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S D Corrêa H, Alessandri I, Verzeletti A. Assessing the usefulness of Raman spectroscopy and lipid analysis of decomposed human bones in forensic genetics and molecular taphonomy. Forensic Sci Int 2024; 354:111881. [PMID: 38000148 DOI: 10.1016/j.forsciint.2023.111881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/18/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023]
Abstract
Bones are among the structures most likely to be recovered after death. However, the low quantity of preserved DNA and complex processing from sample to DNA profile make forensic DNA analysis of bones a challenging task. Raman spectroscopy and gas chromatography-mass spectrometry (GC/MS), have the potential to be useful as screening tools for DNA analysis and in decomposition studies. The objective of this research was to assess the usefulness of such molecular investigations. Femur samples collected from 50 decomposing human bodies were subjected to Raman spectroscopy and GC/MS. Assessment of nuclear DNA quantity and short tandem repeat (STR) genotyping efficiency were also performed. Raman parameters (crystallinity, carbonate-to-phosphate ratio, mineral-to-matrix ratio) and detected lipids were recorded. Background fluorescence proved problematic for Raman analysis of forensic bones. Regardless, it was not associated with less preserved DNA or less detected STR alleles. Fatty acids, hydrocarbons, and five types of fatty acid methyl esters (FAMEs) were detected. The main phosphate peak position in Raman spectra was significantly correlated with preserved DNA (p = 0.03713), while significantly more STR alleles were detected in bones containing methyl hexadecenoate (p = 0.04236). Detection of FAMEs in the bone matrix suggests a reaction between methanol produced by bacteria and free fatty acids, which are not associated with the level of preservation of endogenous DNA. The techniques assessed have shown to be useful in molecular taphonomy studies and forensic genetics.
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Affiliation(s)
- Heitor S D Corrêa
- Institute of Legal Medicine, Department of Medico-surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy; Forensic DNA Laboratory, Politec/MT, Cuiabá, Brazil.
| | - Ivano Alessandri
- INSTM and Sustainable Chemistry and Materials Laboratory, Department of Information Engineering, University of Brescia, Brescia, Italy
| | - Andrea Verzeletti
- Institute of Legal Medicine, Department of Medico-surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
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Kaur S, Kujur M, Rawat B, Upadhyaya M, ChandraVarshney K. Journey of Unidentified Bodies towards DNA Identification: A Social, Medico-legal and Forensic Perspective from New Delhi in India. Forensic Sci Int 2022; 341:111470. [DOI: 10.1016/j.forsciint.2022.111470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/12/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022]
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Emmons AL, Mundorff AZ, Keenan SW, Davoren J, Andronowski J, Carter DO, DeBruyn JM. Characterizing the postmortem human bone microbiome from surface-decomposed remains. PLoS One 2020; 15:e0218636. [PMID: 32639969 PMCID: PMC7343130 DOI: 10.1371/journal.pone.0218636] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 05/19/2020] [Indexed: 01/19/2023] Open
Abstract
Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.
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Affiliation(s)
- Alexandra L. Emmons
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Amy Z. Mundorff
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Sarah W. Keenan
- Department of Geology and Geological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, United States of America
| | - Jonathan Davoren
- Bode Cellmark Forensics, Lorton, Virginia, United States of America
| | - Janna Andronowski
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - David O. Carter
- Division of Natural Sciences and Mathematics, Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Chaminade University of Honolulu, Honolulu, Hawaii, United States of America
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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Astolphi RD, de Seixas Alves MT, Evison MP, Francisco RA, Guimarães MA, Iwamura ESM. The impact of burial period on compact bone microstructure: Histological analysis of matrix loss and cell integrity in human bones exhumed from tropical soil. Forensic Sci Int 2019; 298:384-392. [PMID: 30928778 DOI: 10.1016/j.forsciint.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/01/2019] [Accepted: 03/07/2019] [Indexed: 01/25/2023]
Abstract
Human bone histological analysis is a useful tool to assess post mortem diagenesis and to predict successful nuclear DNA typing of forensic material. This study is part of a series of studies developed by the authors intended to improve the understanding of post mortem diagenesis and to develop applications for DNA analysis of skeletal species from tropical soils, in order to optimize genetic and anthropological protocols. The aim of this study was to analyze the impact of burial period on the integrity of exhumed compact bone microstructure from tropical climate. In fragments of exhumed human femora from 39 individuals from the same cemetery (exhumed group) and 5 fresh femora from routine autopsies (control group), sections stained by hematoxylin-eosin were analyzed in order to measure bone microstructural integrity. We found that bone integrity index in exhumed group was negatively influenced by the period of burial (r = -0.37, p < 0.05) and highly significantly decreased (p < 0.0001) in comparison to control group. The period of burial and nitric acid decalcification time was positively correlated (r = 0.51; p < 0.01), leading to imply a bone petrification process during inhumation. Exhumed group showed higher level of matrix bone loss (p < 0.001), as expected, and 87% of cases analyzed were "tunneled" as described by Hackett. Bone integrity index and bone matrix tend to decrease in bones buried in tropical soil between 8-14 years of inhumation. This period is short if we consider cases in which there are preserved bones interred for longer periods in other environments. These data must be considered in cases where genetic identification of exhumed skeletons from tropical environment is required. The diagenesis in these bones and the variations of results found are discussed, clarifying some challenges for forensic laboratories, especially in DNA analysis.
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Affiliation(s)
- Rafael Dias Astolphi
- Department of Pathology, Escola Paulista de Medicina - Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | | | | | - Raffaela Arrabaça Francisco
- Department of Pathology and Legal Medicine, Faculdade de Medicina de Ribeirão Preto - Universidade de São Paulo, SP, Brazil
| | - Marco Aurelio Guimarães
- Department of Pathology and Legal Medicine, Faculdade de Medicina de Ribeirão Preto - Universidade de São Paulo, SP, Brazil
| | - Edna Sadayo Miazato Iwamura
- Department of Pathology, Escola Paulista de Medicina - Universidade Federal de São Paulo, São Paulo, SP, Brazil; Northumbria University, Newcastle Upon Tyne, United Kingdom.
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Singh S, Bavle RM, Konda P, Venugopal R, Bopaiah S, Kumar S. Assessment of the most reliable sites in mandibular bone for the best deoxyribonucleic acid yield for expeditive human identification in forensics. J Oral Maxillofac Pathol 2018; 21:447-453. [PMID: 29391725 PMCID: PMC5763873 DOI: 10.4103/jomfp.jomfp_47_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: In recent years, the techniques used to identify human remains post accidents, trauma or in case of criminal investigation have been expanded, improved and rendered more complex by the emergence of technologies based on deoxyribonucleic acid (DNA) analysis. In the head and neck area, tooth has been proven to be the best quantitative source for DNA but in certain cases where the mandible specimen is edentulous or the tooth is extensively destroyed with caries, large dental restorations, mobile, or if they show any perimortem or postmortem fractures, sampling of such tooth specimen is usually avoided. In such situations, bone is considered the next best site for DNA analysis. Mandible being the largest, strongest and dense cortical bone is the most prominent facial bone that can be easily disarticulated. It can be analyzed for the best short tandem repeat (STR) segment qualitative amplification using polymerase chain reaction (PCR) technique for forensic analysis which can be used for gender and age determination. Aim: The aim of this study is to determine the best site for optimum quantitative and qualitative yield of DNA for amplification using specific and standard STR segment by conventional PCR technique. Methodology: Fifteen mandibular samples exposed to different environmental conditions were collected. Bone pieces of 1 cm × 1 cm were cut from each mandible from three sites, i.e., the ramus, angle and body, wherein the genomic DNA was isolated and was subjected to PCR using restricted number of 25 cycles. Results: The STR segment D3S1358 from clone RP11-438F9 used for the study showed very good amplification in restricted number of PCR cycles in the ramus region with number of repeats in every 15th genomic region. Conclusion: This study highlights the use of mandibular bone for the expeditive human identification. As per the study, the ramus of the mandible gave high quantitative and qualitative yield of DNA with thick amplification band of the STR segment as compared to the body and angle of the mandible. Thus ramus of the mandible can be preferred over other sites for molecular forensic investigations.
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Affiliation(s)
- Shruti Singh
- Oral Pathologist-Private Dental Practitioner, Vishakapatnam, India
| | - Radhika Manoj Bavle
- Department of Oral and Maxillofacial Pathology, Krishnadevaraya College of Dental Sciences, Bengaluru, Karnataka, India
| | - Paremala Konda
- Department of Oral and Maxillofacial Pathology, Krishnadevaraya College of Dental Sciences, Bengaluru, Karnataka, India
| | - Reshma Venugopal
- Department of Oral and Maxillofacial Pathology, Krishnadevaraya College of Dental Sciences, Bengaluru, Karnataka, India
| | - Shiny Bopaiah
- Oral Pathologist-Private Dental Practitioner, Bengaluru, Karnataka, India
| | - Sameer Kumar
- Oral Pathologist-Private Dental Practitioner, Bengaluru, Karnataka, India
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Francisco RA, Evison MP, Costa Junior MLD, Silveira TCP, Secchieri JM, Guimarães MA. Validation of a standard forensic anthropology examination protocol by measurement of applicability and reliability on exhumed and archive samples of known biological attribution. Forensic Sci Int 2017; 279:241-250. [DOI: 10.1016/j.forsciint.2017.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 08/07/2017] [Accepted: 08/14/2017] [Indexed: 10/18/2022]
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Mallett X, Evison MP. Critical issues in the historical and contemporary development of forensic anthropology in Australia: An international comparison. Forensic Sci Int 2017; 275:314.e1-8. [PMID: 28449842 DOI: 10.1016/j.forsciint.2017.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 11/23/2022]
Abstract
The aim of this brief critical qualitative analysis is to examine the development of forensic anthropology in Australia, at a time of significant change in the discipline. It will briefly summarise its historical establishment, making comparative reference to other regions-particularly the United Kingdom and United States, and the influence of the Bali Bombings of 2002, Indian Ocean earthquake and tsunami of 2004 and Black Saturday Bushfires of 2009. The analysis goes on to consider key factors in research in forensic anthropology in the United States, and the development of standards and regulation in the US and UK. The significance of research in post-mortem diagenesis in Brazil-a country sharing aspects of climate, soil types and demography with Australia-is also considered, as well as the significance of patterns of casework encountered in Australia compared with those of other jurisdictions. While forensic anthropology as a discipline has grown remarkably in recent years, this analysis suggests that research and training tailored to the specific pattern of casework encountered in Australia is now essential to support the development of national standards in science, education, and professional regulation. The significance of the establishment of the first taphonomy research facility outside of the US-the Australian Facility for Taphonomic Experimental Research-is briefly considered with reference to what this facility may offer to the development of forensic anthropology in Australia.
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Mello RB, Silva MR, Alves MT, Evison MP, Guimarães MA, Francisco RA, Astolphi RD, Iwamura ES. Tissue Microarray Analysis Applied to Bone Diagenesis. Sci Rep 2017; 7:39987. [PMID: 28051148 DOI: 10.1038/srep39987] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 11/29/2016] [Indexed: 11/08/2022] Open
Abstract
Taphonomic processes affecting bone post mortem are important in forensic, archaeological and palaeontological investigations. In this study, the application of tissue microarray (TMA) analysis to a sample of femoral bone specimens from 20 exhumed individuals of known period of burial and age at death is described. TMA allows multiplexing of subsamples, permitting standardized comparative analysis of adjacent sections in 3-D and of representative cross-sections of a large number of specimens. Standard hematoxylin and eosin, periodic acid-Schiff and silver methenamine, and picrosirius red staining, and CD31 and CD34 immunohistochemistry were applied to TMA sections. Osteocyte and osteocyte lacuna counts, percent bone matrix loss, and fungal spheroid element counts could be measured and collagen fibre bundles observed in all specimens. Decalcification with 7% nitric acid proceeded more rapidly than with 0.5 M EDTA and may offer better preservation of histological and cellular structure. No endothelial cells could be detected using CD31 and CD34 immunohistochemistry. Correlation between osteocytes per lacuna and age at death may reflect reported age-related responses to microdamage. Methodological limitations and caveats, and results of the TMA analysis of post mortem diagenesis in bone are discussed, and implications for DNA survival and recovery considered.
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Mundorff A, Davoren JM. Examination of DNA yield rates for different skeletal elements at increasing post mortem intervals. Forensic Sci Int Genet 2013; 8:55-63. [PMID: 24315589 DOI: 10.1016/j.fsigen.2013.08.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 11/28/2022]
Abstract
Identification of contemporary human remains by DNA STR testing is mainly limited by the ability to isolate sufficient amounts of DNA from the skeletal samples. A key part of this work relies on selection of the skeletal element with the best chance of obtaining a DNA STR profile. DNA was extracted from 55 bone samples, from 3 recently skeletonized individuals, representing most element types in the human body. Comparison of DNA yields from samples within an individual showed that the small cancellous bones on average have much higher amounts of DNA per unit mass than dense cortical bones. Complete 16 locus STR profiles were obtained for all 3 individuals from 36 of the element types, 10 had full profiles for 2 of the 3 individuals, 3 had full profiles for 1 of the 3 and 5 did not have any full profiles. The sample types with the least STR loci were from the arms. Ten skeletal elements were tested from 12 additional skeletons ranging from 3-21 years post mortem interval (PMI). At increasing PMI the small cancellous bones continued to yield more DNA and STR loci than the cortical bones. These findings suggest that the current recommendation for selection of long cortical bone samples for DNA testing of skeletal remains should be re-evaluated.
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Affiliation(s)
- Amy Mundorff
- Department of Anthropology, The University of Tennessee, 250 South Stadium Hall, Knoxville, TN 37996, USA
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Li R, Klempner S. The effect of an enzymatic bone processing method on short tandem repeat profiling of challenged bone specimens. Leg Med (Tokyo) 2013; 15:171-6. [PMID: 23384499 DOI: 10.1016/j.legalmed.2012.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 12/21/2012] [Accepted: 12/26/2012] [Indexed: 11/21/2022]
Abstract
Forensic analysis of DNA from bone can be important in investigating a variety of cases involving violent crimes and mass fatality cases. To remove the potential presence of co-mingled remains and to eliminate contaminants that interfere with forensic DNA analysis, the outer surface of the bone fragment must be cleaned. This study evaluated two methods for processing bone specimens prior to DNA isolation. Mechanical sanding and enzymatic trypsin methods were compared in this study. The effects of these methods on the yield of DNA isolated and the quality of DNA analysis were studied. It was revealed that comparable values of DNA yields between the two methods were observed. Additionally, to evaluate the capabilities of the cleaning effect of the bone processing methods, the presence of polymerase chain reaction inhibitors in the DNA extracts was monitored using the internal positive control. Similar Ct values of the internal positive control were observed as the DNA extracts of the trypsin method compared with that of the sanding method. The characterization of the effects of the trypsin treatment on the quality of DNA profiling was also carried out. To evaluate the integrity of the nuclear DNA isolated, the percentage of allele calls and the peak-height values of alleles of the short tandem repeat profiles were compared between the two methods. A paired-sample t-test revealed no significant difference between the two methods. Our data suggested that the trypsin method can be used as an alternative cleaning method to mechanical cleaning methods. This method can be used to process multiple samples simultaneously. This can be very important for achieving high-throughput DNA isolation through potential automation, which can be extremely valuable for situations such as the forensic DNA analysis of skeletal remains from mass fatality incidents.
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Raimann PE, Picanço JB, Silva DS, Albuquerque TC, Paludo FJO, Alho CS. Procedures to recover DNA from pre-molar and molar teeth of decomposed cadavers with different post-mortem intervals. Arch Oral Biol 2012; 57:1459-66. [PMID: 23040740 DOI: 10.1016/j.archoralbio.2012.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 07/10/2012] [Accepted: 08/31/2012] [Indexed: 11/25/2022]
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Li R, Liriano L. A bone sample cleaning method using trypsin for the isolation of DNA. Leg Med (Tokyo) 2011; 13:304-8. [DOI: 10.1016/j.legalmed.2011.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/27/2011] [Accepted: 07/11/2011] [Indexed: 11/28/2022]
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Westen AA, Gerretsen RRR, Maat GJR. Femur, rib, and tooth sample collection for DNA analysis in disaster victim identification (DVI). Forensic Sci Med Pathol 2007; 4:15-21. [DOI: 10.1007/s12024-007-0027-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2007] [Indexed: 10/23/2022]
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Zehner R. “Foreign” DNA in tissue adherent to compact bone from tsunami victims. Forensic Sci Int Genet 2007; 1:218-22. [DOI: 10.1016/j.fsigen.2007.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 01/27/2007] [Indexed: 10/23/2022]
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Abstract
Anthropologists frequently encounter cases in which only partial human remains are recovered. This study reports how the percentage of the body recovered affects identification (ID) rates and cause and manner of death determination. A total of 773 cases involving anthropology consults were drawn from the New Mexico medical examiner's office (1974-2006). Results indicate a significant correlation between body percent recovered and ID rates, which ranged from 89% for complete bodies to 56% when less than half the body was present. Similar patterns were evident in cause/manner determination, which were the highest (83% and 79%, respectively) in complete bodies but declined to 40% when less than half the body was found. The absence of a skull also negatively impacted ID and ruling rates. Findings are compared with general autopsy ID rates (94-96%) and cause/manner determination rates (96-99%) as well as prior published rates for individual casework and mass death events.
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Affiliation(s)
- Debra A Komar
- Office of the Medical Investigator, MSC11 6030, and Department of Anthropology, MSC01 1040, University of New Mexico, Albuquerque, NM 87131-0001, USA.
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