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Haarkötter C, Gálvez X, Vinueza-Espinosa DC, Medina-Lozano MI, Saiz M, Lorente JA, Álvarez JC. A comparison of five DNA extraction methods from degraded human skeletal remains. Forensic Sci Int 2023; 348:111730. [PMID: 37224759 DOI: 10.1016/j.forsciint.2023.111730] [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: 03/24/2023] [Revised: 04/19/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023]
Abstract
Extracting DNA from degraded human remains poses a challenge for any forensic genetics laboratory, as it requires efficient high-throughput methods. While little research has compared different techniques, silica in suspension has been identified in the literature as the best method for recovering small fragments, which are often present in these types of samples. In this study, we tested five DNA extraction protocols on 25 different degraded skeletal remains. Including the humerus, ulna, tibia, femur, and petrous bone. The five protocols were organic extraction by phenol/chloroform/isoamyl alcohol, silica in suspension, High Pure Nucleic Acid Large Volume silica columns (Roche), InnoXtract™ Bone (InnoGenomics), and PrepFiler™ BTA with AutoMate™ Express robot (ThermoFisher). We analysed five DNA quantification parameters (small human target quantity, large human target quantity, human male target quantity, degradation index, and internal PCR control threshold), and five DNA profile parameters (number of alleles with peak height higher than analytic and stochastic threshold, average relative fluorescence units (RFU), heterozygous balance, and number of reportable loci) were analysed. Our results suggest that organic extraction by phenol/chloroform/isoamyl alcohol was the best performing method in terms of both quantification and DNA profile results. However, Roche silica columns were found to be the most efficient method.
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Affiliation(s)
- Christian Haarkötter
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - Xiomara Gálvez
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain.
| | - Diana C Vinueza-Espinosa
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - María Isabel Medina-Lozano
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - María Saiz
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - José Antonio Lorente
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
| | - Juan Carlos Álvarez
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11 Torre C Planta 9, 18016 Granada, Spain
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Date Chong M, Sheehan S, Battaglia J, Wescott DJ, Wallin J. Comparative study of Rapid DNA versus conventional methods on compromised bones. Forensic Sci Int Genet 2023; 63:102825. [PMID: 36592573 DOI: 10.1016/j.fsigen.2022.102825] [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: 08/15/2022] [Revised: 12/02/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022]
Abstract
Equivalent amounts of compromised bones were used to directly compare STR success of conventional and Rapid DNA methods. Conventional DNA extraction methods, including manual full demineralization and semi-automated PrepFiler BTA/ AutoMate Express (ThermoFisher Scientific), provided insights regarding the DNA quantity and extent of degradation of each compromised bone analyzed with ANDE 6C (ANDE Corp) and RapidHIT ID (ThermoFisher Scientific) Rapid systems. Full demineralization provided higher DNA yields than extraction with the AutoMate Express for quality control (QC) and environmentally challenged bones. The degradation indices ranged from ∼1.8 to 73. Both demineralization and AutoMate Express extracts benefited from additional clean-up with NucleoSpin XS devices, which usually resulted in more alleles being detected than without further clean-up. Complete "CODIS 20″ profiles could be obtained with bone QC1 with all methods. However, among the 14 compromised bones with low DNA content, complete CODIS 20 profiles were detected for 7, 4, and 0 bones analyzed with demineralization, AutoMate Express and ANDE methods, respectively. The RapidHIT ID was the least sensitive method, providing the fewest detectable alleles for the bones tested. Whereas extracted DNA of approximately 0.1 ng can yield complete GlobalFiler STR profiles, at least 30 ng was required for complete FlexPlex 27 profiles using the ANDE 6C Rapid DNA system. In addition to being less sensitive than conventional methods, the tested Rapid DNA approaches were less predictable when attempting to improve STR success and proved to be less reliable in genotyping accuracy.
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Affiliation(s)
- Mavis Date Chong
- State of California, Department of Justice, Jan Bashinski DNA Laboratory, 1001 W. Cutting Blvd, Richmond, CA 94804, USA.
| | - Sandra Sheehan
- State of California, Department of Justice, Jan Bashinski DNA Laboratory, 1001 W. Cutting Blvd, Richmond, CA 94804, USA
| | - Jessica Battaglia
- State of California, Department of Justice, Jan Bashinski DNA Laboratory, 1001 W. Cutting Blvd, Richmond, CA 94804, USA
| | - Daniel J Wescott
- Texas State University, Department of Anthropology, Forensic Anthropology Center, 601 University Drive, San Marcos, TX 78666, USA
| | - Jeanette Wallin
- State of California, Department of Justice, Jan Bashinski DNA Laboratory, 1001 W. Cutting Blvd, Richmond, CA 94804, USA
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Genealogy: The Tree Where History Meets Genetics. GENEALOGY 2021. [DOI: 10.3390/genealogy5040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Although biological relationships are a universal reality for all human beings, the concepts of “family” and “family bond” depend on both the geographic region and the historical moment to which they refer. However, the concept of “family” can be determinant in a large variety of societies, since it can influence the lines of succession, inheritances and social relationships, as well as where and with whom an individual is buried. The relation between a deceased person and other members of a community, other individuals of the same necropolis, or even with those who are buried in the same tomb can be analysed from the genetic point of view, considering different perspectives: archaeological, historical, and forensic. In the present work, the concepts of “family” and “kinship” are discussed, explaining the relevance of genetic analysis, such as nuclear and lineage markers, and their contribution to genealogical research, for example in the heritage of surnames and Y-chromosome, as well as those cases where some discrepancies with historical record are detected, such as cases of adoption. Finally, we explain how genetic genealogical analyses can help to solve some cold cases, through the analysis of biologically related relatives.
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Mckinnon M, Henneberg M, Higgins D. A review of the current understanding of burned bone as a source of DNA for human identification. Sci Justice 2021; 61:332-338. [PMID: 34172121 DOI: 10.1016/j.scijus.2021.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/16/2021] [Accepted: 03/13/2021] [Indexed: 10/21/2022]
Abstract
Identification of incinerated human remains may rely on genetic analysis of burned bone which can prove far more challenging than fresh tissues. Severe thermal insult results in the destruction or denaturation of DNA in soft tissues, however genetic material may be preserved in the skeletal tissues. Considerations for DNA retrieval from these samples include low levels of exogenous DNA, the dense, mineralised nature of bone, and the presence of contamination, and qPCR inhibitors. This review collates current knowledge in three areas relating to optimising DNA recovery from burned bone: 1) impact of burning on bone and subsequent effects on sample collection, 2) difficulties of preparing burned samples for DNA extraction, and 3) protocols for bone decalcification and DNA extraction. Bone decalcification and various DNA extraction protocols have been tested and optimised for ancient bone, suggesting that prolonged EDTA (Ethylenediaminetetraacetic acid) demineralisation followed by solid-phased silica-based extraction techniques provide the greatest DNA yield. However, there is significantly less literature exploring the optimal protocol for incinerated bones. Although burned bone, like ancient and diagenetic bone, can be considered "low-copy", the taphonomic processes occurring are likely different. As techniques developed for ancient samples are tailored to deal with bone that has been altered in a particular way, it is important to understand if burned bone undergoes similar or different changes. Currently the effects of burning on bone and the DNA within it is not fully understood. Future research should focus on increasing our understanding of the effects of heat on bone and on comparing the outcome of various DNA extraction protocols for these tissues.
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Affiliation(s)
- Meghan Mckinnon
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Adelaide, Australia.
| | - Maciej Henneberg
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Adelaide, Australia
| | - Denice Higgins
- Forensic Odontology Unit, Adelaide Dental School, the University of Adelaide, Adelaide, Australia
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5
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Grela M, Jakubczak A, Kowalczyk M, Listos P, Gryzińska M. Effectiveness of various methods of DNA isolation from bones and teeth of animals exposed to high temperature. J Forensic Leg Med 2021; 78:102131. [PMID: 33561692 DOI: 10.1016/j.jflm.2021.102131] [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: 11/16/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 11/17/2022]
Abstract
In the event of fires, natural disasters, and other events associated with high temperature, bones and teeth are the only source of genetic material for identifying human or animal carcasses. To obtain reliable final results of identification tests, the use of appropriate nucleic acid extraction methods is crucial. Therefore, the main objective of this research was to evaluate the effectiveness of selected methods of DNA isolation from animal burnt bones and teeth. In addition, the effect of the duration of high temperature on the stability of nuclear and mitochondrial DNA in these tissues was determined, as well as the possibility of using the genetic material obtained for species identification of remains of unknown origin. Bones and teeth collected during necropsy of dogs were burnt in a laboratory oven at 400 °C (752 °F; 673.15 K) for 5, 10, 15, 30, 45 and 60 min. DNA was isolated according to four different protocols, using three commercial kits, i.e. the PrepFiler® Forensic DNA Extraction Kit from Applied Biosystems, the QIAamp® DNA Investigator Kit from QIAGEN, and the DNA Mini Kit from Syngen, as well as a classic organic method. The effectiveness of these methods was compared by assessing the amount of isolated DNA using Real-Time PCR and its purity using a NanoDrop™ spectrophotometer. Each isolate was also subjected to PCR with primers designed to amplify fragments of dog mitochondrial DNA. The effectiveness of species identification was assessed for the method showing the best DNA recovery and for the organic method, considered the gold standard for analysis of difficult material. The QIAamp® DNA Investigator Kit showed the highest efficiency of DNA isolation from bones and teeth burnt for 15 min (the longest burning time for which DNA could still be recovered from bones and teeth). The results of the experiment clearly indicate that DNA stability in hard tissues depends on how long they burn. In the case of exposure to 400 °C, reliable genetic testing, including species identification, is possible when the burning time does not exceed 15 min. Among the hard tissues examined, bones proved more suitable than teeth for identification purposes. It was also concluded that identification of bone remains with extreme heat damage should be based on mitochondrial DNA analysis.
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Affiliation(s)
- Małgorzata Grela
- Department and Clinic of Animal Internal Diseases, Sub-Department of Pathomorphology and Forensic Medicine, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Głęboka 30, 20-612, Lublin, Poland.
| | - Andrzej Jakubczak
- Institute of Biological Basis of Animal Production, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland.
| | - Marek Kowalczyk
- Institute of Quality Evaluation and Processing of Animal Products, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland.
| | - Piotr Listos
- Department and Clinic of Animal Internal Diseases, Sub-Department of Pathomorphology and Forensic Medicine, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Głęboka 30, 20-612, Lublin, Poland.
| | - Magdalena Gryzińska
- Institute of Biological Basis of Animal Production, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland.
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Booncharoen P, Khacha-ananda S, Kanchai C, Ruengdit S. Factors influencing DNA extraction from human skeletal remains: bone characteristic and total demineralization process. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2021. [DOI: 10.1186/s41935-021-00216-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The extraction of DNA from skeletal remains with good quality and quantity is often challenging for the ability to generate DNA typing. Previous studies demonstrated the DNA extraction with total demineralization from fresh teeth and bones; however, the application in old skeletal remains has been less performed. To obtain good quality and high yield of DNA amount extracted from skeletal remains, the objective of this study was focused on exploring the factors influencing the total demineralization process to obtain developing effective methods.
Results
The concentration of EDTA was found to significantly enhance calcium chelation from the bone while pH of EDTA solution, incubation temperature, incubation time, and volume of EDTA solution were not significant. The optimal condition of total demineralization obtained from Placket-Burmann results represented good-quality DNA and the highest concentration of extracted DNA yield. Subsequently, the STR typing in some bone specimens processed by total demineralization process prior to DNA extraction was improved.
Conclusions
EDTA concentration was a key influencing factor on the total demineralization process to chelate calcium from human skeletal remains. The total demineralization process in old bone specimens probably improved the STR profiles.
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Calacal GC, Gallardo BG, Apaga DLT, De Ungria MCA. Improved autosomal STR typing of degraded femur samples extracted using a custom demineralization buffer and DNA IQ™. Forensic Sci Int Synerg 2021; 3:100131. [PMID: 33532721 PMCID: PMC7829153 DOI: 10.1016/j.fsisyn.2020.100131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/18/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022]
Abstract
Bone samples are utilized as a source of DNA in disaster victim identification and human remains investigations. However, DNA recovery from bones is time consuming and prone to contamination. A logical approach for postmortem identification is to validate efficient DNA extraction methods requiring less bone material using improved molecular kits with less hands-on time and workflows that facilitate faster turn-around time for processing. In this study, we evaluated DNA yield and amplification efficiency of DNA extracts using a new custom bone demineralization buffer (DMB; Promega) and extracted via manual and automated DNA IQ™ workflows. Including the demineralization step, the bone protocol can be completed in ∼4 h and even less with minimal sample handling when automated. Overall, a rapid and simple DNA extraction with improved allele recovery was validated using degraded bone samples exposed to tropical environments and post-disaster recovery as well as adverse conditions of embalming prior to internment.
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Affiliation(s)
- Gayvelline C. Calacal
- DNA Analysis Laboratory, Natural Sciences Research Institute, Miranda Hall, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Bea G. Gallardo
- DNA Analysis Laboratory, Natural Sciences Research Institute, Miranda Hall, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Dame Loveliness T. Apaga
- DNA Analysis Laboratory, Natural Sciences Research Institute, Miranda Hall, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Maria Corazon A. De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, Miranda Hall, University of the Philippines, Diliman, 1101, Quezon City, Philippines
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Quintin DM, Scheinman JE, Adamowicz MS, San Pietro D. Assessment of PowerPlex® Fusion 5C's ability to type degraded DNA. Sci Justice 2020; 60:423-431. [PMID: 32873382 DOI: 10.1016/j.scijus.2020.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/19/2020] [Accepted: 05/25/2020] [Indexed: 11/18/2022]
Abstract
DNA samples collected at crime scenes are often degraded so this research focused on the ability of the Promega PowerPlex® Fusion 5C amplification kit to type both naturally and artificially degraded DNA. DNA was degraded naturally by placing equal volumes of blood on white fabric that was stored either inside, outside in a shaded area, or outside in direct sunlight. Samples were then collected every 10 days for 60 days and the DNA extracted (QIAamp® DNA Investigator). Artificially degraded samples were created by exposing extracted DNA to either UV light or 95 °C heat for varying times. DNA was also degraded artificially by placing blood samples into a 50% bleach solution for varying times prior to extraction. Following sample treatment, standard forensic DNA analysis was performed including quantification (Investigator® Quantiplex) and amplification (PowerPlex® Fusion 5C). Separation and detection were performed on an ABI 3130xl capillary electrophoresis unit and analysis was performed using GeneMapper ID v3.2.1. While the time and shade samples showed similar amounts of degradation, the samples exposed to direct sun showed more degradation. The artificially degraded samples showed more signs of degradation such as reduced overall peak height and peak height imbalance at heterozygous loci. There were also some cases where an allele that was known to be in the profile exhibited total dropout. Although there were some instances of both allelic dropout and heterozygote peak imbalance, PowerPlex® Fusion was able to reliably type degraded DNA as all alleles detected were consistent with the known donor profile. The results show that PowerPlex® Fusion is a robust kit capable of handling forensically challenged samples.
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Affiliation(s)
- Danielle M Quintin
- Henry C. Lee College, University of New Haven, Dodds Hall, 300 Boston Post Road, West Haven, CT 06516, USA
| | - John E Scheinman
- Connecticut-DESPP, Division of Scientific Services, 278 Colony Street, Meriden, CT 06451, USA
| | - Michael S Adamowicz
- College of Agricultural Sciences & Natural Resources, University of Nebraska-Lincoln, 103 Agriculture Hall, Lincoln, NE 68583-0702, USA
| | - David San Pietro
- Henry C. Lee College, University of New Haven, Dodds Hall, 300 Boston Post Road, West Haven, CT 06516, USA.
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9
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Saragoni VG, Celis RC, Intriago M, Melillán-Sanzana AA, Reyes P, Prieto L, Gill P. Overcoming the undetected inhibition of bone DNA extracts obtained by total demineralization. Forensic Sci Int Genet 2020; 48:102363. [DOI: 10.1016/j.fsigen.2020.102363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
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10
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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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Hasap L, Chotigeat W, Pradutkanchana J, Vongvatcharanon U, Kitpipit T, Thanakiatkrai P. A novel, 4-h DNA extraction method for STR typing of casework bone samples. Int J Legal Med 2020; 134:461-471. [PMID: 31897668 DOI: 10.1007/s00414-019-02232-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/11/2019] [Indexed: 10/25/2022]
Abstract
Bones are often found in mass grave crime scene. To increase DNA identification success rates, a highly efficient DNA extraction method should be selected. Several DNA extraction methods for human bones have been published yet never been systematically compared, and some are time-consuming or complex. As such, a quick and highly efficient DNA extraction method was developed and compared with three published methods (Hi-Flow silica-based, total demineralization (TD) and PrepFiler BTA) using 70 fresh and 22 casework bones from different body parts. The highest median DNA concentrations were obtained from developed method (135.85 ng/μL and 0.224 ng/μL for fresh and casework bones, respectively). For residual PCR inhibitors, the threshold cycle (Ct) of the internal positive control (IPC) showed that developed method and PrepFiler BTA removed most PCR inhibitors. Similarly, 95.45% of casework STR profiles obtained using the developed protocol meet the standard requirements for Australian National Criminal Investigative DNA Database (NCIDD) entry, followed by 86.35% using TD, 81.82% using PrepFiler BTA, and 45.45% using Hi-Flow. Additionally, DNA extracts from seven different bones revealed that the 1st distal phalange of the hand contained the highest DNA concentration of 338.43 ng/μL, which was three times higher than the tibia and femur. Our findings suggest that developed method was highly efficient for casework bone analysis. It significantly reduced the extraction processing time down to 4 h and is two to four times cheaper compared with other methods. In practice, both the extraction method and the bone sampling must be considered by a forensic DNA analyst to increase the chances of successful identification.
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Affiliation(s)
- Laila Hasap
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Wilaiwan Chotigeat
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Jintana Pradutkanchana
- Forensic Medicine and Toxicology Unit, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Uraporn Vongvatcharanon
- Department of Anatomy, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Thitika Kitpipit
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand
| | - Phuvadol Thanakiatkrai
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, 90112, Thailand.
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Zupanič Pajnič I, Obal M, Zupanc T. Identifying victims of the largest Second World War family massacre in Slovenia. Forensic Sci Int 2020; 306:110056. [DOI: 10.1016/j.forsciint.2019.110056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/25/2023]
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13
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Hasap L, Chotigeat W, Pradutkanchana J, Asawutmangkul W, Kitpipit T, Thanakiatkrai P. Comparison of two DNA extraction methods: PrepFiler® BTA and modified PCI-silica based for DNA analysis from bone. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Caldeira M, Bento A, Gouveia N, Brito P, Porto M. Evaluation of DNA levels recovered from forensic bone samples through the optimization of a semi-automated extraction method. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Harrel M, Hughes-Stamm S. A Powder-free DNA Extraction Workflow for Skeletal Samples. J Forensic Sci 2019; 65:601-609. [PMID: 31577371 DOI: 10.1111/1556-4029.14197] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/28/2019] [Accepted: 08/31/2019] [Indexed: 12/01/2022]
Abstract
The processing of skeletal material poses several challenges for forensic laboratories. Current methods can be laborious, time-consuming, require dedicated equipment, and are vulnerable to contamination. In this study, various sample mass (1 × 50 mg, 3 × 50 mg, and 1 × 150 mg chip(s)) and incubation times (2, 4, and 16 h) were tested using the PrepFiler® BTA™ Forensic DNA Extraction Kit to digest whole bone chips in lieu of powdering. The most effective method was then applied to bones and tooth fragments collected from contemporary human cadavers exposed to various environmental conditions using an automated platform. Over a third of the samples tested generated full DNA profiles without having to powder the bone/tooth fragment or further alter the manufacturer's protocol. However, for most samples resulting in incomplete STR profiles due to low amounts of DNA, slightly better results were achieved with powdered tissue. Overall, this work demonstrates the potential use of a faster, nonpowdering DNA extraction method for processing skeletal samples as an effective first-pass screening tool.
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Affiliation(s)
- Michelle Harrel
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, 77340
| | - Sheree Hughes-Stamm
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, 77340.,School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St. Lucia, QLD, 4072, Australia
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Caputo M, Corach D. Reply to comment “A DNA extraction method of small quantities of bone for high-quality genotyping”. Forensic Sci Int Genet 2019; 41:e18-e19. [DOI: 10.1016/j.fsigen.2019.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 11/26/2022]
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17
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Comment on 'A DNA extraction method for small quantities of bone for high-qualitygenotyping' by Caputo et al. Forensic Sci Int Genet 2019; 40:e243-e244. [PMID: 30770290 DOI: 10.1016/j.fsigen.2019.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/30/2018] [Accepted: 01/30/2019] [Indexed: 01/20/2023]
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18
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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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19
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Dash HR, Das S. Microbial Degradation of Forensic Samples of Biological Origin: Potential Threat to Human DNA Typing. Mol Biotechnol 2018; 60:141-153. [PMID: 29214499 DOI: 10.1007/s12033-017-0052-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Forensic biology is a sub-discipline of biological science with an amalgam of other branches of science used in the criminal justice system. Any nucleated cell/tissue harbouring DNA, either live or dead, can be used as forensic exhibits, a source of investigation through DNA typing. These biological materials of human origin are rich source of proteins, carbohydrates, lipids, trace elements as well as water and, thus, provide a virtuous milieu for the growth of microbes. The obstinate microbial growth augments the degradation process and is amplified with the passage of time and improper storage of the biological materials. Degradation of these biological materials carriages a huge challenge in the downstream processes of forensic DNA typing technique, such as short tandem repeats (STR) DNA typing. Microbial degradation yields improper or no PCR amplification, heterozygous peak imbalance, DNA contamination from non-human sources, degradation of DNA by microbial by-products, etc. Consequently, the most precise STR DNA typing technique is nullified and definite opinion can be hardly given with degraded forensic exhibits. Thus, suitable precautionary measures should be taken for proper storage and processing of the biological exhibits to minimize their decaying process by micro-organisms.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, Madhya Pradesh, 470001, India
| | - Surajit Das
- Department of Life Science, Laboratory of Environmental Microbiology and Ecology (LEnME), National Institute of Technology, Rourkela, Odisha, 769008, India.
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Harrel M, Gangitano D, Hughes-Stamm S. The effects of extra PCR cycles when amplifying skeletal samples with the GlobalFiler ® PCR Amplification Kit. Int J Legal Med 2018; 133:745-750. [PMID: 29845343 DOI: 10.1007/s00414-018-1860-2] [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: 03/20/2018] [Accepted: 05/11/2018] [Indexed: 11/29/2022]
Abstract
When samples with low amounts of DNA are amplified using short tandem repeats (STRs), stochastic effects such as allele and locus dropout or drop-in, allele imbalance, and increased stutter often occur making data interpretation more difficult. The most common approach to improving STR results from low template samples is to increase the number of PCR cycles. Although more alleles may be recovered, stochastic effects may be exaggerated resulting in more complicated STR profiles. This work reports the effect of additional PCR cycles (29 vs. 30, 31, and 32) on STR success from environmentally challenged bone and tooth samples using the GlobalFiler® DNA Amplification Kit (Thermo Fisher Scientific). In addition, we compared the efficiency of two DNA extraction kits for skeletal samples: QIAamp® DNA Investigator (QIAGEN) and PrepFiler® BTA™ Forensic DNA Extraction (Thermo Fisher Scientific) kits. Results showed that more DNA was recovered from samples using the PrepFiler® BTA™ kit; but regardless of the extraction method, the number of alleles detected and the peak heights both increased with an increase in PCR cycle number. Although more alleles were reported in almost all samples, the most notable improvement was observed in samples with the DNA template < 120 pg. A general increase in the number of PCR artifacts was detected in STR profiles generated using 30-32 cycles. Overall, this study provides supporting evidence that STR profile completeness and quality may be improved when low template skeletal samples are amplified with extra PCR cycles (up to 32 cycles) using the GlobalFiler® DNA Amplification Kit.
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Affiliation(s)
- Michelle Harrel
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA.
| | - David Gangitano
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA
| | - Sheree Hughes-Stamm
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA
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Harrel M, Mayes C, Gangitano D, Hughes-Stamm S. Evaluation Of A Powder-Free DNA Extraction Method For Skeletal Remains. J Forensic Sci 2018; 63:1819-1823. [PMID: 29411392 DOI: 10.1111/1556-4029.13749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/27/2017] [Accepted: 01/15/2018] [Indexed: 11/26/2022]
Abstract
Bones are often recovered in forensic investigations, including missing persons and mass disasters. While traditional DNA extraction methods rely on grinding bone into powder prior to DNA purification, the TBone Ex buffer (DNA Chip Research Inc.) digests bone chips without powdering. In this study, six bones were extracted using the TBone Ex kit in conjunction with the PrepFiler® BTA™ DNA extraction kit (Thermo Fisher Scientific) both manually and via an automated platform. Comparable amounts of DNA were recovered from a 50 mg bone chip using the TBone Ex kit and 50 mg of powdered bone with the PrepFiler® BTA™ kit. However, automated DNA purification decreased DNA yield (p < 0.05). Nevertheless, short tandem repeat (STR) success was comparable across all methods tested. This study demonstrates that digestion of whole bone fragments is an efficient alternative to powdering bones for DNA extraction without compromising downstream STR profile quality.
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Affiliation(s)
- Michelle Harrel
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, 77340
| | - Carrie Mayes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, 77340
| | - David Gangitano
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, 77340
| | - Sheree Hughes-Stamm
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, TX, 77340
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Neither femur nor tooth: Petrous bone for identifying archaeological bone samples via forensic approach. Forensic Sci Int 2018; 283:144-149. [DOI: 10.1016/j.forsciint.2017.12.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/12/2017] [Indexed: 11/22/2022]
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23
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Liu Q, Liu L, Zhang M, Zhang Q, Wang Q, Ding X, Shao L, Zhou Z, Wang S. A Simple and Efficient Method of Extracting DNA from Aged Bones and Teeth. J Forensic Sci 2017; 63:824-828. [PMID: 29240980 DOI: 10.1111/1556-4029.13603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 04/27/2017] [Accepted: 07/03/2017] [Indexed: 11/30/2022]
Abstract
DNA is often difficult to extract from old bones and teeth due to low levels of DNA and high levels of degradation. This study established a simple yet efficient method for extracting DNA from 20 aged bones and teeth (approximately 60 years old). Based on the concentration and STR typing results, the new method of DNA extraction (OM) developed in this study was compared with the PrepFiler™ BTA Forensic DNA Extraction Kit (BM). The total amount of DNA extracted using the OM method was not significantly different from that extracted using the commercial kit (p > 0.05). However, the number of STR loci detected was significantly higher in the samples processed using the OM method than using the BM method (p < 0.05). This study aimed to establish a DNA extraction method for aged bones and teeth to improve the detection rate of STR typing and reduce costs compared to the BM technique.
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Affiliation(s)
- Qiqi Liu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Liyan Liu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Minli Zhang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qingzhen Zhang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qiong Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xiaoran Ding
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Liting Shao
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Zhe Zhou
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
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Corrêa HSD, Pedro FLM, Volpato LER, Pereira TM, Siebert Filho G, Borges ÁH. Forensic DNA typing from teeth using demineralized root tips. Forensic Sci Int 2017; 280:164-168. [DOI: 10.1016/j.forsciint.2017.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/28/2017] [Accepted: 10/04/2017] [Indexed: 10/18/2022]
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Alghafri R, Zupanič Pajnič I, Zupanc T, Balažic J, Shrivastava P. Rapidly mutating Y-STR analyses of compromised forensic samples. Int J Legal Med 2017; 132:397-403. [PMID: 28466124 DOI: 10.1007/s00414-017-1600-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/24/2017] [Indexed: 11/25/2022]
Abstract
Rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) were identified to improve differentiation of unrelated males and also to enable separating closely and distantly related males in human identity testing in forensic and other applications. RM-Yplex assay was developed as a single multiplex that is capable of simultaneously amplifying all currently known RM Y-STRs, and reproducibility and sensitivity testing were performed on reference samples. Additional analyses are necessary to test its suitability for analysing compromised forensic samples. For this purpose, we applied the RM-Yplex assay to approximately 70-year-old skeletons that were used as a model for poorly preserved, challenging forensic samples. We analysed 57 male skeletal remains (bones and teeth) from 55 skeletons excavated from the Second World War (WWII) mass graves in Slovenia. The RM-Yplex typing was successful in all 57 samples; there were 56% full profiles obtained, and in partial profiles, up to 7 locus drop-outs were observed and they appeared correlated with low DNA quantities and degradation of DNA obtained from WWII bone and tooth samples. The longest loci, DYS403S1b, DYS547, DYS627 and DYS526b, were the most often dropped-out RM Y-STRs. In spite of high frequency of drop-out events, the RM-Yplex typing was successful in all WWII samples, showing the possibility of successful amplification of at least half of the RM Y-STRs even from the most compromised samples analysed.
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Affiliation(s)
- Rashed Alghafri
- General Department of Forensic Sciences and Criminology, Dubai Police General Head Quarters, Al Tawar 1, Dubai, United Arab Emirates
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Jože Balažic
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Govt. of Madhya Pradesh, Sagar, 470001, India
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Zupanič Pajnič I, Zupanc T, Balažic J, Geršak ŽM, Stojković O, Skadrić I, Črešnar M. Prediction of autosomal STR typing success in ancient and Second World War bone samples. Forensic Sci Int Genet 2017; 27:17-26. [DOI: 10.1016/j.fsigen.2016.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/08/2016] [Accepted: 11/18/2016] [Indexed: 01/31/2023]
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27
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Chaitanya L, Pajnič IZ, Walsh S, Balažic J, Zupanc T, Kayser M. Bringing colour back after 70 years: Predicting eye and hair colour from skeletal remains of World War II victims using the HIrisPlex system. Forensic Sci Int Genet 2016; 26:48-57. [PMID: 27780108 DOI: 10.1016/j.fsigen.2016.10.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 09/26/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
Abstract
Retrieving information about externally visible characteristics from DNA can provide investigative leads to find unknown perpetrators, and can also help in disaster victim and other missing person identification cases. Aiming for the application to both types of forensic casework, we previously developed and forensically validated the HIrisPlex test system enabling parallel DNA prediction of eye and hair colour. Although a recent proof-of-principle study demonstrated the general suitability of the HIrisPlex system for successfully analysing DNA from bones and teeth of various storage times and conditions, practical case applications to human remains are scarce. In this study, we applied the HIrisPlex system to 49 DNA samples obtained from bones or teeth of World War II victims excavated at six sites, mostly mass graves, in Slovenia. PCR-based DNA quantification ranged from 4pg/μl to 313pg/μl and on an average was 41pg/μl across all samples. All 49 samples generated complete HIrisPlex profiles with the exception of one MC1R DNA marker (N29insA) missing in 83.7% of the samples. In 44 of the 49 samples (89.8%) complete 15-loci autosomal STR (plus amelogenin) profiles were obtained. Of 5 pairs of skeletal remains for which STR profiling suggested an origin in the same individuals, respectively, 4 showed the same HIrisPlex profiles and predicted eye and hair colours, respectively, while discrepancies in one pair (sample 26 and 43) are likely to be explained by DNA quantity and quality issues observed in sample 43. Sample 43 had the lowest DNA concentration of only 4pg/μl, producing least reliable STR results and could be misleading in concluding that samples 43 and 26 originate from the same individual. The HIrisPlex-predicted eye and hair colours from two skeletal samples, suggested to derive from two brothers via STR profiling together with a living sister, were confirmed by the living sister's report. Overall, we demonstrate that after more than 70 years, HIrisPlex-based eye and hair colour prediction from skeletal remains is feasible with high success rate. Our results further encourage the use of the HIrisPlex system in missing person/disaster victim identification to aid the identification process in cases where ante-mortem samples or putative relatives are not directly available, and DNA predicted eye and hair colour information provides leads for locating them, allowing STRbased individual identification.
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Affiliation(s)
- Lakshmi Chaitanya
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Jože Balažic
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
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28
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Abstract
In recent years the recovery and analysis of DNA from skeletal remains has been applied to several contexts ranging from disaster victim identification to the identification of the victims of conflict. Here are described procedures for processing the bone and tooth samples including mechanical and chemical cleaning, cutting and powdering in the presence of liquid nitrogen, complete demineralization of bone and tooth powder, DNA extraction, DNA purification using magnetic beads, and the precautions and strategies implemented to avoid and detect contamination. It has proven highly successful in the analysis of bones and teeth from Second World War victims' skeletal remains that have been excavated from mass graves in Slovenia and is also suitable for genetic identification of relatively fresh human remains.
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Affiliation(s)
- Irena Zupanič Pajnič
- Laboratory of Molecular Genetics, Institute of Forensic Medicine, Vrazov trg 2, 1104, Ljubljana, Slovenia.
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