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Kinebuchi T, Idota N, Tsuboi H, Takaso M, Bando R, Ikegaya H. The genome profiling method can be applied for species identification of biological materials collected at crime scenes. BMC Genet 2019; 20:50. [PMID: 31182029 PMCID: PMC6558897 DOI: 10.1186/s12863-019-0753-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Various biological materials unrelated to humans are found at crime scenes and it is often important to elucidate the origin of these materials. A genetic locus common to several species is conventionally PCR-amplified with universal primers to identify species. However, not all species can be identified using a single locus. In this study, DNA from 13 commonly handled taxa was analyzed to identify species by a genome profiling (GP) method, which involves random PCR and temperature gradient gel electrophoresis. RESULTS In a clustering analysis, we successfully obtained a single cluster for each species. CONCLUSION The GP method is cost-effective and does not require advanced techniques and knowledge in molecular biology. The random sampling of the whole genome using multiple primers provides substantial genomic information. Therefore, the method is effective for classifying a wide range of species, including animals, plants, and insects, and is useful for crime scene investigations.
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Affiliation(s)
- Takako Kinebuchi
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Nozomi Idota
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Hajime Tsuboi
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Marin Takaso
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Risa Bando
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Hiroshi Ikegaya
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan.
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Xie T, Hu L, Guo YX, Li YC, Chen F, Zhu BF. Genetic polymorphism analysis of mitochondrial DNA from Chinese Xinjiang Kazak ethnic group by a novel mitochondrial DNA genotyping panel. Mol Biol Rep 2018; 46:17-25. [DOI: 10.1007/s11033-018-4375-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/10/2018] [Indexed: 11/24/2022]
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Human blood identification using the genome profiling method. Leg Med (Tokyo) 2012; 14:121-5. [PMID: 22285643 DOI: 10.1016/j.legalmed.2012.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 11/23/2022]
Abstract
In criminal investigations, usually it is necessary to identify whether blood spots found at crime scenes are from humans or not. Nowadays, immunohistochemical methods and DNA analysis are usually used for this purpose. However, such methods and DNA analysis are labor intensive and expensive, and require highly trained skilled technicians. Recently, the genome profiling method (GP method) was developed. However, its use as a human DNA analysis method has not been reported. In this report, an attempt was made to differentiate human blood samples from animal blood samples using the GP method for forensic purposes. DNA extracted from a rat, squirrel, cat, dog, cow, and antelope along with human blood samples were analyzed. Following cluster analysis the human samples clustered into a single group separate from the animal samples. Therefore, although the number of samples was small the results suggest that the GP method might enable us to differentiate human samples from various animal samples. It may become a powerful tool in the field of forensic science.
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Houshmand M, Banoei MM, Tabarsi P, Panahi MSS, Hooshiar Kashani B, Ebrahimi G, Zargar L, Farnia P, Morris MW, Mansouri D, Velayati AA, Mirsaeidi MS. Do mitochondrial DNA haplogroups play a role in susceptibility to tuberculosis? Respirology 2008; 12:823-7. [PMID: 17986109 DOI: 10.1111/j.1440-1843.2007.01163.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVES Mitochondrial DNA has a unique role in ATP production and subsequent mitochondrial reactive oxygen species (ROS) production in eukaryotic cells and there is a potential role for ROS and oxygen burst against Mycobacterium tuberculosis, an intracellular pathogen. This study aimed to determine whether the frequency of different mitochondrial haplogroups was significantly different in patients with tuberculosis (TB) compared with a normal population. METHODS Mitochondrial DNA haplogroups M, N, J and K were studied by PCR-restriction fragment length polymorphism and sequencing. Cases were 54 patients with confirmed smear positive pulmonary TB. Controls were 256 healthy persons. RESULTS There were no statistically significant differences between those with TB and the control group. CONCLUSIONS There was no statistically significant association between mtDNA haplogroups and the presence of TB infection.
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Affiliation(s)
- Massoud Houshmand
- National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
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5
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Szibor R, Plate I, Schmitter H, Wittig H, Krause D. Forensic mass screening using mtDNA. Int J Legal Med 2006; 120:372-6. [PMID: 16583247 DOI: 10.1007/s00414-006-0085-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Accepted: 02/17/2006] [Indexed: 11/25/2022]
Abstract
At the forensic autopsy of a sexual murder victim, some trace hairs, possibly belonging to the perpetrator, were saved. Initially, the analysis of a pubic hair shaft only revealed the presence of the mitochondrial (mt) DNA haplotype profile consisting of the (CA)(6) allele and the complete hypervariable region 1 (HV1) and 2 (HV2) sequence. Later, typing of some further telogene trace hairs, which had been stored for several years, yielded a nuclear short tandem repeat (STR) profile. We used both the mtDNA haplotype and the STR profile to start a DNA mass screening project involving 2,335 male citizens of the relevant communities. MtDNA screening was carried out by using the CA repeat amplification in combination with an SNP typing procedure based on the restriction site analysis of amplified d-loop sequences. The aim of our paper is to put mass screening with mtDNA up for discussion.
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Affiliation(s)
- Reinhard Szibor
- Institut für Rechtsmedizin, Otto-von-Guericke-Universität Magdeburg, Leipziger Strasse 44, 39120 Magdeburg, Germany.
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Yao YG, Bravi CM, Bandelt HJ. A call for mtDNA data quality control in forensic science. Forensic Sci Int 2004; 141:1-6. [PMID: 15066707 DOI: 10.1016/j.forsciint.2003.12.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2003] [Revised: 11/14/2003] [Accepted: 12/10/2003] [Indexed: 10/26/2022]
Abstract
There is increasing evidence that many of the mitochondrial DNA (mtDNA) databases published in the fields of forensic science and molecular anthropology are flawed. An a posteriori phylogenetic analysis of the sequences could help to eliminate most of the errors and thus greatly improve data quality. However, previously published caveats and recommendations along these lines were not yet picked up by all researchers. Here we call for stringent quality control of mtDNA data by haplogroup-directed database comparisons. We take some problematic databases of East Asian mtDNAs, published in the Journal of Forensic Sciences and Forensic Science International, as examples to demonstrate the process of pinpointing obvious errors. Our results show that data sets are not only notoriously plagued by base shifts and artificial recombination but also by lab-specific phantom mutations, especially in the second hypervariable region (HVR-II).
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Affiliation(s)
- Yong-Gang Yao
- Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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7
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Poetsch M, Wittig H, Krause D, Lignitz E. Mitochondrial diversity of a northeast German population sample. Forensic Sci Int 2004; 137:125-32. [PMID: 14609647 DOI: 10.1016/j.forsciint.2003.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mitochondrial DNA sequences of the hypervariable regions HV I and HV II were analyzed in 300 unrelated individuals born and living in the northeast corner of Germany (Western Pomerania) to generate a database for forensic identification purposes in this region. Sequence polymorphism were detected using PCR and direct sequencing analysis. A total of 242 different haplotypes were found as determined by 147 variable positions. The most frequent haplotype (263G, 315.1C) was found in 10 individuals and is also the most common sequence in Europe. Three other haplotypes were shared by 5 individuals, 2 sequences by 4, 8 haplotypes by 3, 15 sequences by 2 persons, and 213 sequences were unique. The genetic diversity was estimated to be 0.99 and the probability of two random individuals showing identical mitochondrial DNA (mtDNA) haplotypes is 0.6%. A comparison with other studies from Germany showed only little differences in the distribution of haplogroups. Nevertheless, one frequent haplotype in northeast Germany (five unrelated individuals) could only rarely be found in other German and European regions. Our results may indicate that despite a high admixture proportion in the German population some regions could demonstrate certain characteristic features.
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Affiliation(s)
- Micaela Poetsch
- Institute of Forensic Medicine, University of Greifswald, Kuhstrasse 30, D-17489 Greifswald, Germany.
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8
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Vanecek T, Vorel F, Sip M. Mitochondrial DNA D-loop hypervariable regions: Czech population data. Int J Legal Med 2003; 118:14-8. [PMID: 14593483 DOI: 10.1007/s00414-003-0407-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2003] [Accepted: 09/29/2003] [Indexed: 11/26/2022]
Abstract
In order to identify polymorphic sites and to find out their frequencies and the frequency of haplotypes, the complete D-loop of mitochondrial DNA (mtDNA) from 93 unrelated Czech Caucasians was sequenced. Sequence comparison showed that 85 haplotypes were found and of these 78 were unique, 6 were observed twice and 1 was observed three times. Genetic diversity (GD) was estimated at 0.999 and the probability of two randomly selected sequences matching (random match probability, RMP) at 1.2%. Additionally these calculations were carried out for hypervariable regions 1, 2 (HV1, HV2), for the area between HV1 and HV2 and for the area of the hypervariable region HV3. The average number of nucleotide differences (ANND) was established to be 10.2 for the complete D-loop. The majority of sequence variations were substitutions, particularly transitions. Deletions were found only in the region where HV3 is situated and insertions in the same place and in poly-C tracts between positions 303 and 315 in HV2. A high degree of length heteroplasmy was found especially in the regions of poly-C tracts between positions 16184 and 16193 in HV1 and between positions 303 and 315 in HV2. Position heteroplasmies were found in two cases.
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Affiliation(s)
- T Vanecek
- Sikl's Department of Pathology, Charles University Hospital, Pilsen, Czech Republic
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9
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Szibor R, Michael M, Plate I, Wittig H, Krause D. Identification of the minor component of a mixed stain by using mismatch primer-induced restriction sites in amplified mtDNA. Int J Legal Med 2003; 117:160-4. [PMID: 12684817 DOI: 10.1007/s00414-002-0342-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2001] [Accepted: 09/16/2002] [Indexed: 11/29/2022]
Abstract
We report a case in which STR typing failed to identify the minor component of a mixed saliva stain, but a mitochondrial restriction analysis succeeded in discriminating between the two components. To identify the nt16093 and nt16265 transitions, the template was amplified with the mismatch primers L16092-mm16085 and H16266-mm16269. In the presence of the transitions the mismatch primers created a BsaB I and a Cac8 I restriction site, respectively. Subsequently, aliquots were restricted separately using the enzymes Cac8 I and BsaB I which clearly identified the minor stain component.
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Affiliation(s)
- R Szibor
- Institut für Rechtsmedizin, Otto-von-Guericke-Universität Magdeburg, Leipziger Strasse 44, 39120 Magdeburg, Germany.
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Lutz-Bonengel S, Schmidt U, Schmitt T, Pollak S. Sequence polymorphisms within the human mitochondrial genes MTATP6, MTATP8 and MTND4. Int J Legal Med 2003; 117:133-42. [PMID: 12734709 DOI: 10.1007/s00414-002-0356-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2002] [Accepted: 11/19/2002] [Indexed: 10/25/2022]
Abstract
By sequencing the control region of mitochondrial DNA, the majority of human DNA samples can be differentiated. A further increase in differentiation probability may be possible, e.g. by extending the sequenced region to coding regions of the mitochondrial genome. Restriction to those positions that do not result in a change of the amino acids guarantees that the information thus obtained does not refer to phenotypically relevant information. In the present study the sequence data of the mitochondrial genes MTATP6, MTATP8 and MTND4 were collected from 109 subjects and analyzed in order to define variable positions suitable for identification purposes. There were 32 variable base positions among 850 bases studied from MTATPase genes and 1,200 bases of the MTND4 gene showed 28 variable positions. "Hot spots" for base exchanges were found in both regions and one position (position 11,719 in the MTND4 gene) seems to be suitable for SNP investigation for forensic purposes.
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Affiliation(s)
- Sabine Lutz-Bonengel
- Institut für Rechtsmedizin, Klinikum der Universität Freiburg, Albertstrasse 9, 79104 Freiburg, Germany.
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Wittig H, Aschenbrenner A, Poetsch M, Krause D, Lignitz E. Variability of mitochondrial DNA in a population sample from Iceland. Leg Med (Tokyo) 2003; 5 Suppl 1:S173-6. [PMID: 12935581 DOI: 10.1016/s1344-6223(02)00103-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over the past decade investigations of human mitochondrial DNA (mtDNA) have considerably contributed to our knowledge about human evolution and migration. The genome of the Icelandic population is of special interest since Iceland has been genetically isolated for centuries. The sequence of the hypervariable regions HVS-I and HVS-II of the mtDNA control region was generated for 100 Icelandic individuals. A total of 75 different mtDNA sequences were observed, of which 19 sequences were shared by more than one individual, 16 sequences were shared by two individuals and two sequences were shared by three individuals; the most frequent haplotype (16129 A, 16239 T, 00263 G and 00315.1 C) was found six times. Both the genetic diversity (0.9925+/-0.0031) and the average number of pairwise nucleotide differences (7.371) were comparable with most of the other European populations. However, we found a smaller number of distinct mitochondrial lineages, suggesting that founder effects and genetic drift may have exerted a visible influence on the Icelandic genetic diversity. We compared these data with 1400 other European sequences from the D-Loop-BASE database. The paper discusses the evolutionary relationship between Icelandic and Central European mtDNA under due consideration of the historical context. Finally, our study has been aimed at increasing the number of mtDNA sequences available throughout the world and contributing to human genome investigations.
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Affiliation(s)
- Holger Wittig
- Institute of Forensic Medicine, Magdeburg University, Leipziger Strasse 44, 39120 Magdeburg, Germany.
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12
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Oikawa H, Tun Z, Young DR, Ozawa H, Yamazaki K, Tanaka E, Honda K. The specific mitochondrial DNA polymorphism found in Klinefelter's syndrome. Biochem Biophys Res Commun 2002; 297:341-5. [PMID: 12237124 DOI: 10.1016/s0006-291x(02)02198-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Hypervariable segments of mitochondrial DNA (mtDNA) (HV1 and HV2) were analyzed in Klinefelter's syndrome and compared to normal population data. One pair of samples consisting of a Japanese mother and affected son with Klinefelter's syndrome (involved in a criminal case), and seven unrelated DNA samples from Caucasian Klinefelter males (two involved in criminal cases and five diagnosed) were collected in Japan and the United States. The diagnosis of Klinefelter's syndrome was established previously by multiplex XY-STR typing detecting two X alleles and one Y allele in the samples. Haplotype analysis of the mtDNA sequence in Klinefelter males was found to be identical, unique, and specific, as it was not found in the normal population. Astonishingly, family data exhibited that the haplotype of the mtDNA in the son was apparently different from the mother's, suggesting that the mtDNA of Klinefelter male would not be inherited from mother to son. Our data indicate that possible interaction of the sex chromosome and the mtDNA exists, and suggests that the specific mtDNA haplotype could cause the abnormal cell to fertilize and reproduce itself.
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Affiliation(s)
- Haruna Oikawa
- Department of Legal Medicine, Institute of Community Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba City, Ibaraki 305-8575, Japan
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13
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Forster P, Calì F, Röhl A, Metspalu E, D'Anna R, Mirisola M, De Leo G, Flugy A, Salerno A, Ayala G, Kouvatsi A, Villems R, Romano V. Continental and subcontinental distributions of mtDNA control region types. Int J Legal Med 2002; 116:99-108. [PMID: 12056528 DOI: 10.1007/s00414-001-0261-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
When the mtDNA profile of a crime scene matches that of a suspect, it is necessary to determine the probability of a chance match by consulting the frequencies of the identified allele in a "reference population". The ceiling principle suggests that that population should be chosen in which the allele of the suspect is found at the highest frequency, in order to give the suspect the maximum benefit of doubt. Recently, we advocated the use of a worldwide mitochondrial database combined with a geographical information system to identify the regions of the world with the highest frequencies of matching mtDNA types. Here, we demonstrate that the alternative approach of defining a ceiling reference population on the basis of continent or phenotype (race) is too coarse for a non-negligible percentage of mtDNA control region types.
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Affiliation(s)
- Peter Forster
- The McDonald Institute for Archaeological Research, University of Cambridge, England.
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14
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Thormann W, Lurie IS, McCord B, Marti U, Cenni B, Malik N. Advances ofcapillary electrophoresis in clinical and forensic analysis (1999-2000). Electrophoresis 2001; 22:4216-43. [PMID: 11824639 DOI: 10.1002/1522-2683(200111)22:19<4216::aid-elps4216>3.0.co;2-w] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this paper, capillary electrophoresis in clinical and forensic analysis is reviewed on the basis of the literature of 1999, 2000 and the first papers in 2001. An overview of progress relevant examples for each major field of application, namely (i) analysis of drug seizures, explosives residues, gunshot residues and inks, (ii) monitoring of drugs, endogenous small molecules and ions in biofluids and tissues, (iii) general screening for serum proteins and analysis of specific proteins (carbohydrate deficient transferrin, alpha1-antitrypsin, lipoproteins and hemoglobins) in biological fluids, and (iv) analysis of nucleic acids and oligonucleotides in biological samples, including oligonucleotide therapeutics, are presented.
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Affiliation(s)
- W Thormann
- Department of Clinical Pharmacology, University of Bern, Switzerland.
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Affiliation(s)
- T A Brettell
- Forensic Science Bureau, New Jersey State Police, West Trenton 08628, USA
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Szibor R, Michael M, Plate I, Krause D. Efficiency of forensic mtDNA analysis. Case examples demonstrating the identification of traces. Forensic Sci Int 2000; 113:71-8. [PMID: 10978604 DOI: 10.1016/s0379-0738(00)00266-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The paper presents results of forensic mitochondrial DNA analyses which were aimed at typing the traces caused by touching or abrasion of skin cells. Five cases of strangulation tool investigation are summarised. Two cases of homicide could be cleared up by identifying the mtDNA of both the victim and the suspect on cables which had obviously been used as strangulation tools. In eight of 10 cases, weapons could be reliably assigned to their users. The mtDNA of the users could be even detected on cartridges after firing. In one case, evidence of a suicide could be provided by means of mtDNA sequencing of the wiping traces on a suicide note.
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Affiliation(s)
- R Szibor
- Institut für Rechtsmedizin, Otto-von-Guericke-Universität Magdeburg, Leipziger Strasse 44, D-39120, Magdeburg, Germany.
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