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C Zapico S, Matos S, Conte J. Assessment of the efficiency of DNA isolation and profiling applying a temperature-driven method in human remains. Electrophoresis 2024; 45:805-813. [PMID: 38247192 DOI: 10.1002/elps.202300273] [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: 11/28/2023] [Revised: 01/02/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
The identification of human remains is of utmost importance in a variety of scenarios. One of the primary identification methods is DNA. DNA extraction from human remains could be difficult, particularly in situations where the remains have been exposed to environmental conditions and other insults. Several studies tried to improve extraction by applying different approaches. ForensicGEM Universal (MicroGem) is a single-tube approach to DNA extraction and a temperature-driven method that could have some advantages with respect to previous techniques, among them, reducing the risk of contamination, not requiring specialized equipment, or several steps to perform. The aim of this study was to assess, for the first time, the efficiency of DNA extraction and quality of STR profiles applying the MicroGem protocol and modifications of this protocol from tooth samples in comparison with automatic extraction (AE). Our results indicated that AE and MicroGem performed similar, though with variability depending on the MicroGem modifications, increasing the DNA yield and STR profile quality when DNA is concentrated with Microcon. These findings demonstrated the efficiency of this methodology for DNA extraction from human remains while also providing a simple and quick technique suitable to apply in a variety of forensic scenarios.
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Affiliation(s)
- Sara C Zapico
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA
- National Museum of Natural History, Anthropology Department and Laboratories of Analytical Biology, Smithsonian Institution, Washington, District of Columbia, USA
| | - Shayla Matos
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Jillian Conte
- Conte Forensic Consulting, LLC, Peckville, Pennsylvania, USA
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Wei YF, Lin CY, Yu YJ, Linacre A, Lee JCI. DNA identification from dental pulp and cementum. Forensic Sci Int Genet 2023; 67:102945. [PMID: 37844374 DOI: 10.1016/j.fsigen.2023.102945] [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: 05/08/2023] [Revised: 09/03/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
Teeth are one of the body tissues remaining after severe decomposition from which a DNA profile can be obtained to aid in human identification. Currently, the standard approach to isolate DNA from teeth requires pulverizing the entire tooth. This destructive approach compromises any further morphological or anthropological study. We report on two methods of DNA isolation that minimizes destruction of the tooth when accessing the DNA within pulp and cementum. Forty-nine teeth, removed as part of normal dental procedures, were buried for up to 92 days, with a further nine teeth acting as unburied controls. Additionally, four teeth samples collected during a forensic examination were included in this study. The two processes were: using a fine drill to access the pulp from the crown and then using endodontic files to collect the biological material; and using a sterile blade to scrape the cementum. It was found that the samples collected from the cementum had greater DNA quality compared to those samples obtained from the pulp. Microbial activity was found to play a role in the degradation of the nuclear material, reducing DNA yields from pulp. DNA profiling data from 24 loci, including 22 STR markers, indicated that multi-rooted teeth provided better DNA quantity and quality than those with a single root. The DNA quantity obtained from pulp samples of teeth which exhibited cavities was adversely affected, although this DNA loss was not from samples collected from the cementum of teeth in similar condition. Obtaining samples from DNA profiling from the cementum was found to be ideal if the morphological preservation of the tooth is required. Obtaining pathogen DNA is of interest when an occlusal approach to retrieve pulp may serve as a good alternative to prepare DNA without destruction of the tooth structure.
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Affiliation(s)
- Yi-Feng Wei
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan
| | - Chun-Yen Lin
- Institute of Forensic Medicine, Ministry of Justice, New Taipei City 23016, Taiwan
| | - Yu-Jen Yu
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide 5001, Australia
| | - James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei 10051, Taiwan.
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Examination of human osteoarchaeological remains as a feasible source of polar and apolar metabolites to study past conditions. Sci Rep 2023; 13:696. [PMID: 36639564 PMCID: PMC9839756 DOI: 10.1038/s41598-023-27401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
Metabolomics is a modern tool that aids in our understanding of the molecular changes in organisms. Archaeological science is a branch of archaeology that explores different archaeological materials using modern analytical tools. Human osteoarchaeological material are a frequent finding in archaeological contexts and have the potential to offer information about previous human populations, which can be illuminating about our current condition. Using a set of samples comprising different skeletal elements and bone structures, here we explore for the first time the possibility of extracting metabolites from osteoarchaeological material. Here, a protocol for extraction and measurement of extracted polar and less-polar/apolar metabolites by ultra-high performance liquid chromatography hyphenated to high resolution mass spectrometry is presented to measure the molecules separated after a reversed phase and hydrophilic interaction liquid chromatography column. Molecular information was obtained, showing that osteoarchaeological material is a viable source of molecular information for metabolomic studies.
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Rahmat RA, Humphries MA, Linacre AMT, Malik A, Saedon NA, Austin JJ. Freeze-drying improves DNA yield from teeth. Forensic Sci Int 2021; 326:110938. [PMID: 34343942 DOI: 10.1016/j.forsciint.2021.110938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
The common method of preparing teeth prior to DNA extraction involves cleaning, decontamination, drying and pulverisation. Moisture in post-mortem teeth can promote bacterial growth and hydrolytic damage that could contribute to DNA degradation, whilst also possibly reducing the efficiency of sample pulverisation and DNA release. Here we compared DNA extraction from pig teeth, with- and without freeze-drying, to examine the impact of removing moisture on DNA yield. Quantitative real-time polymerase chain reaction (qPCR) was used to quantify an 83 bp mitochondrial DNA fragment and two nuclear DNA fragments of 82 bp and 150 bp. The comparative results showed that sample preparation with freeze-drying resulted in a higher DNA yield without compromising the DNA quality. This study highlights the advantage of incorporating a freeze-drying to improve the DNA yield and minimising the loss of DNA during sample preparation of teeth.
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Affiliation(s)
- Rabiah A Rahmat
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur 50603, Malaysia; School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5006, Australia.
| | - Melissa A Humphries
- School of Mathematical Sciences, Faculty of Engineering, Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia 5006, Australia; ARC Centre of Excellence for Mathematical and Statistical Frontiers, University of Adelaide, Adelaide, South Australia, Australia.
| | - Adrian M T Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia.
| | - Arif Malik
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5006, Australia.
| | - Nor A Saedon
- Forensic DNA Division, Forensic Science Analysis Centre, Department of Chemistry, Selangor 46661, Malaysia.
| | - Jeremy J Austin
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5006, Australia.
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Thornton I, Cartozzo C, Mays D, Singh B, Simmons T. Development of a quantitative PCR-based method for studying temporal DNA degradation in waterlogged bone. J Forensic Sci 2020; 66:1114-1123. [PMID: 33275292 DOI: 10.1111/1556-4029.14641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/31/2020] [Accepted: 11/10/2020] [Indexed: 11/27/2022]
Abstract
While several studies have examined temporal DNA degradation in bones collected from terrestrial environments, studies on temporal DNA degradation in bones collected from aquatic environments are limited and mostly based on case studies. The objective of this study was to assess the impact of long-term submersion, aquatic environment, bone type and DNA extraction method on DNA quality and quantity. Bone samples (scapulae and ribs), collected every ~1000 ADD from a freshwater lake and river, underwent DNA extraction via ChargeSwitch® gDNA Plant Kit and organic phenol-chloroform methods, and DNA quantitation using both TaqMan and SYBR Green-based quantitative PCR (qPCR) methods. Results suggest that in both bone types, quality of recovered DNA (i.e., degradation index) declined significantly with increase in submersion time. Among two bone types, quality of recovered DNA from scapulae declined faster than rib samples. There was no significant difference in recovered DNA quantity between bone types, DNA extraction methods, or locations but various interactions between these variables showed significant difference. Overall, it can be concluded that DNA can be extracted from waterlogged bone in sufficient quantity to generate an STR profile up to 4000 ADD.
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Affiliation(s)
- Isis Thornton
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Claire Cartozzo
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - D'Arcy Mays
- Department of Statistics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Baneshwar Singh
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Tal Simmons
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
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Inostroza C, Carrasco P, Godoy M, Gatti G, Paulino B. Dental Forensic Kit (DFK®) and Quick Extract™ FFPE DNA extraction kit, a new workflow for obtaining dental DNA for human genetic identity. J Forensic Leg Med 2020; 73:101992. [DOI: 10.1016/j.jflm.2020.101992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/18/2020] [Accepted: 05/23/2020] [Indexed: 10/24/2022]
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Edson SM. The effect of chemical compromise on the recovery of DNA from skeletonized human remains: A study of three World War II era incidents recovered from tropical locations. Forensic Sci Med Pathol 2019; 15:10.1007/s12024-019-00179-2. [PMID: 31712986 DOI: 10.1007/s12024-019-00179-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 12/21/2022]
Abstract
The use of DNA extracted from skeletonized human remains is a common challenge for those working in human identification. Thermal age and chemical compromise should be considered prior to performing DNA testing on skeletonized remains. Both heat and chemical contamination may cause damage to the DNA present in the osseous materials and a subsequent increase in both the difficulty and expense of DNA testing. For this study, three World War II era mass fatality events involving the US military, the USS Oklahoma, the Battle of Tarawa, and the Cabanatuan Prison Camps, were examined for the overall success of DNA testing using five DNA modalities: Sanger sequencing of mitochondrial DNA, AmpFlSTR® MiniFiler™; PowerPlex® Fusion; a modified AmpFlSTR® Yfiler™; and a Next Generation Sequencing (NGS) protocol. Decedents from the three chosen incidents were buried in tropical environments and have the same approximate post mortem interval of 75 years, however, the chemical conditions that decedents were exposed to at each of the incidents vary. Remains from the USS Oklahoma were soaked in fuel oil and salt water immediately post-mortem; Cabanatuan Prison Camp remains were treated with a 'hardening' compound; and those from the Battle of Tarawa were not treated. Skeletal elements from each incident were compared across the 5 tested DNA modalities for success. Chemical insult to skeletal materials appears to have the greatest impact on every modality of DNA testing examined.
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Affiliation(s)
- Suni M Edson
- Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System, Dover AFB, Dover, DE, USA.
- College of Science and Engineering, Flinders University, Adelaide, South Australia.
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