fsigen.2017.01.011] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 12/08/2016] [Accepted: 01/23/2017] [Indexed: 01/01/2023]
Abstract
Human DNA profiling using PCR at polymorphic short tandem repeat (STR) loci followed by capillary electrophoresis (CE) size separation and length-based allele typing has been the standard in the forensic community for over 20 years. Over the last decade, Next-Generation Sequencing (NGS) matured rapidly, bringing modern advantages to forensic DNA analysis. The MiSeq FGx™ Forensic Genomics System, comprised of the ForenSeq™ DNA Signature Prep Kit, MiSeq FGx™ Reagent Kit, MiSeq FGx™ instrument and ForenSeq™ Universal Analysis Software, uses PCR to simultaneously amplify up to 231 forensic loci in a single multiplex reaction. Targeted loci include Amelogenin, 27 common, forensic autosomal STRs, 24 Y-STRs, 7 X-STRs and three classes of single nucleotide polymorphisms (SNPs). The ForenSeq™ kit includes two primer sets: Amelogenin, 58 STRs and 94 identity informative SNPs (iiSNPs) are amplified using DNA Primer Set A (DPMA; 153 loci); if a laboratory chooses to generate investigative leads using DNA Primer Set B, amplification is targeted to the 153 loci in DPMA plus 22 phenotypic informative (piSNPs) and 56 biogeographical ancestry SNPs (aiSNPs). High-resolution genotypes, including detection of intra-STR sequence variants, are semi-automatically generated with the ForenSeq™ software. This system was subjected to developmental validation studies according to the 2012 Revised SWGDAM Validation Guidelines. A two-step PCR first amplifies the target forensic STR and SNP loci (PCR1); unique, sample-specific indexed adapters or "barcodes" are attached in PCR2. Approximately 1736 ForenSeq™ reactions were analyzed. Studies include DNA substrate testing (cotton swabs, FTA cards, filter paper), species studies from a range of nonhuman organisms, DNA input sensitivity studies from 1ng down to 7.8pg, two-person human DNA mixture testing with three genotype combinations, stability analysis of partially degraded DNA, and effects of five commonly encountered PCR inhibitors. Calculations from ForenSeq™ STR and SNP repeatability and reproducibility studies (1ng template) indicate 100.0% accuracy of the MiSeq FGx™ System in allele calling relative to CE for STRs (1260 samples), and >99.1% accuracy relative to bead array typing for SNPs (1260 samples for iiSNPs, 310 samples for aiSNPs and piSNPs), with >99.0% and >97.8% precision, respectively. Call rates of >99.0% were observed for all STRs and SNPs amplified with both ForenSeq™ primer mixes. Limitations of the MiSeq FGx™ System are discussed. Results described here demonstrate that the MiSeq FGx™ System meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities.
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Affiliation(s)
- Anne C Jäger
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | | | - Carey P Davis
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Ernesto Guzmán
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Yonmee Han
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Lisa Way
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | | | - David Silva
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Nguyen Pham
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Glorianna Caves
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | - Jocelyne Bruand
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | | | | | - Joe Varlaro
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
| | | | - Cydne L Holt
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
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108
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Investigation into ethylene oxide treatment and residuals on DNA and downstream DNA analysis. Sci Justice 2017; 57:13-20. [PMID: 28063580 DOI: 10.1016/j.scijus.2016.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 09/09/2016] [Accepted: 09/10/2016] [Indexed: 11/22/2022]
Abstract
Recent years have seen a significant increase in the sensitivity of DNA testing, enabling the determination of DNA profiles from low levels of cellular material. However, the increased sensitivity is in many ways a double-edged sword as background contaminating DNA generated during the manufacture of consumables and sampling devices is now being detected and may compromise the interpretation of the DNA profile results. This study initially demonstrated the effectiveness of ethylene oxide (EO) as a post-production treatment to eliminate DNA on swabs, used as a sampling device for the recovery of cellular material. Subsequently, the potential adverse effects of any residual EO remaining on the swabs on the downstream DNA analysis on both rayon and cotton swabs were investigated and the levels of remaining EO measured. Two main variables were tested: the amount of time elapsed since EO treatment of the swabs prior to use, and the time elapsed between cellular material collection and DNA analysis. Residual levels of EO were found to be below quantitation levels and therefore also international standards. The results indicated that while there was a negligible effect of EO treatment on DNA recovered from rayon swabs, there was however an adverse effect on the DNA profiles recovered from cotton swabs. The adverse effect was negatively correlated with time since EO treatment and positively correlated with time to DNA analysis.
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109
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Ostojic L, Wurmbach E. Analysis of fingerprint samples, testing various conditions, for forensic DNA identification. Sci Justice 2017; 57:35-40. [DOI: 10.1016/j.scijus.2016.08.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 01/28/2023]
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110
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Bond JW, Weart JR. The Effectiveness of Trace DNA Profiling-A Comparison Between a U.S. and a U.K. Law Enforcement Jurisdiction. J Forensic Sci 2016; 62:753-760. [DOI: 10.1111/1556-4029.13317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/17/2016] [Accepted: 08/06/2016] [Indexed: 11/30/2022]
Affiliation(s)
- John W. Bond
- Department of Criminology; University of Leicester; 154 Upper New Walk Leicester LE1 7QA U.K
| | - Jocelyn R. Weart
- Santa Clara County Crime Laboratory; 250 West Hedding Street San Jose CA 95110
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111
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Cloete KW, Ristow PG, Kasu M, D'Amato ME. Design, installation, and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis. Electrophoresis 2016; 38:617-623. [PMID: 27859383 DOI: 10.1002/elps.201600257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
CE equipment detects and deconvolutes mixtures containing up to six fluorescently labeled DNA fragments. This deconvolution is done by the collection software that requires a spectral calibration file. The calibration file is used to adjust for the overlap that occurs between the emission spectra of fluorescence dyes. All commercial genotyping and sequencing kits require the installation of a corresponding matrix standard to generate a calibration file. Due to the differences in emission spectrum overlap between fluorescent dyes, the application of existing commercial matrix standards to the electrophoretic separation of DNA labeled with other fluorescent dyes can yield undesirable results. Currently, the number of fluorescent dyes available for oligonucleotide labeling surpasses the availability of commercial matrix standards. Therefore, in this study we developed and evaluated a customized matrix standard using ATTO 633, ATTO 565, ATTO 550, ATTO Rho6G, and 6-FAM dyes for which no commercial matrix standard is available. We highlighted the potential genotyping errors of using an incorrect matrix standard by evaluating the relative performance of our custom dye set using six matrix standards. The specific performance of two genotyping kits (UniQTyper™ Y-10 version 1.0 and PowerPlex® Y23 System) was also evaluated using their specific matrix standards. The procedure we followed for the construction of our custom dye matrix standard can be extended to other fluorescent dyes.
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Affiliation(s)
- Kevin Wesley Cloete
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Peter Gustav Ristow
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Mohaimin Kasu
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
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112
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Hess S, Haas C. Recovery of Trace DNA on Clothing: A Comparison of Mini-tape Lifting and Three Other Forensic Evidence Collection Techniques. J Forensic Sci 2016; 62:187-191. [DOI: 10.1111/1556-4029.13246] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 03/07/2016] [Accepted: 04/24/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Sabine Hess
- Forensic Science Institute Zurich; P.O. Box 8021 Zurich Switzerland
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, Forensic Genetics; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
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113
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Abstract
Imagine a scenario where personal belongings such as pens, keys, phones, or handbags are found at an investigative site. It is often valuable to the investigative team that is trying to trace back the belongings to an individual to understand their personal habits, even when DNA evidence is also available. Here, we develop an approach to translate chemistries recovered from personal objects such as phones into a lifestyle sketch of the owner, using mass spectrometry and informatics approaches. Our results show that phones' chemistries reflect a personalized lifestyle profile. The collective repertoire of molecules found on these objects provides a sketch of the lifestyle of an individual by highlighting the type of hygiene/beauty products the person uses, diet, medical status, and even the location where this person may have been. These findings introduce an additional form of trace evidence from skin-associated lifestyle chemicals found on personal belongings. Such information could help a criminal investigator narrowing down the owner of an object found at a crime scene, such as a suspect or missing person.
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114
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Amorim A, Crespillo M, Luque JA, Prieto L, Garcia O, Gusmão L, Aler M, Barrio PA, Saragoni VG, Pinto N. Formulation and communication of evaluative forensic science expert opinion—A GHEP-ISFG contribution to the establishment of standards. Forensic Sci Int Genet 2016; 25:210-213. [DOI: 10.1016/j.fsigen.2016.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/30/2016] [Accepted: 09/02/2016] [Indexed: 11/29/2022]
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115
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Buckingham AK, Harvey ML, van Oorschot RA. The origin of unknown source DNA from touched objects. Forensic Sci Int Genet 2016; 25:26-33. [DOI: 10.1016/j.fsigen.2016.07.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 07/01/2016] [Accepted: 07/27/2016] [Indexed: 10/21/2022]
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116
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Parker GJ, Leppert T, Anex DS, Hilmer JK, Matsunami N, Baird L, Stevens J, Parsawar K, Durbin-Johnson BP, Rocke DM, Nelson C, Fairbanks DJ, Wilson AS, Rice RH, Woodward SR, Bothner B, Hart BR, Leppert M. Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome. PLoS One 2016; 11:e0160653. [PMID: 27603779 PMCID: PMC5014411 DOI: 10.1371/journal.pone.0160653] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 07/21/2016] [Indexed: 12/28/2022] Open
Abstract
Human identification from biological material is largely dependent on the ability to characterize genetic polymorphisms in DNA. Unfortunately, DNA can degrade in the environment, sometimes below the level at which it can be amplified by PCR. Protein however is chemically more robust than DNA and can persist for longer periods. Protein also contains genetic variation in the form of single amino acid polymorphisms. These can be used to infer the status of non-synonymous single nucleotide polymorphism alleles. To demonstrate this, we used mass spectrometry-based shotgun proteomics to characterize hair shaft proteins in 66 European-American subjects. A total of 596 single nucleotide polymorphism alleles were correctly imputed in 32 loci from 22 genes of subjects' DNA and directly validated using Sanger sequencing. Estimates of the probability of resulting individual non-synonymous single nucleotide polymorphism allelic profiles in the European population, using the product rule, resulted in a maximum power of discrimination of 1 in 12,500. Imputed non-synonymous single nucleotide polymorphism profiles from European-American subjects were considerably less frequent in the African population (maximum likelihood ratio = 11,000). The converse was true for hair shafts collected from an additional 10 subjects with African ancestry, where some profiles were more frequent in the African population. Genetically variant peptides were also identified in hair shaft datasets from six archaeological skeletal remains (up to 260 years old). This study demonstrates that quantifiable measures of identity discrimination and biogeographic background can be obtained from detecting genetically variant peptides in hair shaft protein, including hair from bioarchaeological contexts.
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Affiliation(s)
- Glendon J. Parker
- Department of Biology, Utah Valley University, Orem, Utah, United States of America
- Protein-Based Identification Technologies L.L.C., Orem, Utah, United States of America
- * E-mail: parker64@llnl;
| | - Tami Leppert
- Protein-Based Identification Technologies L.L.C., Orem, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Deon S. Anex
- Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Jonathan K. Hilmer
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Nori Matsunami
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Lisa Baird
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jeffery Stevens
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Krishna Parsawar
- Mass Spectrometry and Proteomics Core Facility, University of Utah, Salt Lake City, Utah, United States of America
| | - Blythe P. Durbin-Johnson
- Department of Public Health Sciences, University of California, Davis, California, United States of America
| | - David M. Rocke
- Department of Public Health Sciences, University of California, Davis, California, United States of America
| | - Chad Nelson
- Mass Spectrometry and Proteomics Core Facility, University of Utah, Salt Lake City, Utah, United States of America
| | - Daniel J. Fairbanks
- Department of Biology, Utah Valley University, Orem, Utah, United States of America
| | - Andrew S. Wilson
- School of Archaeological Sciences, University of Bradford, Bradford, United Kingdom
| | - Robert H. Rice
- Department of Environmental Toxicology, University of California, Davis, California, United States of America
| | - Scott R. Woodward
- Sorenson Molecular Genealogical Foundation, Salt Lake City, Utah, United States of America
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Bradley R. Hart
- Forensic Science Center, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Mark Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
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117
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Forsberg C, Jansson L, Ansell R, Hedman J. High-throughput DNA extraction of forensic adhesive tapes. Forensic Sci Int Genet 2016; 24:158-163. [DOI: 10.1016/j.fsigen.2016.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/23/2016] [Accepted: 06/05/2016] [Indexed: 11/28/2022]
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118
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Oldoni F, Castella V, Hall D. Shedding light on the relative DNA contribution of two persons handling the same object. Forensic Sci Int Genet 2016; 24:148-157. [DOI: 10.1016/j.fsigen.2016.07.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/11/2016] [Accepted: 07/05/2016] [Indexed: 10/21/2022]
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119
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Microfluidic Devices for Forensic DNA Analysis: A Review. BIOSENSORS-BASEL 2016; 6:bios6030041. [PMID: 27527231 PMCID: PMC5039660 DOI: 10.3390/bios6030041] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/07/2016] [Accepted: 07/25/2016] [Indexed: 12/16/2022]
Abstract
Microfluidic devices may offer various advantages for forensic DNA analysis, such as reduced risk of contamination, shorter analysis time and direct application at the crime scene. Microfluidic chip technology has already proven to be functional and effective within medical applications, such as for point-of-care use. In the forensic field, one may expect microfluidic technology to become particularly relevant for the analysis of biological traces containing human DNA. This would require a number of consecutive steps, including sample work up, DNA amplification and detection, as well as secure storage of the sample. This article provides an extensive overview of microfluidic devices for cell lysis, DNA extraction and purification, DNA amplification and detection and analysis techniques for DNA. Topics to be discussed are polymerase chain reaction (PCR) on-chip, digital PCR (dPCR), isothermal amplification on-chip, chip materials, integrated devices and commercially available techniques. A critical overview of the opportunities and challenges of the use of chips is discussed, and developments made in forensic DNA analysis over the past 10–20 years with microfluidic systems are described. Areas in which further research is needed are indicated in a future outlook.
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120
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Frippiat C, Noel F. Comparison of performance of genetics 4N6 FLOQSwabs™ with or without surfactant to rayon swabs. J Forensic Leg Med 2016; 42:96-9. [DOI: 10.1016/j.jflm.2016.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/18/2016] [Accepted: 06/05/2016] [Indexed: 10/21/2022]
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121
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Blackie R, Taylor D, Linacre A. DNA profiles from clothing fibers using direct PCR. Forensic Sci Med Pathol 2016; 12:331-5. [DOI: 10.1007/s12024-016-9784-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
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122
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Gill P. Analysis and implications of the miscarriages of justice of Amanda Knox and Raffaele Sollecito. Forensic Sci Int Genet 2016; 23:9-18. [DOI: 10.1016/j.fsigen.2016.02.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 10/22/2022]
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123
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Caraballo NI, Mendel J, Holness H, La Salvia J, Moroose T, Eckenrode B, Stockham R, Furton K, Mills D. An investigation into the concurrent collection of human scent and epithelial skin cells using a non-contact sampling device. Forensic Sci Int 2016; 266:148-159. [PMID: 27281052 DOI: 10.1016/j.forsciint.2016.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
In criminal investigations, the collection of human scent often employs a non-contact, dynamic airflow device, known as the Scent Transfer Unit 100 (STU-100), to transfer volatile organic compounds (VOCs) from an object/person onto a collection material that is subsequently presented to human scent discriminating canines. Human scent is theorized to be linked to epithelial skin cells that are shed at a relatively constant rate allowing both scent and cellular material to be deposited into the environment and/or onto objects. Simultaneous collection of cellular material, with adequate levels of nuclear deoxyribonucleic acid (nDNA), and human scent using a non-invasive methodology would facilitate criminal investigations. This study evaluated the STU-100 for the concurrent collection of human scent and epithelial skin cells from a porous (paper) and non-porous (stainless steel bar) object that was held for a specified period of time in the dominant hand of twenty subjects (10 females and 10 males). Human scent analysis was performed using headspace static solid-phase microextraction with gas chromatography-mass spectrometry (HS-SPME/GC-MS). A polycarbonate filter was used to trap epithelial skin cells which, upon extraction, were subsequently analyzed, inter-laboratory, using the quantitative polymerase chain reaction (qPCR). The STU-100 proved to be inadequate for collecting the minimum number of epithelial skin cells required to obtain nuclear DNA concentrations above the limit of detection for the qPCR kit. With regard to its use for human scent collection, a reduction in the number and mass of compounds was observed when compared to samples that were directly collected. However, when the indirect collection of human scent from the two different objects was compared, a greater number and mass of compounds was observed from the non-porous object than from the porous object. This outcome suggests that the matrix composition of the scent source could affect the efficacy of the human scent collected when using a non-contact, dynamic airflow sampling device. The findings from this study are of importance because although the STU-100 proved to not be suitable for collecting epithelial skin cells for DNA analysis, its non-contact capability allows for the possibility of other potential forensic evidence, like that of human scent, to be obtained.
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Affiliation(s)
- Norma Iris Caraballo
- International Forensic Research Institute, Florida International University, Miami, FL, United States; Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | - Julian Mendel
- International Forensic Research Institute, Florida International University, Miami, FL, United States; Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Howard Holness
- International Forensic Research Institute, Florida International University, Miami, FL, United States; Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | - Joel La Salvia
- International Forensic Research Institute, Florida International University, Miami, FL, United States; Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Tina Moroose
- Forensic and Investigative Science, West Virginia University, Morgantown, WV, United States
| | - Brian Eckenrode
- Counterterrorism and Forensic Science Research Unit, FBI Laboratory, Quantico, VA, United States
| | - Rex Stockham
- Evidence Response Team Unit, FBI Laboratory, Quantico, VA, United States
| | - Kenneth Furton
- International Forensic Research Institute, Florida International University, Miami, FL, United States; Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | - DeEtta Mills
- International Forensic Research Institute, Florida International University, Miami, FL, United States; Department of Biological Sciences, Florida International University, Miami, FL, United States.
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124
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125
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Lim S, Subhani Z, Daniel B, Frascione N. Touch DNA—The prospect of DNA profiles from cables. Sci Justice 2016; 56:210-215. [DOI: 10.1016/j.scijus.2016.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 01/29/2016] [Accepted: 02/11/2016] [Indexed: 11/28/2022]
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126
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Prevalence of human cell material: DNA and RNA profiling of public and private objects and after activity scenarios. Forensic Sci Int Genet 2016; 21:81-9. [DOI: 10.1016/j.fsigen.2015.12.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/11/2015] [Accepted: 12/19/2015] [Indexed: 11/22/2022]
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127
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Buś MM, Nilsson M, Allen M. Analysis of Mitochondrial DNA from a Burned, Ninhydrin-Treated Paper Towel. J Forensic Sci 2016; 61:828-832. [DOI: 10.1111/1556-4029.13054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 08/11/2015] [Accepted: 08/15/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Magdalena M. Buś
- Department of Immunology, Genetics and Pathology; Science for Life Laboratory; Uppsala University; Box 815 S-751 08 Uppsala Sweden
| | - Martina Nilsson
- Swedish Police Authority; Stockholm Region; Division of investigation; Forensic Section; S-106 75 Stockholm Sweden
| | - Marie Allen
- Department of Immunology, Genetics and Pathology; Science for Life Laboratory; Uppsala University; Box 815 S-751 08 Uppsala Sweden
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128
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Lacerenza D, Aneli S, Omedei M, Gino S, Pasino S, Berchialla P, Robino C. A molecular exploration of human DNA/RNA co-extracted from the palmar surface of the hands and fingers. Forensic Sci Int Genet 2016; 22:44-53. [PMID: 26844918 DOI: 10.1016/j.fsigen.2016.01.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/28/2015] [Accepted: 01/19/2016] [Indexed: 11/25/2022]
Abstract
"Touch DNA" refers to the DNA that is left behind when a person touches or comes into contact with an item. However, the source of touch DNA is still debated and the large variability in DNA yield from casework samples suggests that, besides skin, various body fluids can be transferred through contact. Another important issue concerning touch DNA is the possible occurrence of secondary transfer, but the data published in the literature in relation to the background levels of foreign DNA present on the hand surfaces of the general population are very limited. As the present study aimed at better understanding the nature and characteristics of touch DNA, samples were collected from the palmar surface of the hands and fingers ("PHF" samples) of 30 male and 30 female donors by tape-lifting/swabbing and subjected to DNA/RNA co-extraction. Multiplex mRNA profiling showed that cellular material different from skin could be observed in 15% of the PHF samples. The total amount of DNA recovered from these samples (median 5.1 ng) was significantly higher than that obtained from samples containing skin cells only (median 1.6 ng). The integrity of the DNA isolated from the donors' hands and fingers as well as the prevalence of DNA mixtures were evaluated by STR typing and compared with reference STR profiles from buccal swabs. DNA integrity appeared significantly higher in the male rather than in the female subsample, as the average percentage of the donors' alleles effectively detected in PHF profiles was 75.1% and 60.1%, respectively. The prevalence of mixtures with a foreign DNA contribution ≥20% was 19.2% (30.0% in the female PHF samples and 8.3% in the male PHF samples). The obtained results support the hypothesis that transfer of cellular material different from skin may underlie the occasional recovery of quality STR profiles from handled items. These results also suggest that gender may represent an important factor influencing the propensity of individuals to carry and transfer DNA through hand contact, possibly because of the differences in personal and hygiene habits between males and females.
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Affiliation(s)
- D Lacerenza
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - S Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy; Human Genetics Foundation, HuGeF, Turin, Italy
| | - M Omedei
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy; Department of Public Health, University of Rome "Tor Vergata", Rome, Italy
| | - S Gino
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - S Pasino
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - P Berchialla
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - C Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy.
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129
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Electrostatic sampling of trace DNA from clothing. Int J Legal Med 2016; 130:661-7. [DOI: 10.1007/s00414-015-1312-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/30/2015] [Indexed: 11/27/2022]
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130
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Abstract
Effective sampling of biological material is critical to the ability to acquire DNA profiles of probative value. The main methods of collection are swabbing, tapelifting, or direct excision. This chapter describes the key aspects to consider when applying these methods, in addition to suggested procedures for swabbing and tapelifting. Important issues to be considered, such as exhibit triaging, pre-examination preparation, contamination risk reduction, sample localization, sample identification, and sample prioritization as well as aspects of record keeping, packaging, and storage, are also raised.
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Affiliation(s)
- Roland A H van Oorschot
- Victoria Police Forensic Services Department, 31 Forensic Drive, Macleod, Melbourne, VIC, 3085, Australia.
| | - Timothy J Verdon
- Victoria Police Forensic Services Department, 31 Forensic Drive, Macleod, Melbourne, VIC, 3085, Australia.,Department of Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Kaye N Ballantyne
- Victoria Police Forensic Services Department, 31 Forensic Drive, Macleod, Melbourne, VIC, 3085, Australia.,School of Psychology and Public Health, La Trobe University, Bundoora, Melbourne, VIC, 3083, Australia
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131
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DNA transfer—a never ending story. A study on scenarios involving a second person as carrier. Int J Legal Med 2015; 130:121-5. [DOI: 10.1007/s00414-015-1284-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
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132
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Wilson CC, Wozney KM, Smith CM. Recognizing false positives: synthetic oligonucleotide controls for environmental
DNA
surveillance. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12452] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chris C. Wilson
- Aquatic Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Trent University 2140 East Bank Drive Peterborough Ontario K9J 7B8 Canada
| | - Kristyne M. Wozney
- Aquatic Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Trent University 2140 East Bank Drive Peterborough Ontario K9J 7B8 Canada
| | - Caleigh M. Smith
- Aquatic Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Trent University 2140 East Bank Drive Peterborough Ontario K9J 7B8 Canada
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133
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134
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Evaluation of samples comprising minute amounts of DNA. Sci Justice 2015; 55:316-22. [DOI: 10.1016/j.scijus.2015.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/01/2015] [Accepted: 05/04/2015] [Indexed: 01/31/2023]
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135
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Bolivar PA, Tracey M, McCord B. Assessing the Risk of Secondary Transfer Via Fingerprint Brush Contamination Using Enhanced Sensitivity DNA Analysis Methods. J Forensic Sci 2015; 61:204-11. [PMID: 26300550 DOI: 10.1111/1556-4029.12911] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/18/2014] [Accepted: 01/30/2015] [Indexed: 11/27/2022]
Abstract
Experiments were performed to determine the extent of cross-contamination of DNA resulting from secondary transfer due to fingerprint brushes used on multiple items of evidence. Analysis of both standard and low copy number (LCN) STR was performed. Two different procedures were used to enhance sensitivity, post-PCR cleanup and increased cycle number. Under standard STR typing procedures, some additional alleles were produced that were not present in the controls or blanks; however, there was insufficient data to include the contaminant donor as a contributor. Inclusion of the contaminant donor did occur for one sample using post-PCR cleanup. Detection of the contaminant donor occurred for every replicate of the 31 cycle amplifications; however, using LCN interpretation recommendations for consensus profiles, only one sample would include the contaminant donor. Our results indicate that detection of secondary transfer of DNA can occur through fingerprint brush contamination and is enhanced using LCN-DNA methods.
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Affiliation(s)
- Paula-Andrea Bolivar
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199
| | - Martin Tracey
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199
| | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199
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136
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de Gruijter M, de Poot CJ, Elffers H. The Influence of New Technologies on the Visual Attention of CSIs Performing a Crime Scene Investigation. J Forensic Sci 2015; 61:43-51. [DOI: 10.1111/1556-4029.12904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 12/09/2014] [Accepted: 12/31/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Madeleine de Gruijter
- Amsterdam University of Applied Sciences - Forensic Sciences; P.O. Box 1025 1000 BA Amsterdam The Netherlands
| | - Christianne J. de Poot
- Amsterdam University of Applied Sciences - Forensic Sciences; P.O. Box 1025 1000 BA Amsterdam The Netherlands
- Dutch Police Academy; Amsterdam The Netherlands
- Research and Documentation Centre of the Dutch Ministry of Security and Justice; Amsterdam The Netherlands
| | - Henk Elffers
- Netherlands Institute for the Study of Crime and Law Enforcement NSCR; Amsterdam The Netherlands
- Department of Criminal Law and Criminology; VU University Amsterdam; Amsterdam The Netherlands
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137
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Breathnach M, Moore E. Background Levels of Salivary-α-amylase Plus Foreign DNA in Cases of Oral Intercourse: a Female Perspective. J Forensic Sci 2015. [DOI: 10.1111/1556-4029.12866] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michelle Breathnach
- Department of Applied Science; Limerick Institute of Technology; Limerick Ireland
| | - Elizabeth Moore
- Department of Applied Science; Limerick Institute of Technology; Limerick Ireland
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138
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Verdon TJ, Mitchell RJ, van Oorschot RAH. Preliminary investigation of differential tapelifting for sampling forensically relevant layered deposits. Leg Med (Tokyo) 2015; 17:553-9. [PMID: 26152832 DOI: 10.1016/j.legalmed.2015.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 06/02/2015] [Accepted: 07/03/2015] [Indexed: 11/18/2022]
Abstract
The analysis of DNA mixtures can be problematic, especially when in trace quantities such as when a biological sample is deposited onto a substrate which contains background DNA (for example, in the case of touch DNA deposited onto a garment containing the wearer's DNA). We conducted a preliminary investigation into the possibility of removing such multi-donor deposits layer by layer using a differential tape-lifting method. Two types of tape were tested using two different numbers of applications for sampling layered deposits of touch DNA/touch DNA and touch DNA/saliva, both on the same polyester-cotton plain woven material. The data showed that there was no significant increase in the ratio of secondary to primary deposit when sampled in this manner, compared to direct extraction from cuttings of the touched fabric. A similar result was also obtained even when the deposits were on opposing surfaces of the fabric and the sampling was carried out on the secondary deposit side. These findings indicate that biological material, whether touch DNA or saliva, does not predominantly remain on the side of the fabric on which it is deposited (at least for plain-woven polyester-cotton). They also highlight the importance of considering substrate properties when making assumptions as to the resulting location of biological materials from a deposition event, and the necessity to conduct further research on the interactions between substrates and deposits.
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Affiliation(s)
- Timothy J Verdon
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, 31 Forensic Drive, Macleod, Victoria 3085, Australia; Department of Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - R John Mitchell
- Department of Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, 31 Forensic Drive, Macleod, Victoria 3085, Australia
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139
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Phetpeng S, Kitpipit T, Thanakiatkrai P. Systematic study for DNA recovery and profiling from common IED substrates: From laboratory to casework. Forensic Sci Int Genet 2015; 17:53-60. [DOI: 10.1016/j.fsigen.2015.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 01/20/2015] [Accepted: 03/11/2015] [Indexed: 10/23/2022]
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140
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Kamphausen T, Fandel SB, Gutmann JS, Bajanowski T, Poetsch M. Everything clean? Transfer of DNA traces between textiles in the washtub. Int J Legal Med 2015. [PMID: 26024792 DOI: 10.1007/s00414-015-1203-5/tables/1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Forensic genetic analysis of items possibly handled by a suspect or a victim is frequently inquired by the law enforcement authorities, since DNA left on touched objects can often be linked to an individual. Due to technical improvement, even poor traces, which seemed to be unsuitable for DNA analysis a few years ago, may be amplified successfully today. Yet, DNA can be transferred to a crime scene artificially or unintentionally without any primary contact between the individual and the object found at the crime scene, the so-called secondary transfer or indirect transfer in general. In this study, "secondary transfer" scenarios with cells and DNA of different origins under wet conditions were investigated. Transfer was simulated as either "washing by hand" in a washtub or as "machine laundry" in a washing machine. As expected, major differences were seen between blood stains and epithelial abrasions. DNA from blood donors could be detected clearly both on the donor and on the acceptor textile, regardless of washing method. Regarding epithelial abrasions, simulating worn clothes, after washing by hand, only little residual DNA was found, and partial profiles were displayed on the donor textile, while transfer to the acceptor textile occurred even less and not in noteworthy amount and quality. Single alleles could be found both on donor textiles and acceptor textiles after simulated machine wash, but no reliable DNA profile could be verified after laundry in machine. Therefore, a DNA transfer from one worn cloth (without blood stains) to another textile in the washing machine seems to be extremely unlikely.
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Affiliation(s)
- Thomas Kamphausen
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, D-45122, Essen, Germany
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141
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Lapointe M, Rogic A, Bourgoin S, Jolicoeur C, Séguin D. Leading-edge forensic DNA analyses and the necessity of including crime scene investigators, police officers and technicians in a DNA elimination database. Forensic Sci Int Genet 2015; 19:50-55. [PMID: 26117338 DOI: 10.1016/j.fsigen.2015.06.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 05/19/2015] [Accepted: 06/08/2015] [Indexed: 11/18/2022]
Abstract
In recent years, sophisticated technology has significantly increased the sensitivity and analytical power of genetic analyses so that very little starting material may now produce viable genetic profiles. This sensitivity however, has also increased the risk of detecting unknown genetic profiles assumed to be that of the perpetrator, yet originate from extraneous sources such as from crime scene workers. These contaminants may mislead investigations, keeping criminal cases active and unresolved for long spans of time. Voluntary submission of DNA samples from crime scene workers is fairly low, therefore we have created a promotional method for our staff elimination database that has resulted in a significant increase in voluntary samples since 2011. Our database enforces privacy safeguards and allows for optional anonymity to all staff members. We also offer information sessions at various police precincts to advise crime scene workers of the importance and success of our staff elimination database. This study, a pioneer in its field, has obtained 327 voluntary submissions from crime scene workers to date, of which 46 individual profiles (14%) have been matched to 58 criminal cases. By implementing our methods and respect for individual privacy, forensic laboratories everywhere may see similar growth and success in explaining unidentified genetic profiles in stagnate criminal cases.
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Affiliation(s)
- Martine Lapointe
- Laboratoire de Sciences Judiciaires et de Médecine Légale, Direction Biologie/ADN, 1701 Parthenais, Montréal, Québec H2K 3S7, Canada.
| | - Anita Rogic
- Laboratoire de Sciences Judiciaires et de Médecine Légale, Direction Biologie/ADN, 1701 Parthenais, Montréal, Québec H2K 3S7, Canada.
| | - Sarah Bourgoin
- Laboratoire de Sciences Judiciaires et de Médecine Légale, Direction Biologie/ADN, 1701 Parthenais, Montréal, Québec H2K 3S7, Canada.
| | - Christine Jolicoeur
- Laboratoire de Sciences Judiciaires et de Médecine Légale, Direction Biologie/ADN, 1701 Parthenais, Montréal, Québec H2K 3S7, Canada.
| | - Diane Séguin
- Laboratoire de Sciences Judiciaires et de Médecine Légale, Direction Biologie/ADN, 1701 Parthenais, Montréal, Québec H2K 3S7, Canada.
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142
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Everything clean? Transfer of DNA traces between textiles in the washtub. Int J Legal Med 2015; 129:709-14. [DOI: 10.1007/s00414-015-1203-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/18/2015] [Indexed: 11/26/2022]
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143
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McNevin D, Edson J, Robertson J, Austin JJ. Reduced reaction volumes and increased Taq DNA polymerase concentration improve STR profiling outcomes from a real-world low template DNA source: telogen hairs. Forensic Sci Med Pathol 2015; 11:326-38. [PMID: 25999132 DOI: 10.1007/s12024-015-9679-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2015] [Indexed: 11/28/2022]
Abstract
PURPOSE The primary method for analysis of low template DNA (LTDNA) is known as the low copy number (LCN) method involving an increased number of PCR cycles (typically 34). In common with other LTDNA methods, LCN profiles are characterized by allelic imbalance, drop in, and drop out that require complicated interpretation rules. They often require replicate PCR reactions to generate a "consensus" profile in a specialized facility. An ideal method for analysis of LTDNA should enhance profiling outcomes without elevated error rates and be performed using standard facilities, with minimum additional cost. METHODS In this study, we present a comparison of four method variations for the amplification of STRs from LTDNA with a widely used, commercially available kit (AmpFℓSTR(®) Profiler Plus(®)): the standard method, the standard method with a post-PCR clean up, the LCN method, and a reduced reaction volume with increased Taq DNA polymerase concentration. RESULTS Using telogen hairs-a common source of LTDNA-and matched reference DNA, the LCN method produced the highest number of concordant and non-concordant (i.e., dropped-in) alleles. In comparison, the reduced reaction volume with increased Taq polymerase yielded more full and concordant DNA profiles (all alleles combined) and less off-ladder alleles from a broad range of input DNA. In addition, this method resulted in less non-concordant alleles than LCN and no more than for standard PCR, which suggests that it may be preferred over increased PCR cycles for LTDNA analysis, either with or without consensus profiling and statistical modelling. CONCLUSIONS Overall, this study highlights the importance and benefit of optimizing PCR conditions and developing improved laboratory methods to amplify and analyze LTDNA.
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Affiliation(s)
- Dennis McNevin
- National Centre for Forensic Studies, University of Canberra, Canberra, ACT, Australia,
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144
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Gill P, Haned H, Bleka O, Hansson O, Dørum G, Egeland T. Genotyping and interpretation of STR-DNA: Low-template, mixtures and database matches-Twenty years of research and development. Forensic Sci Int Genet 2015; 18:100-17. [PMID: 25866376 DOI: 10.1016/j.fsigen.2015.03.014] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 03/19/2015] [Accepted: 03/24/2015] [Indexed: 12/17/2022]
Abstract
The introduction of Short Tandem Repeat (STR) DNA was a revolution within a revolution that transformed forensic DNA profiling into a tool that could be used, for the first time, to create National DNA databases. This transformation would not have been possible without the concurrent development of fluorescent automated sequencers, combined with the ability to multiplex several loci together. Use of the polymerase chain reaction (PCR) increased the sensitivity of the method to enable the analysis of a handful of cells. The first multiplexes were simple: 'the quad', introduced by the defunct UK Forensic Science Service (FSS) in 1994, rapidly followed by a more discriminating 'six-plex' (Second Generation Multiplex) in 1995 that was used to create the world's first national DNA database. The success of the database rapidly outgrew the functionality of the original system - by the year 2000 a new multiplex of ten-loci was introduced to reduce the chance of adventitious matches. The technology was adopted world-wide, albeit with different loci. The political requirement to introduce pan-European databases encouraged standardisation - the development of European Standard Set (ESS) of markers comprising twelve-loci is the latest iteration. Although development has been impressive, the methods used to interpret evidence have lagged behind. For example, the theory to interpret complex DNA profiles (low-level mixtures), had been developed fifteen years ago, but only in the past year or so, are the concepts starting to be widely adopted. A plethora of different models (some commercial and others non-commercial) have appeared. This has led to a confusing 'debate' about the 'best' to use. The different models available are described along with their advantages and disadvantages. A section discusses the development of national DNA databases, along with details of an associated controversy to estimate the strength of evidence of matches. Current methodology is limited to searches of complete profiles - another example where the interpretation of matches has not kept pace with development of theory. STRs have also transformed the area of Disaster Victim Identification (DVI) which frequently requires kinship analysis. However, genotyping efficiency is complicated by complex, degraded DNA profiles. Finally, there is now a detailed understanding of the causes of stochastic effects that cause DNA profiles to exhibit the phenomena of drop-out and drop-in, along with artefacts such as stutters. The phenomena discussed include: heterozygote balance; stutter; degradation; the effect of decreasing quantities of DNA; the dilution effect.
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Affiliation(s)
- Peter Gill
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway; Department of Forensic Medicine, Sognsvannsveien 20, Rikshospitalet, 0372 Oslo, Norway.
| | - Hinda Haned
- Netherlands Forensic Institute, Department of Human Biological Traces, The Hague, The Netherlands
| | - Oyvind Bleka
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway
| | - Oskar Hansson
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway
| | - Guro Dørum
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Aas, Norway
| | - Thore Egeland
- Norwegian Institute of Public Health, Department of Forensic Biology, PO Box 4404 Nydalen, 0403 Oslo, Norway; Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Aas, Norway
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145
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Goray M, van Oorschot RA. The complexities of DNA transfer during a social setting. Leg Med (Tokyo) 2015; 17:82-91. [DOI: 10.1016/j.legalmed.2014.10.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/10/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
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146
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Liu JY. PE-Swab Direct STR Amplification of Forensic Touch DNA Samples. J Forensic Sci 2015; 60:693-701. [DOI: 10.1111/1556-4029.12705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/21/2014] [Accepted: 04/21/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Jason Y. Liu
- Thermo Fisher Scientific 180 Oyster Point Blvd.; South San Francisco CA 94080
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147
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Ostojic L, Klempner SA, Patel RA, Mitchell AA, Axler-DiPerte GL, Wurmbach E. Qualitative and quantitative assessment of single fingerprints in forensic DNA analysis. Electrophoresis 2014; 35:3165-72. [DOI: 10.1002/elps.201400177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/26/2014] [Accepted: 07/18/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Lana Ostojic
- Department of Forensic Biology; Office of Chief Medical Examiner; New York NY USA
| | - Stacey A. Klempner
- Department of Forensic Biology; Office of Chief Medical Examiner; New York NY USA
| | - Rosni A. Patel
- Department of Forensic Biology; Office of Chief Medical Examiner; New York NY USA
| | | | | | - Elisa Wurmbach
- Department of Forensic Biology; Office of Chief Medical Examiner; New York NY USA
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148
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Hedell R, Dufva C, Ansell R, Mostad P, Hedman J. Enhanced low-template DNA analysis conditions and investigation of allele dropout patterns. Forensic Sci Int Genet 2014; 14:61-75. [PMID: 25282604 DOI: 10.1016/j.fsigen.2014.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 06/27/2014] [Accepted: 09/09/2014] [Indexed: 11/26/2022]
Abstract
Forensic DNA analysis applying PCR enables profiling of minute biological samples. Enhanced analysis conditions can be applied to further push the limit of detection, coming with the risk of visualising artefacts and allele imbalances. We have evaluated the consecutive increase of PCR cycles from 30 to 35 to investigate the limitations of low-template (LT) DNA analysis, applying the short tandem repeat (STR) analysis kit PowerPlex ESX 16. Mock crime scene DNA extracts of four different quantities (from around 8-84 pg) were tested. All PCR products were analysed using 5, 10 and 20 capillary electrophoresis (CE) injection seconds. Bayesian models describing allele dropout patterns, allele peak heights and heterozygote balance were developed to assess the overall improvements in EPG quality with altered PCR/CE settings. The models were also used to evaluate the impact of amplicon length, STR marker and fluorescent label on the risk for allele dropout. The allele dropout probability decreased for each PCR cycle increment from 30 to 33 PCR cycles. Irrespective of DNA amount, the dropout probability was not affected by further increasing the number of PCR cycles. For the 42 and 84 pg samples, mainly complete DNA profiles were generated applying 32 PCR cycles. For the 8 and 17 pg samples, the allele dropouts decreased from 100% using 30 cycles to about 75% and 20%, respectively. The results for 33, 34 and 35 PCR cycles indicated that heterozygote balance and stutter ratio were mainly affected by DNA amount, and not directly by PCR cycle number and CE injection settings. We found 32 and 33 PCR cycles with 10 CE injection seconds to be optimal, as 34 and 35 PCR cycles did not improve allele detection and also included CE saturation problems. We find allele dropout probability differences between several STR markers. Markers labelled with the fluorescent dyes CXR-ET (red in electropherogram) and TMR-ET (shown as black) generally have higher dropout risks compared with those labelled with JOE (green) and fluorescein (blue). Overall, the marker D10S1248 has the lowest allele dropout probability and D8S1179 the highest. The marker effect is mainly pronounced for 30-32 PCR cycles. Such effects would not be expected if the amplification efficiencies were identical for all markers. Understanding allele dropout risks and the variability in peak heights and balances is important for correct interpretation of forensic DNA profiles.
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Affiliation(s)
- Ronny Hedell
- Swedish National Laboratory of Forensic Science (SKL), SE-581 94 Linköping, Sweden; Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Sweden.
| | - Charlotte Dufva
- Swedish National Laboratory of Forensic Science (SKL), SE-581 94 Linköping, Sweden.
| | - Ricky Ansell
- Swedish National Laboratory of Forensic Science (SKL), SE-581 94 Linköping, Sweden; Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden.
| | - Petter Mostad
- Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Sweden; Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden.
| | - Johannes Hedman
- Swedish National Laboratory of Forensic Science (SKL), SE-581 94 Linköping, Sweden; Division of Applied Microbiology, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
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149
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Evaluation of a novel material, Diomics X-Swab™, for collection of DNA. Forensic Sci Int Genet 2014; 12:192-8. [DOI: 10.1016/j.fsigen.2014.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 11/23/2022]
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150
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LoCIM-tool: An expert's assistant for inferring the major contributor's alleles in mixed consensus DNA profiles. Forensic Sci Int Genet 2014; 11:154-65. [DOI: 10.1016/j.fsigen.2014.03.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 11/23/2022]
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