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Oh CS, Koh BJ, Yoo DS, Park JB, Min SR, Kim YS, Lee SS, Ge J, Seo SB, Shin DH. Joseon funerary texts tested using ancient DNA analysis of a Korean mummy. Anat Rec (Hoboken) 2015; 298:1191-207. [PMID: 25998652 DOI: 10.1002/ar.23142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 01/30/2015] [Indexed: 01/23/2023]
Abstract
In Korea, ancient DNA (aDNA) analysis has been applied to investigations into the genetic affiliations of mummies found in Joseon Dynasty tombs (1392-1910 CE), becoming now indispensable tool for researches studying human remains from archaeological sites. In the course of our recent examinations on a Korean mummy of Joseon Dynasty, we discovered many teeth contained in a pouch. And in fact, the historical literature on the topic of Joseon funerals contain general accounts of pouches in which an individual's lost teeth were collected over the course of a lifetime and, after death, placed in the coffin with the body. To test the veracity of the historical texts, the present study undertook aDNA analyses and compared the results between specifically questioned (Q) samples (teeth) and known (K) samples (brain and bone) from the mummy to ensure that they came from the same individual. Although the Q-K comparison of autosomal short tandem repeat results did not show full concordance due to allelic drop-outs in some loci, our statistical calculation indicated that the teeth in the pouch are highly likely those of the mummy. Additionally, Q-K comparison of mitochondrial DNA sequence results showed 100% matches between samples. There results, in short, could not gainsay the conjecture that the teeth samples originated from the person buried in the tomb; and if so, he must have kept his teeth for a long time after their loss. As the application of aDNA analysis to Korean mummy studies develops, there will be other opportunities to test historical documents, particularly those referring to funerary rites.
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Affiliation(s)
- Chang Seok Oh
- Anthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul, 110-799, Korea
| | - Bou-Ja Koh
- Dankook University, 152, Jukjeon-Ro, Suji-Gu, Yongin-Si, Gyeonggi-Do, 448-701, Korea
| | - Dong Soo Yoo
- Department of Radiology, Dankook University College of Medicine, San 29, Anseo-Dong, Chonan City, Chungcheongnam-Do, 330-715, Korea
| | - Jun Bum Park
- Seoul Institute of Cultural Heritages, 833, Tongil-Ro, Eunpyeong-Gu, Seoul, 122-842, Korea
| | - So Ri Min
- Korean Institute for Archaeology and Environment, 26, Mogwanamu-1 Gil, Jochiwon-Eup, Sejong-Si, 339-806, Korea
| | - Yi-Suk Kim
- Department of Anatomy, Graduate School of Medicine, Ewha Womans University, 911-1, Mok-Dong, Yangcheon-Gu, Seoul, 158-710, Korea
| | - Sang Sup Lee
- National Forensic Service, 331-1 Shinwol 7-Dong, Yangcheon-Gu, Seoul, 158-707, Korea
| | - Jianye Ge
- Department of Forensic and Investigative Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Seung Bum Seo
- Department of Forensic and Investigative Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Dong Hoon Shin
- Anthropology and Paleopathology Lab, Department of Anatomy, Seoul National University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul, 110-799, Korea
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Sahib Zar M, Ali Shahid A, Saqib Shahzad M, Shin KJ, Young Lee H, Israr M, Husnain T. Comparative study of STR loci for typing old skeletal remains with modified protocols of AmpFlSTR Identifiler and AmpFlSTR MiniFiler STR Kits. AUST J FORENSIC SCI 2014. [DOI: 10.1080/00450618.2014.925976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Robertson JM, Dineen SM, Scott KA, Lucyshyn J, Saeed M, Murphy DL, Schweighardt AJ, Meiklejohn KA. Assessing PreCR™ repair enzymes for restoration of STR profiles from artificially degraded DNA for human identification. Forensic Sci Int Genet 2014; 12:168-80. [PMID: 24997322 DOI: 10.1016/j.fsigen.2014.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 04/08/2014] [Accepted: 05/21/2014] [Indexed: 11/28/2022]
Abstract
Forensic scientists have used several approaches to obtain short tandem repeat (STR) profiles from compromised DNA samples, including supplementing the polymerase chain reaction (PCR) with enhancers and using procedures yielding reduced-length amplicons. For degraded DNA, the peak intensities of the alleles separated by electrophoresis generally decrease as the length of the allele increases. When the intensities of the alleles decrease below an established threshold, they are described as drop-outs, thus contributing to a partial STR profile. This work assesses the use of repair enzymes to improve the STR profiles from artificially degraded DNA. The commercial PreCR™ repair kit of DNA repair enzymes was tested on both purified DNA and native DNA in body fluids exposed to oxidizing agents, hydrolytic conditions, ultraviolet (UV) and ionizing radiation, and desiccation. The strategy was to restrict the level of DNA damage to that which yields partial STR profiles in order to test for allele restoration as opposed to simple allele enhancement. Two protocols were investigated for allele restoration: a sequential protocol using the manufacturer's repair procedure and a modified protocol reportedly designed for optimal STR analysis of forensic samples. Allele restoration was obtained with both protocols, but the peak height appeared to be higher for the modified protocol (determined by Mann-Kendall Trend Test). The success of the approach using the PreCR™ repair enzymes was sporadic; it led to allele restoration as well as allele drop-out. Additionally, allele restoration with the PreCR™ enzymes was compared with restoration by alternative, but commonly implemented approaches using Restorase™, PCRBoost™, bovine serum albumin (BSA) and the Minifiler™ STR system. The alternative methods were also successful in improving the STR profile, but their success also depended on the quality of the template encountered. Our results indicate the PreCR™ repair kit may be useful for restoring STR profiles from damaged DNA, but further work is required to develop a generalized approach.
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Affiliation(s)
- James M Robertson
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States.
| | - Shauna M Dineen
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
| | - Kristina A Scott
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
| | - Jonathan Lucyshyn
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States; Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System, 115 Purple Heart Ave., Dover Air Force Base, Dover, DE 19902, United States; American Registry of Pathology, P.O. Box 495, Dover, DE 19903, United States
| | - Maria Saeed
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
| | - Devonie L Murphy
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
| | - Andrew J Schweighardt
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
| | - Kelly A Meiklejohn
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, United States
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Forensic DNA typing strategy of degraded DNA on discarded cigarette ends using the AmpFℓSTR® Identifiler®, Identifiler® Plus and MiniFiler™ PCR amplification kits. Sci Justice 2014; 54:311-5. [PMID: 25002050 DOI: 10.1016/j.scijus.2014.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 03/21/2014] [Accepted: 04/30/2014] [Indexed: 11/21/2022]
Abstract
DNA left on a forensic sample is often prone to degradation, especially if left to the elements. To maximize the chance of retrieving the most information from such compromised DNA, an appropriate profiling scheme using the available technologies needs to be devised. In this study, a total of 62 cigarette ends collected under different conditions of environmental exposure were employed to test the effectiveness of three DNA amplification kits, namely the Applied Biosystems™ AmpFℓSTR® Identifiler®, Identifiler® Plus and MiniFiler™ PCR Amplification Kits, in the profiling of such compromised DNA. We demonstrated that Identifiler® Plus could substitute Identifiler® to improve the effectiveness of profiling for those inhibited cigarette samples. MiniFiler™, on the other hand, could supplement Identifiler®/Identifiler® Plus profiles and provide additional genetic information to enhance the evidential value of the samples, especially for those that have suffered from DNA degradation to a greater extent. The findings in this work allowed us to propose a DNA profiling strategy as follow: 1) samples yielding complete Identifiler®/Identifiler® Plus profiles require no further testing with MiniFiler™; 2) samples yielding partial single-source profiles to be tested with MiniFiler™ to add genetic information; 3) samples yielding no results are unlikely to yield any results with MiniFiler™.
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Validation of two canine STR multiplex-assays following the ISFG recommendations for non-human DNA analysis. Forensic Sci Int Genet 2013; 8:90-100. [PMID: 24315595 DOI: 10.1016/j.fsigen.2013.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 06/07/2013] [Accepted: 07/01/2013] [Indexed: 11/22/2022]
Abstract
To gain general acceptance forensic DNA testing in animals needs to improve standardization of analysis methods and data interpretation. Recently, the International Society of Forensic Genetics (ISFG) took particular care of this topic by publishing recommendations for forensic non-human DNA analysis following the successful example of human DNA analysis in order to provide a basis for harmonization of the still existing inter-laboratory variability. By following these recommendations we demonstrate the performance of two short tandem repeat (STR) multiplexes for forensic identity testing of canine biological material. Thirteen STRs and two sex-specific markers were selected and validated according to the ISFG guidelines. Population genetic parameters were calculated based on 295 dog samples collected in Austria (124) and Germany (171). A repeat-based nomenclature of the mainly tetrameric STRs and corresponding allelic ladders are presented. All 146 different alleles included in the ladders were sequenced for correct allele calling. Additionally, a canine cell line (DH82-D3167) was evaluated as standard reference material.
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