1
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Liu Y, Fan J, Zhang M, Liu Z, Wang J, Liu J, Li Z, Yang F, Zhang G. A human identification system for hair shaft using RNA polymorphism. Forensic Sci Int Genet 2023; 67:102929. [PMID: 37611365 DOI: 10.1016/j.fsigen.2023.102929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023]
Abstract
Hair is one of the common pieces of evidence at crime scenes, with abundant mitochondrial DNA but limited nuclear DNA in its shaft. It also helps to narrow the investigation scope to maternal lineage but fails to provide unique individual information. We assumed that RNA in hair shafts would be an alternative resource used to perform human identification based on the facts that (1) RNA retains the polymorphic information; (2) the multi-copy of RNA in a cell resists degradation as compared to the one-copy of nuclear DNA. In this study, we explored the potential of RNA polymorphism in hair shafts for forensic individual identification. A SNaPshot typing system was constructed using 18 SNPs located on 11 genes (ABCA13, AHNAK, EXPH5, KMT2D, KRT35, PPP1R15A, RBM33, S100A5, TBC1D4, TMC5, TRPV2). The RNA typing system was evaluated for sensitivity, species specificity, and feasibility for aged hair samples. Hair samples from a Shanxi population in China were used for the population study of the system. The detection limit of the assay was 2 ng RNA. The CDP of these 11 genes was 0.999969 in the Shanxi population. We also identified the concordance of the RNA and DNA typing results. In summary, we developed an RNA typing method to perform human identification from hair shafts, which performed as accurately as nuclear DNA typing. Our method provides a potential basis for solving the human identification problem from hair shafts, as well as other biological materials that lack nuclear DNA.
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Affiliation(s)
- Yao Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiajia Fan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Mingming Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
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2
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Liu Z, Simayijiang H, Wang Q, Yang J, Sun H, Wu R, Yan J. DNA and protein analyses of hair in forensic genetics. Int J Legal Med 2023; 137:613-633. [PMID: 36732435 DOI: 10.1007/s00414-023-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China.
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3
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Karim N, Plott TJ, Durbin-Johnson BP, Rocke DM, Salemi M, Phinney BS, Goecker ZC, Pieterse MJM, Parker GJ, Rice RH. Elucidation of familial relationships using hair shaft proteomics. Forensic Sci Int Genet 2021; 54:102564. [PMID: 34315035 DOI: 10.1016/j.fsigen.2021.102564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 07/08/2021] [Accepted: 07/14/2021] [Indexed: 01/01/2023]
Abstract
This study examines the potential of hair shaft proteomic analysis to delineate genetic relatedness. Proteomic profiling and amino acid sequence analysis provide information for quantitative and statistically-based analysis of individualization and sample similarity. Protein expression levels are a function of cell-specific transcriptional and translational programs. These programs are greatly influenced by an individual's genetic background, and are therefore influenced by familial relatedness as well as ancestry and genetic disease. Proteomic profiles should therefore be more similar among related individuals than unrelated individuals. Likewise, profiles of genetically variant peptides that contain single amino acid polymorphisms, the result of non-synonymous SNP alleles, should behave similarly. The proteomically-inferred SNP alleles should also provide a basis for calculation of combined paternity and sibship indices. We test these hypotheses using matching proteomic and genetic datasets from a family of two adults and four siblings, one of which has a genetic condition that perturbs hair structure and properties. We demonstrate that related individuals, compared to those who are unrelated, have more similar proteomic profiles, profiles of genetically variant peptides and higher combined paternity indices and combined sibship indices. This study builds on previous analyses of hair shaft protein profiling and genetically variant peptide profiles in different real-world scenarios including different human hair shaft body locations and pigmentation status. It also validates the inclusion of proteomic information with other biomolecular substrates in forensic hair shaft analysis, including mitochondrial and nuclear DNA.
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Affiliation(s)
- Noreen Karim
- Department of Environmental Toxicology, University of California, Davis, USA
| | - Tempest J Plott
- Department of Environmental Toxicology, University of California, Davis, USA; Forensic Science Program, University of California, Davis, USA
| | - Blythe P Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational, Science Center Biostatistics Core, University of California, Davis, USA
| | - David M Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational, Science Center Biostatistics Core, University of California, Davis, USA
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, USA
| | - Brett S Phinney
- Proteomics Core Facility, University of California, Davis, USA
| | - Zachary C Goecker
- Department of Environmental Toxicology, University of California, Davis, USA
| | - Marc J M Pieterse
- Department of Environmental Toxicology, University of California, Davis, USA
| | - Glendon J Parker
- Department of Environmental Toxicology, University of California, Davis, USA; Forensic Science Program, University of California, Davis, USA
| | - Robert H Rice
- Department of Environmental Toxicology, University of California, Davis, USA; Forensic Science Program, University of California, Davis, USA
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4
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Gutierrez R, LaRue B, Houston R. Novel extraction chemistry and alternative amplification strategies for use with rootless hair shafts. J Forensic Sci 2021; 66:1929-1936. [PMID: 34057738 DOI: 10.1111/1556-4029.14763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/14/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
Abstract
Rootless hair shafts are often considered unsuitable for STR genotyping due to the known high failure rate. The same samples can be reliably processed with mitochondrial sequencing. However, the minimal discriminatory power of widely implemented control region mitochondrial sequencing techniques limits its utility in some forensic casework. In this research, multiple variables were tested to provide information on rootless hair shaft sample genotyping success. Results showed external decontamination procedures decreased drop-in alleles but also greatly reduced profile recovery. The novel InnoXtract™ chemistry was comparable to automated EZ1 DNA Investigator extraction. With thoroughly decontaminated hairs, InnoTyper® 21 amplification generated random match probabilities higher than STR chemistry in 71.875% of samples and 18.75% of samples benefitted from the use of InnoTyper® 21 amplification compared with estimated mtDNA profile rarity. Compared with the capillary electrophoresis-based amplification chemistries tested, the ForenSeq™ DNA Signature Prep chemistry paired with massively parallel sequencing was the most discriminatory amplification strategy tested.
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Affiliation(s)
- Ryan Gutierrez
- Department of Forensic Science, Sam Houston State University, Huntsville, TX, USA
| | | | - Rachel Houston
- Department of Forensic Science, Sam Houston State University, Huntsville, TX, USA
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5
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Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.
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Holt CL, Stephens KM, Walichiewicz P, Fleming KD, Forouzmand E, Wu SF. Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software. Genes (Basel) 2021; 12:genes12040599. [PMID: 33921728 PMCID: PMC8073089 DOI: 10.3390/genes12040599] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGxTM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.
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7
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Hao T, Guo J, Liu J, Wang J, Liu Z, Cheng X, Li J, Ren J, Li Z, Yan J, Zhang G. Predicting human age by detecting DNA methylation status in hair. Electrophoresis 2021; 42:1255-1261. [PMID: 33629357 DOI: 10.1002/elps.202000349] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 02/07/2021] [Indexed: 12/29/2022]
Abstract
Age prediction is of great importance for criminal investigation and judicial expertise. DNA methylation status is considered a promising method to infer tissue age by virtue of age-dependent changes on methylation sites. In recent years, forensic scientists have established various models to predict the chronological age of blood, saliva, and semen based on DNA methylation status. However, hair-inferred age has not been studied in the field of forensic science. In this study, we measured the methylation statuses of potential age-related CpG sites by using the multiplex methylation SNaPshot method. A total of 10 CpG sites from the LAG3, SCGN, ELOVL2, KLF14, C1orf132, SLC12A5, GRIA2, and PDE4C genes were found to be tightly associated with age in hair follicles. A correlation coefficient above 0.7 was found for four CpG sites (cg24724428 and Chr6:11044628 in ELOVL2, cg25148589 in GRIA2, and cg07547549 in SLC12A5). Among four age-prediction models, the multiple linear regression model consisting of 10 CpG sites provided the best-fitting results, with a median absolute deviation of 3.68 years. It is feasible to obtain both human identification and age information from a single scalp hair follicle. No significant differences in methylation degree were found between different sexes, hair types, or hair colors. In conclusion, we established a method to evaluate chronological age by assessing DNA methylation status in hair follicles.
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Affiliation(s)
- Ting Hao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jiangling Guo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Xiaojuan Cheng
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jintao Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jianbo Ren
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
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8
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Burrill J, Rammenou E, Alawar F, Daniel B, Frascione N. Corneocyte lysis and fragmented DNA considerations for the cellular component of forensic touch DNA. Forensic Sci Int Genet 2020; 51:102428. [PMID: 33338861 DOI: 10.1016/j.fsigen.2020.102428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 01/28/2023]
Abstract
DNA deposited by individuals' hands is a routine part of forensic analysis, yet little is understood about the precise cellular contents left by handling. "Dead" skin cells known as corneocytes make up the majority of the cellular material left in touch deposits by people's hands but are known to lack nuclei, making their DNA content ambiguous. Here we measure DNA released from anucleate corneocytes following various lysis methods to determine how much DNA may be present in these cells and how best to recover it from inside the cornified envelope. We demonstrate that enhanced lysis methods using a reducing agent and longer incubation may be valuable for hand deposit samples. Corneocyte DNA can be characterized as highly degraded based on the quantification, STR profiling and fluorescence microscopy of the cells from freshly washed hands. Purification to target shorter DNA fragments is demonstrated. DNA from the washed corneocyte cells is shown to constitute the majority of recoverable DNA with these methods. We consider the use of new methods adapted to cornified cells and fragmented DNA for future research into this sample type.
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Affiliation(s)
- Julia Burrill
- King's Forensics, Department of Analytical, Environmental & Forensic Sciences, School of Population Health & Environmental Sciences, King's College London, London, United Kingdom.
| | - Elli Rammenou
- King's Forensics, Department of Analytical, Environmental & Forensic Sciences, School of Population Health & Environmental Sciences, King's College London, London, United Kingdom.
| | - Fatima Alawar
- King's Forensics, Department of Analytical, Environmental & Forensic Sciences, School of Population Health & Environmental Sciences, King's College London, London, United Kingdom.
| | - Barbara Daniel
- King's Forensics, Department of Analytical, Environmental & Forensic Sciences, School of Population Health & Environmental Sciences, King's College London, London, United Kingdom.
| | - Nunzianda Frascione
- King's Forensics, Department of Analytical, Environmental & Forensic Sciences, School of Population Health & Environmental Sciences, King's College London, London, United Kingdom.
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9
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Heß SA, Trapani S, Boronat MDM, Theunissen GMG, Rolf B, Jäger R. Ribosomal DNA as target for the assessment of DNA degradation of human and canine DNA. Leg Med (Tokyo) 2020; 48:101819. [PMID: 33248354 DOI: 10.1016/j.legalmed.2020.101819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022]
Abstract
The assessment of DNA amount and DNA integrity can support forensic DNA analysis, in particular of problematic traces such as single telogen hairs where STR typing success is often hampered by low amounts and strong degradation of nuclear DNA. Common strategies consist of quantitative polymerase chain reaction (qPCR)-based analysis of the abundance of a short versus a long nuclear amplicon, the latter prone to DNA degradation. To increase sensitivity, commercial qPCR solutions rest on amplification of multi-copy DNA sequences. Here we show that ribosomal DNA (rDNA) sequences are well suited for the same purpose. Because rDNA sequences are present in high copy number in most eukaryotic species, qPCR strategies can easily be adapted to non-human species. In this paper, we establish qPCR-based assays for human or dog DNA, respectively, which allow for sensitive analysis of DNA amounts and DNA degradation. We show that the human system can be applied to DNA of single telogen hairs, where STR typing success correlates with measured amounts and integrity of the DNA. By adapting the system to dog rDNA sequences we found that single telogen dog hairs often displayed less DNA degradation than human telogen hairs, in most cases allowing for successful STR typing. Thus, qPCR-based analysis of rDNA represents a cost-effective, highly sensitive strategy to assess DNA amount and integrity that can be adapted to hairs or other traces from various animal species.
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Affiliation(s)
- Sarah Aurora Heß
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany; Institute of Safety and Security Research, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Salvatore Trapani
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany; Università degli Studi di Palermo, University of Palermo, 90133 Palermo, PA, Italy
| | - Maria Del Mar Boronat
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany
| | - Glenn M G Theunissen
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany; Institute of Safety and Security Research, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Burkhard Rolf
- Eurofins Medigenomix Forensik GmbH, Anzinger Str. 7a, 85560 Ebersberg, Germany
| | - Richard Jäger
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany; Institute of Safety and Security Research, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany; Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757, Sankt Augustin, Germany.
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Jones KF, Carlson TL, Eckenrode BA, Donfack J. Assessing protein sequencing in human single hair shafts of decreasing lengths. Forensic Sci Int Genet 2020; 44:102145. [DOI: 10.1016/j.fsigen.2019.102145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 10/25/2022]
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11
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Applications and challenges of forensic proteomics. Forensic Sci Int 2019; 297:350-363. [DOI: 10.1016/j.forsciint.2019.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/23/2022]
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12
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Brandhagen MD, Loreille O, Irwin JA. Fragmented Nuclear DNA is the Predominant Genetic Material in Human Hair Shafts. Genes (Basel) 2018; 9:genes9120640. [PMID: 30567392 PMCID: PMC6316335 DOI: 10.3390/genes9120640] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/03/2018] [Accepted: 12/10/2018] [Indexed: 01/18/2023] Open
Abstract
While shed hairs are one of the most commonly encountered evidence types, they are among the most limited in terms of DNA quantity and quality. As a result, nuclear DNA short tandem repeat (STR) profiling is generally unsuccessful and DNA testing of shed hair is instead performed by targeting the mitochondrial DNA control region. Although the high copy number of mitochondrial DNA relative to nuclear DNA routinely permits the recovery of mitochondrial DNA (mtDNA) data in these cases, mtDNA profiles do not offer the discriminatory power of nuclear DNA profiles. In order to better understand the total content and degradation state of DNA in single shed hairs and assess the feasibility of recovering highly discriminatory nuclear DNA data from this common evidence type, high throughput shotgun sequencing was performed on both recently collected and aged (approximately 50-year-old) hair samples. The data reflect trends that have been demonstrated previously with other technologies, namely that mtDNA quantity and quality decrease along the length of the hair shaft. In addition, the shotgun data reveal that nuclear DNA is present in shed hair and surprisingly abundant relative to mitochondrial DNA, even in the most distal fragments. Nuclear DNA comprised, at minimum, 88% of the total human reads in any given sample, and generally more than 95%. Here, we characterize both the nuclear and mitochondrial DNA content of shed hairs and discuss the implications of these data for forensic investigations.
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Affiliation(s)
- Michael D Brandhagen
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Odile Loreille
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Jodi A Irwin
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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Current and emerging tools for the recovery of genetic information from post mortem samples: New directions for disaster victim identification. Forensic Sci Int Genet 2018; 37:270-282. [DOI: 10.1016/j.fsigen.2018.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/27/2018] [Accepted: 08/27/2018] [Indexed: 01/14/2023]
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14
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Cavanaugh SE, Bathrick AS. Direct PCR amplification of forensic touch and other challenging DNA samples: A review. Forensic Sci Int Genet 2018; 32:40-49. [DOI: 10.1016/j.fsigen.2017.10.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 01/08/2023]
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15
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Lee SY, Ha EJ, Woo SK, Lee SM, Lim KH, Eom YB. A rapid nuclear staining test using cationic dyes contributes to efficient STR analysis of telogen hair roots. Electrophoresis 2017; 38:1771-1779. [PMID: 28401988 DOI: 10.1002/elps.201700024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/05/2017] [Accepted: 04/05/2017] [Indexed: 11/10/2022]
Abstract
Telogen hairs presented in the crime scene are commonly encountered as trace evidence. However, short tandem repeat (STR) profiling of the hairs currently have low and limited use due to poor success rate. To increase the success rate of STR profiling of telogen hairs, we developed a rapid and cost-effective method to estimate the number of nuclei in the hair roots. Five cationic dyes, Methyl green (MG), Harris hematoxylin (HH), Methylene blue (MB), Toluidine blue (TB), and Safranin O (SO) were evaluated in this study. We conducted a screening test based on microscopy and the percentage of loss with nuclear DNA, in order to select the best dye. MG was selected based on its specific nuclei staining and low adverse effect on the hair-associated nuclear DNA. We examined 330 scalp and 100 pubic telogen hairs with MG. Stained hairs were classified into five groups and analyzed by STR. The fast staining method revealed 70% (head hair) and 33.4% (pubic hair) of full (30 alleles) and high partial (18-29 alleles) STR profiling proportion from the lowest nuclei count group (one to ten nuclei). The results of this study demonstrated a rapid, specific, nondestructive, and high yield DNA profiling method applicable for screening telogen hairs.
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Affiliation(s)
- So-Yeon Lee
- Department of Medical Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Eun-Ju Ha
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Seung-Kyun Woo
- Department of Medical Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - So-Min Lee
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Kyung-Hee Lim
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Yong-Bin Eom
- Department of Medical Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, Republic of Korea.,Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam, Republic of Korea
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Nishi E, Watanabe K, Tashiro Y, Sakai K. Terminal restriction fragment length polymorphism profiling of bacterial flora derived from single human hair shafts can discriminate individuals. Leg Med (Tokyo) 2017; 25:75-82. [DOI: 10.1016/j.legalmed.2017.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/13/2016] [Accepted: 01/09/2017] [Indexed: 01/28/2023]
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17
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Castillo-Peinado LS, Luque de Castro MD. An overview on forensic analysis devoted to analytical chemists. Talanta 2017; 167:181-192. [PMID: 28340709 DOI: 10.1016/j.talanta.2017.01.087] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/28/2017] [Accepted: 01/29/2017] [Indexed: 12/01/2022]
Abstract
The present article has as main aim to show analytical chemists interested in forensic analysis the world they will face if decision in favor of being a forensic analytical chemist is adopted. With this purpose, the most outstanding aspects of forensic analysis in dealing with sampling (involving both bodily and no bodily samples), sample preparation, and analytical equipment used in detection, identification and quantitation of key sample components are critically discussed. The role of the great omics in forensic analysis, and the growing role of the youngest of the great omics -metabolomics- are also discussed. The foreseeable role of integrative omics is also outlined.
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Affiliation(s)
- L S Castillo-Peinado
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; University of Córdoba, Agrifood Excellence Campus, ceiA3, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, E-14071 Córdoba, Spain
| | - M D Luque de Castro
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; University of Córdoba, Agrifood Excellence Campus, ceiA3, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, E-14071 Córdoba, Spain.
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18
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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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Haines AM, Linacre A. A rapid screening method using DNA binding dyes to determine whether hair follicles have sufficient DNA for successful profiling. Forensic Sci Int 2016; 262:190-5. [DOI: 10.1016/j.forsciint.2016.03.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/16/2016] [Accepted: 03/12/2016] [Indexed: 12/24/2022]
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20
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Tridico SR, Koch S, Michaud A, Thomson G, Kirkbride KP, Bunce M. Interpreting biological degradative processes acting on mammalian hair in the living and the dead: which ones are taphonomic? Proc Biol Sci 2015; 281:20141755. [PMID: 25339725 DOI: 10.1098/rspb.2014.1755] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although the taphonomic (post-mortem) degradation processes relevant to teeth and bones have been well described, those taking place with regards to mammalian hairs have not been characterized to the same extent. This present article describes, in detail, microscopic changes resulting from the actions of biological agents that digest and degrade hairs. The most noteworthy and prevalent agents responsible for the destruction of hair structure are fungi, which use a range of strategies to invade and digest hairs. One of the most important finds to emerge from this study is that taphonomic structures and processes can easily be interpreted by the unwary as 'real', or as class characteristics for a particular animal taxon. Moreover, under certain conditions, 'taphonomic' processes normally associated with the dead are also present on the hairs of the living. This work will improve the reliability of hair examinations in forensic, archaeological and palaeontological applications-in addition, the finding has relevance in the protection of mammalian collections susceptible to infestation. This article also addresses the popular myth that ancient peoples were often red-haired and discusses phenomena responsible for this observation. Insights gained from detailed characterization of taphonomic processes in 95 hairs from a variety of species demonstrate the range and breadth of degradative effects on hair structure and colour. Lastly, the study demonstrates that hairs often tell a story and that there is value of extracting as much morphological data as possible from hairs, prior to destructive sampling for biomolecules.
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Affiliation(s)
- Silvana R Tridico
- Trace and Environmental DNA (TrEnD) Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6845, Australia School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - Sandra Koch
- Department of Anthropology, The Pennsylvania State University, 403C Carpenter Building, University Park, PA 16801, USA
| | - Amy Michaud
- Bureau of Alcohol, Tobacco, Firearms and Explosives, 6000 Ammendale Road, Beltsville, MD 20705, USA
| | - Gordon Thomson
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - K Paul Kirkbride
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6845, Australia School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
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21
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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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22
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Kumar R, Shakyawar DB, Pareek PK, Raja ASM, Prince LLL, Kumar S, Naqvi SMK. Development of PCR-based technique for detection of purity of Pashmina fiber from textile materials. Appl Biochem Biotechnol 2015; 175:3856-62. [PMID: 25712909 DOI: 10.1007/s12010-015-1552-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 02/15/2015] [Indexed: 10/23/2022]
Abstract
Pashmina fiber is one of major specialty animal fiber in India. The quality of Pashmina obtained from Changthangi and Chegu goats in India is very good. Due to restricted availability and high prices, adulteration of natural prized fibers is becoming a common practice by the manufacturers. Sheep wool is a cheap substitute, which is usually used for adulteration and false declaration of Pashmina-based products. Presently, there is lack of cost-effective and readily available methodology to identify the adulteration of Pashmina products from other similar looking substitutes like sheep wool. Polymerase chain reaction (PCR)-based detection method can be used to identify origin of animal fiber. Extraction of quality DNA from dyed and processed animal fiber and textile materials is a limiting factor in the development of such detection methods. In the present study, quality DNA was extracted from textile materials, and PCR-based technique using mitochondrial gene (12S rRNA) specific primers was developed for detection of the Pashmina in textile blends. This technique has been used for detection of the adulteration of the Pashmina products with sheep wool. The technique can detect adulteration level up to 10 % of sheep/goat fibers in textile blends.
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Affiliation(s)
- Rajiv Kumar
- Animal Biotechnology Section, ICAR-Central Sheep and Wool Research Institute, Avikanagar, CSWRI Campus, Jaipur, Rajasthan, 304501, India,
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23
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Nissimov JN, Das Chaudhuri AB. Hair curvature: a natural dialectic and review. Biol Rev Camb Philos Soc 2014; 89:723-66. [PMID: 24617997 DOI: 10.1111/brv.12081] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 12/18/2013] [Accepted: 01/01/2014] [Indexed: 12/19/2022]
Abstract
Although hair forms (straight, curly, wavy, etc.) are present in apparently infinite variations, each fibre can be reduced to a finite sequence of tandem segments of just three types: straight, bent/curly, or twisted. Hair forms can thus be regarded as resulting from genetic pathways that induce, reverse or modulate these basic curvature modes. However, physical interconversions between twists and curls demonstrate that strict one-to-one correspondences between them and their genetic causes do not exist. Current hair-curvature theories do not distinguish between bending and twisting mechanisms. We here introduce a multiple papillary centres (MPC) model which is particularly suitable to explain twisting. The model combines previously known features of hair cross-sectional morphology with partially/completely separated dermal papillae within single follicles, and requires such papillae to induce differential growth rates of hair cortical material in their immediate neighbourhoods. The MPC model can further help to explain other, poorly understood, aspects of hair growth and morphology. Separate bending and twisting mechanisms would be preferentially affected at the major or minor ellipsoidal sides of fibres, respectively, and together they exhaust the possibilities for influencing hair-form phenotypes. As such they suggest dialectic for hair-curvature development. We define a natural-dialectic (ND) which could take advantage of speculative aspects of dialectic, but would verify its input data and results by experimental methods. We use this as a top-down approach to first define routes by which hair bending or twisting may be brought about and then review evidence in support of such routes. In particular we consider the wingless (Wnt) and mammalian target of rapamycin (mTOR) pathways as paradigm pathways for molecular hair bending and twisting mechanisms, respectively. In addition to the Wnt canonical pathway, the Wnt/Ca(2+) and planar cell polarity (PCP) pathways, and others, can explain many alternatives and specific variations of hair bending phenotypes. Mechanisms for hair papilla budding or its division by bisection or fission can explain MPC formation. Epithelial-to-mesenchymal (EMT) and mesenchymal-to-epithelial (MET) transitions, acting in collaboration with epithelial-mesenchymal communications are also considered as mechanisms affecting hair growth and its bending and twisting. These may be treated as sub-mechanisms of an overall development from neural-crest stem cell (NCSC) lineages to differentiated hair follicle (HF) cell types, thus providing a unified framework for hair growth and development.
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24
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Allen-Hall A, McNevin D. Non-cryogenic forensic tissue preservation in the field: a review. AUST J FORENSIC SCI 2013. [DOI: 10.1080/00450618.2013.789077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Guan Z, Zhou Y, Liu J, Jiang X, Li S, Yang S, Chen A. A simple method to extract DNA from hair shafts using enzymatic laundry powder. PLoS One 2013; 8:e69588. [PMID: 23922747 PMCID: PMC3726667 DOI: 10.1371/journal.pone.0069588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 06/09/2013] [Indexed: 12/04/2022] Open
Abstract
A simple method to extract DNA from hair shafts was developed by using enzymatic laundry powder at the first step of the process. The whole extraction can be finished in less than 2 hours. The simple extraction reagent proposed here contains only two cheap components: ordinary enzymatic laundry powder and PCR buffer. After extraction, an ultra sensitive fluorescent nucleic acid stain, PicoGreen, was used for quantifying trace amount of double-stranded DNA in the solution extracted. For further validation of DNA extraction, four primers were employed to amplify DNA microsatellite loci. Both fluorescence spectroscopy and PCR results suggested that this method can extract DNA from hair shafts with good efficiency and repeatability. The study will greatly facilitate the use of hair shafts in future for DNA analyses on genome-wide scale.
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Affiliation(s)
- Zheng Guan
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Yu Zhou
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Jinchuan Liu
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Xiaoling Jiang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Sicong Li
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Shuming Yang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
| | - Ailiang Chen
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Agro-food Quality and Safety, Ministry of Agriculture, Beijing, China
- * E-mail:
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26
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Ottens R, Taylor D, Abarno D, Linacre A. Successful direct amplification of nuclear markers from a single hair follicle. Forensic Sci Med Pathol 2012; 9:238-43. [PMID: 23275022 DOI: 10.1007/s12024-012-9402-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2012] [Indexed: 11/29/2022]
Abstract
We report on successful amplification of DNA profiles from a single hair. Direct amplification was used on the root tip of both anagen and telogen hairs using a kit to amplify 15 STR loci. All 30 anagen hairs tested from five different people gave full DNA profiles after 29 cycles with no allelic drop-in or heterozygous imbalance. Six of the 30 telogen hairs tested resulted in a full DNA profile, and a further four telogen hair samples tested produced a DNA profile of five or more complete loci that could be up-loaded to the National DNA Database (Australia). A full DNA profile was also obtained from the shaft of an anagen hair. Current practice for many laboratories is that a single hair may not be subjected to DNA testing as there is little chance of success, hence this 100 % success rate from anagen hairs is a significant advancement. A full DNA profile was obtained from a 5 year-old single hair illustrating the success when using direct PCR rather than attempting an extraction prior to the amplification step. The process described deliberately uses current DNA profiling methods with no increase in cycle number, such that the methodology can be incorporated readily into operational practice. For the first time in the field of human identification, single hairs can be analyzed with confidence that a meaningful DNA profile will be generated and the data accepted by the criminal justice system.
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Affiliation(s)
- Renée Ottens
- School of Biological Sciences, Flinders University, Bedford Park, Adelaide, SA, Australia
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27
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Belinchón-Lorenzo S, Iniesta V, Parejo JC, Fernández-Cotrina J, Muñoz-Madrid R, Soto M, Alonso C, Gómez Nieto LC. Detection of Leishmania infantum kinetoplast minicircle DNA by Real Time PCR in hair of dogs with leishmaniosis. Vet Parasitol 2012; 192:43-50. [PMID: 23218222 DOI: 10.1016/j.vetpar.2012.11.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 11/05/2012] [Accepted: 11/06/2012] [Indexed: 10/27/2022]
Abstract
It is known that hair can accumulate environmental toxics and excrete foreign chemical or biological substances. In this context, we hypothesized that foreign DNA could be found in the hair of an infected organism, and thus, be detected by Real Time PCR in the hair of Leishmania infantum naturally infected dogs. A population of 28 dogs living in Leishmania endemic areas was divided into two groups: A (13 Leishmania infected dogs) and B (15 healthy dogs). Blood, lymph node and ear hair samples from all of them were tested for the presence of parasite kinetoplast DNA (kDNA). For the same purpose, hair of several body areas and hair sections of two infected dogs were also analyzed. Epidermal keratinocytes from an infected animal were also analyzed for reactivity against Leishmania antigens by ELISA and for the presence of kDNA. Regarding to dogs from group A, parasite kDNA was detected in the 100% of lymph node samples. The sensitivity of Real Time PCR in ear hair was similar to that obtained in blood (9 positive out of 13 versus 8 positive out of 13, respectively). Moreover, the presence of L. infantum kDNA was also detected in the hair of all the analyzed body zones, in all hair sections and in epidermal keratinocytes. In infected dogs, parasite kDNA could be detected and quantified from just one single hair, whereas it was not detected in any of the samples of the healthy dogs. This work describes a new method for a reliable and non-invasive diagnosis of canine leishmaniosis using hair samples of infected animals. The data presented also provide some insights for the understanding of the physiology of keratinocytes and the role of hair as a specialized tissue in the kidnapping and removal of foreign DNA.
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Affiliation(s)
- Silvia Belinchón-Lorenzo
- LeishmanCeres Laboratory (GLP Compliance Certified), Parasitology Unit, Veterinary Faculty, University of Extremadura, Avenida de la Universidad s/n, 10003 Cáceres, Spain.
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Edson J, Brooks EM, McLaren C, Robertson J, McNevin D, Cooper A, Austin JJ. A quantitative assessment of a reliable screening technique for the STR analysis of telogen hair roots. Forensic Sci Int Genet 2012; 7:180-8. [PMID: 23116723 DOI: 10.1016/j.fsigen.2012.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 09/04/2012] [Accepted: 10/03/2012] [Indexed: 10/27/2022]
Abstract
Human telogen hairs are commonly recovered as trace evidence but currently have limited use for forensic DNA analysis. Recent studies have revealed that telogen roots may be shed with adhering material that may contain cells, thus providing a potential source of nuclear DNA. A simple histological stain can be used to screen telogen roots for the presence of nuclei, thus increasing the chance of selecting roots that may yield nuclear DNA. Using this method to visualise nuclei, we surveyed 998 hairs from 136 individuals, quantified the number of nuclei, extracted DNA and evaluated corresponding DNA yield and STR profiling success. Of the hairs screened, 35% of telogen roots contained nuclei and in total 6% of all roots screened had more than 100 nuclei. The number of nuclei associated with telogen roots was independent of the presence or absence of visibly adhering material, highlighting the importance of using histological staining rather than simple microscopic examination. DNA yield and STR profiling were significantly and positively correlated with nuclei number. The methods presented here can be incorporated into routine trace and DNA analysis providing an efficient and cost effective method to screen telogen hairs, and predict STR profiling success prior to destructive DNA analysis. The results of this study indicate telogen hairs may provide a reliable source of nuclear DNA for use in routine casework.
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Affiliation(s)
- Janette Edson
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences & The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia.
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29
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Olsen ME, Bengtsson CF, Bertelsen MF, Willerslev E, Gilbert MTP. DNA from keratinous tissue. Ann Anat 2012; 194:31-5. [DOI: 10.1016/j.aanat.2011.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 03/10/2011] [Accepted: 03/10/2011] [Indexed: 10/18/2022]
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30
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Validation of the PowerPlex® ESX17 and ESI17 kits for STR typing of telogen hair roots in forensic casework. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.09.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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31
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In situ labeling of DNA reveals interindividual variation in nuclear DNA breakdown in hair and may be useful to predict success of forensic genotyping of hair. Int J Legal Med 2011; 126:63-70. [PMID: 21475959 PMCID: PMC3252700 DOI: 10.1007/s00414-011-0566-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 02/14/2011] [Indexed: 12/20/2022]
Abstract
Hair fibers are formed by keratinocytes of the hair follicle in a process that involves the breakdown of the nucleus including DNA. Accordingly, DNA can be isolated with high yield from the hair bulb which contains living keratinocytes, whereas it is difficult to prepare from the distal portions of hair fibers and from shed hair. Nevertheless, forensic investigations are successful in a fraction of shed hair samples found at crime scenes. Here, we report that interindividual differences in the completeness of DNA removal from hair corneocytes are major determinants of DNA content and success rates of forensic investigations of hair. Distal hair samples were permeabilized with ammonia and incubated with the DNA-specific dye Hoechst 33258 to label DNA in situ. Residual nuclear DNA was visualized under the fluorescence microscope. Hair from some donors did not contain any stainable nuclei, whereas hair of other donors contained a variable number of DNA-positive nuclear remnants. The number of DNA-containing nuclear remnants per millimeter of hair correlated with the amount of DNA that could be extracted and amplified by quantitative PCR. When individual hairs were investigated, only hairs in which DNA could be labeled in situ gave positive results in short tandem repeat typing. This study reveals that the completeness of DNA degradation during cornification of the hair is a polymorphic trait. Furthermore, our results suggest that in situ labeling of DNA in hair may be useful for predicting the probability of success of forensic analysis of nuclear DNA in shed hair.
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Bengtsson CF, Olsen ME, Brandt LØ, Bertelsen MF, Willerslev E, Tobin DJ, Wilson AS, Gilbert MTP. DNA from keratinous tissue. Part I: hair and nail. Ann Anat 2011; 194:17-25. [PMID: 21530205 DOI: 10.1016/j.aanat.2011.03.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 03/05/2011] [Accepted: 03/22/2011] [Indexed: 11/26/2022]
Abstract
Keratinous tissues such as nail, hair, horn, scales and feather have been used as a source of DNA for over 20 years. Particular benefits of such tissues include the ease with which they can be sampled, the relative stability of DNA in such tissues once sampled, and, in the context of ancient genetic analyses, the fact that sampling generally causes minimal visual damage to valuable specimens. Even when freshly sampled, however, the DNA quantity and quality in the fully keratinized parts of such tissues is extremely poor in comparison to other tissues such as blood and muscle - although little systematic research has been undertaken to characterize how such degradation may relate to sample source. In this review paper we present the current understanding of the quality and limitations of DNA in two key keratinous tissues, nail and hair. The findings indicate that although some fragments of nuclear and mitochondrial DNA appear to be present in almost all hair and nail samples, the quality of DNA, both in quantity and length of amplifiable DNA fragments, vary considerably not just by species, but by individual, and even within individual between hair types.
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Affiliation(s)
- Camilla Friis Bengtsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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Brooks EM, Cullen M, Sztydna T, Walsh SJ. Nuclear staining of telogen hair roots contributes to successful forensic nDNA analysis. AUST J FORENSIC SCI 2010. [DOI: 10.1080/00450610903258136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Schmid D, Bayer B, Anslinger K. Comparison of telogen hair analyses: genRES® MPX-2SP kit versus genRES® MPX-SP1 and genRES® MPX-SP2 kits. Forensic Sci Int Genet 2008; 3:22-6. [DOI: 10.1016/j.fsigen.2008.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 06/17/2008] [Accepted: 07/03/2008] [Indexed: 11/26/2022]
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Bourguignon L, Hoste B, Boonen T, Vits K, Hubrecht F. A fluorescent microscopy-screening test for efficient STR-typing of telogen hair roots. Forensic Sci Int Genet 2008; 3:27-31. [DOI: 10.1016/j.fsigen.2008.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Revised: 07/29/2008] [Accepted: 08/27/2008] [Indexed: 11/24/2022]
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Boonen T, Vits K, Hoste B, Hubrecht F. The visualization and quantification of cell nuclei in telogen hair roots by fluorescence microscopy, as a pre-DNA analysis assessment. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2008. [DOI: 10.1016/j.fsigss.2007.10.098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Müller K, Klein R, Miltner E, Wiegand P. Improved STR typing of telogen hair root and hair shaft DNA. Electrophoresis 2007; 28:2835-42. [PMID: 17702067 DOI: 10.1002/elps.200600669] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Today the STR typing of telogen hair and hair shafts is regarded as a challenge. The small DNA quantity in the hair is highly degraded. Another problem are PCR inhibitors in the hair. In particular hair pigments, the melanins, are known to inhibit PCR. Hairs are exposed to sunlight and partly to chemical oxidation processes, which make them even more difficult to analyze. To increase the chances of a correct typing of hair, the small amount of DNA must be successfully isolated and the inhibitors have to be removed or neutralized. Furthermore, miniSTR typing improves the analysis of stains with degraded DNA like it is the case with hair. We introduce a nonorganic extraction method and in addition a miniSTR concept which is promising in typing stains with little and degraded DNA, especially hairs. The miniSTR concept including five database STRs (SE33, VWA, TH01, FGA, D3S1358) and the gender typing system Amelogenin was optimized for the amplification of hair DNA. Compared to commercial STR kits, this approach resulted in considerably higher success rates.
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Affiliation(s)
- Kathrin Müller
- Institute of Legal Medicine, University Hospital Ulm, Ulm, Germany
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GUNN MELISSAR, HARTNUP KATIE, BOUTIN STAN, SLATE JON, COLTMAN DAVIDW. TECHNICAL ARTICLE: A test of the efficacy of whole-genome amplification on DNA obtained from low-yield samples. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01696.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Leanza SM, Burk RD, Rohan TE. Whole genome amplification of DNA extracted from hair samples: Potential for use in molecular epidemiologic studies. ACTA ACUST UNITED AC 2007; 31:480-8. [DOI: 10.1016/j.cdp.2007.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2007] [Indexed: 10/22/2022]
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