51
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Claerhout S, Vanpaemel S, Gill MS, Antiga LG, Baele G, Decorte R. YMrCA: Improving Y-chromosomal ancestor time estimation for DNA kinship research. Hum Mutat 2021; 42:1307-1320. [PMID: 34265144 DOI: 10.1002/humu.24259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022]
Abstract
The Y-chromosome is a valuable kinship indicator in family history and forensic research. To reconstruct genealogies, the time to the most recent common ancestor (tMRCA) between paternal relatives can be estimated through Y-STR analysis. Existing models are the stepwise mutation model (SMM, only one-step Y-STR changes) and the infinite allele model (IAM, new allele per Y-STR change). In this study, these mutation models and all existing tMRCA calculators were validated through a genetic-genealogy database containing 1,120 biologically related genealogical pairs confirmed by 46 Y-STRs with known tMRCA (18,109 generations). Consistent under- and overestimation and broad confidence intervals were observed, leading to dubious tMRCA estimates. This is because they do not include individual mutation rates or multi-step changes and ignore hidden multiple, back, or parallel modifications. To improve tMRCA estimation, we developed a user-friendly calculator, the "YMrCA", including all previously mentioned mutation characteristics. After extensive validation, we observed that the YMrCA calculator demonstrated a promising performance. The YMrCA yields a significantly higher tMRCA success rate (96%; +20%) and a lower tMRCA error (7; -3) compared to the mutation models and all online tMRCA calculators. Therefore, YMrCA offers the next step towards more objective tMRCA estimation for DNA kinship research.
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Affiliation(s)
- Sofie Claerhout
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium
| | - Simon Vanpaemel
- Department of Mechanical Engineering, KU Leuven, Noise and Vibration Engineering, Heverlee, Belgium.,DMMS Lab, Flanders Make, Heverlee, Belgium
| | - Mandev S Gill
- Department of Microbiology, KU Leuven, Immunology and Transplantation, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Laura G Antiga
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium.,Bioinformatics for Health Science, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guy Baele
- Department of Microbiology, KU Leuven, Immunology and Transplantation, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Ronny Decorte
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium.,Laboratory of Forensic Genetics, Department of Forensic Medicine, UZ Leuven, Leuven, Belgium
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52
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Strategies for pairwise searches in forensic kinship analysis. Forensic Sci Int Genet 2021; 54:102562. [PMID: 34274795 DOI: 10.1016/j.fsigen.2021.102562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/29/2021] [Accepted: 07/03/2021] [Indexed: 11/20/2022]
Abstract
Testing kinship between pairs of individuals is central to a wide range of applications. We focus on cases where many tests are done jointly. Typical examples include cases where DNA profiles are available from a burial site, a plane crash or a database of convicted offenders. The task is to determine the relationships between DNA profiles or individuals. Our approach generalises previous methods and implementations in several respects. We model general, possibly inbred, pairwise relationships which is important for non-human applications and in archaeological studies of ancient inbred populations. Furthermore, we do not restrict attention to autosomal markers. Some cases, such as distinguishing between maternal and paternal half siblings, can be solved using X-chromosomal markers. When many tests are done, the risk of errors increases. We address this problem by building on the theory of multiple testing and show how optimal thresholds for tests can be determined. We point out that the likelihood ratios in a blind search may be dependent so multiple testing methods and interpretation need to account for this. In addition, we show how a Bayesian approach can be helpful. Our examples, using simulated and real data, demonstrate the practical importance of the methods and implementation is based on freely available software.
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53
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Abstract
We address computational and statistical aspects of DNA-based identification of victims in the aftermath of disasters. Current methods and software for such identification typically consider each victim individually, leading to suboptimal power of identification and potential inconsistencies in the statistical summary of the evidence. We resolve these problems by performing joint identification of all victims, using the complete genetic data set. Individual identification probabilities, conditional on all available information, are derived from the joint solution in the form of posterior pairing probabilities. A closed formula is obtained for the a priori number of possible joint solutions to a given DVI problem. This number increases quickly with the number of victims and missing persons, posing computational challenges for brute force approaches. We address this complexity with a preparatory sequential step aiming to reduce the search space. The examples show that realistic cases are handled efficiently. User-friendly implementations of all methods are provided in the R package dvir, freely available on all platforms.
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54
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The DNAxs software suite: A three-year retrospective study on the development, architecture, testing and implementation in forensic casework. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2021.100212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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55
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Zieger M, Gouy A, Utz S. Expanding the Swiss autosomal marker set to 32 STRs. Int J Legal Med 2021; 135:2309-2310. [PMID: 34143274 PMCID: PMC8523451 DOI: 10.1007/s00414-021-02624-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/24/2021] [Indexed: 12/03/2022]
Abstract
By genotyping 1198 individuals with the Qiagen Investigator® HDplex Kit, we expand the Swiss autosomal STR dataset to 32 loci, providing additional resources for complex kinship cases. We present the first high-quality allele frequency dataset for loci D2S1360, D5S2500, D7S1517, and D10S2325 that will be accessible through the ENFSI reference database STRidER. For loci D3S1744, D4S2366, D6S474, D8S1132, and D21S2055, we provide a first European STRidER dataset.
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Affiliation(s)
- Martin Zieger
- Institute of Forensic Medicine, Forensic Molecular Biology Department, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland
| | - Alexandre Gouy
- Gouy Data Consulting, Sentier de Renges 4A, 1026 Denges, Switzerland
| | - Silvia Utz
- Institute of Forensic Medicine, Forensic Molecular Biology Department, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland
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56
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Vullo CM, Catelli L, Ibarra Rodriguez AA, Papaioannou A, Merino JCÁ, Lopez-Parra AM, Gaviria A, Baeza-Richer C, Romanini C, González-Moya E, Casals F, Calafell F, Berardi G, Iannacone GC, Vicuña Giraldo GC, Zorba GK, Boschi I, Olarte JV, Ruiz Gomez JE, Acierno JP, Soto ML, Miranda MV, García King MD, Marrucci MA, Porto MJ, Piñero MH, Aler M, Stephenson Ojea MM, Navarrete SC, Toscanini U, Saragoni VG, Bozzo W, Posada Posada YC, Bajunovic Z, Solla LP, Parsons T. Second GHEP-ISFG exercise for DVI: "DNA-led" victims' identification in a simulated air crash. Forensic Sci Int Genet 2021; 53:102527. [PMID: 34034006 DOI: 10.1016/j.fsigen.2021.102527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/22/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
The Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) has organized a second collaborative exercise on a simulated case of Disaster Victim Identification (DVI), with the participation of eighteen laboratories. The exercise focused on the analysis of a simulated plane crash case of medium-size resulting in 66 victims with varying degrees of fragmentation of the bodies (with commingled remains). As an additional difficulty, this second exercise included 21 related victims belonging to 6 families among the 66 missings to be identified. A total number of 228 post-mortem samples were represented with aSTR and mtDNA profiles, with a proportion of partial aSTR profiles simulating charred remains. To perform the exercise, participants were provided with aSTR and mtDNA data of 51 reference pedigrees -some of which deficient-including 128 donors for identification purposes. The exercise consisted firstly in the comparison of the post-mortem genetic profiles in order to re-associate fragmented remains to the same individual and secondly in the identification of the re-associated remains by comparing aSTR and mtDNA profiles with reference pedigrees using pre-established thresholds to report a positive identification. Regarding the results of the post-mortem samples re-associations, only a small number of discrepancies among participants were detected, all of which were from just a few labs. However, in the identification process by kinship analysis with family references, there were more discrepancies in comparison to the correct results. The identification results of single victims yielded fewer problems than the identification of multiple related victims within the same family groups. Several reasons for the discrepant results were detected: a) the identity/non-identity hypotheses were sometimes wrongly expressed in the likelihood ratio calculations, b) some laboratories failed to use all family references to report the DNA match, c) In families with several related victims, some laboratories firstly identified some victims and then unnecessarily used their genetic information to identify the remaining victims within the family, d) some laboratories did not correctly use "prior odds" values for the Bayesian treatment of the episode for both post-mortem/post-mortem re-associations as well as the ante-mortem/post-mortem comparisons to evaluate the probability of identity. For some of the above reasons, certain laboratories failed to identify some victims. This simulated "DNA-led" identification exercise may help forensic genetic laboratories to gain experience and expertize for DVI or MPI in using genetic data and comparing their own results with the ones in this collaborative exercise.
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Affiliation(s)
- Carlos M Vullo
- Argentine Forensic Anthropology Team (EAAF), Córdoba, Argentina.
| | - Laura Catelli
- Argentine Forensic Anthropology Team (EAAF), Córdoba, Argentina.
| | | | | | - J Carlos Álvarez Merino
- Laboratorio de Identificación Genética, Facultad de Medicina, Universidad de Granada, Granada, Spain.
| | - A M Lopez-Parra
- Laboratory of Forensic and Population Genetics, Dept of Toxicology and Health Legislation, Madrid, Spain.
| | - Aníbal Gaviria
- Lab de Genética Molecular Cruz Vital - Cruz Roja Ecuatoriana, Quito, Ecuador.
| | - Carlos Baeza-Richer
- Laboratory of Forensic and Population Genetics, Dept of Toxicology and Health Legislation, Madrid, Spain.
| | - Carola Romanini
- Argentine Forensic Anthropology Team (EAAF), Córdoba, Argentina.
| | | | - Ferran Casals
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain.
| | | | | | - Gian Carlo Iannacone
- Laboratorio De Biología Molecular y Genética Del Instituto De Medicina Legal, Lima, Peru.
| | | | - Gulbanu K Zorba
- Committee on Missing Persons Cyprus (CMP) Anthropological Laboratory, Nicosia, Cyprus.
| | - Ilaria Boschi
- Istituto di Sanità Pubblica-Medicina Legale Policlinico Gemelli, Roma, Italy.
| | - Jane Valdivia Olarte
- Laboratorio De Biología Molecular y Genética Del Instituto De Medicina Legal, Lima, Peru.
| | | | | | - Manuel López Soto
- Instituto Nacional de Toxicología y Ciencias Forenses (INTCF), Madrid, Spain.
| | | | | | | | - Maria J Porto
- Instituto Nacional de Medicina Legal e Ciências Forenses, Coimbra, Portugal.
| | | | - Mercedes Aler
- Instituto de Medicina Legal y Ciencias Forenses, Valencia, Spain.
| | | | | | | | - Victor G Saragoni
- Unidad de Genética Forense, Servicio Médico Legal, Santiago de Chile, Chile.
| | - Walter Bozzo
- Banco Nacional De Datos Genéticos, CABA, Argentina.
| | | | | | - Lourdes Prieto Solla
- Grupo de Medicina Xenómica, Instituto de Ciencias Forenses, USC, Santiago de Compostela, Spain; Comisaría General de Policía Científica. Madrid.
| | - Thomas Parsons
- International Commission for Missing Persons (ICMP), USA.
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57
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Kruijver M, Taylor D, Bright JA. Evaluating DNA evidence possibly involving multiple (mixed) samples, common donors and related contributors. Forensic Sci Int Genet 2021; 54:102532. [PMID: 34130043 DOI: 10.1016/j.fsigen.2021.102532] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/18/2022]
Abstract
Forensic DNA profiling is used in various circumstances to evaluate support for two competing propositions with the assignment of a likelihood ratio. Many software implementations exist that tackle a range of inference problems spanning identification and relationship testing. We propose a flexible likelihood ratio framework that caters to inference problems in forensic genetics. The framework allows for investigation of the degree of support for the contribution of multiple persons to multiple samples allowing for persons to be related according to a pedigree, including inbred relationships. We explain how a number of routine as well as more complex problems can be treated within this framework.
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Affiliation(s)
- Maarten Kruijver
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand.
| | - Duncan Taylor
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Jo-Anne Bright
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand
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58
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Marsico FL, Vigeland MD, Egeland T, Piñero MH. Making decisions in missing person identification cases with low statistical power. Forensic Sci Int Genet 2021; 54:102519. [PMID: 34139527 DOI: 10.1016/j.fsigen.2021.102519] [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: 09/16/2020] [Revised: 02/11/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
The present work proposes a general strategy for dealing with missing person identification cases through DNA-database search. Our main example is the identification of abducted children in the last civic-dictatorship of Argentina, known as the "Missing Grandchildren of Argentina". Particularly we focus on those pedigrees where few, or only distant relatives of the missing person are available, resulting in low statistical power. For such complex cases we provide a statistical method for selecting a likelihood ratio (LR) threshold for each pedigree based on error rates. Furthermore, we provide an open-source user friendly software for computing LR thresholds and error rates. The strategy described in the paper could be applied to other large-scale cases of DNA-based identification hampered by low statistical power.
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Affiliation(s)
- Franco L Marsico
- Banco Nacional de Datos Genéticos, Avda. Córdoba 831, C1054AAH Caba, Argentina.
| | - Magnus D Vigeland
- Department of Medical Genetics, University of Oslo, PB 4956 Nydalen, 0424 Oslo, Norway.
| | - Thore Egeland
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Chr. M Falsens vei 1, 1433 Aas, Norway.
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59
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Alterauge A, Lösch S, Sulzer A, Gysi M, Haas C. Beyond simple kinship and identification: aDNA analyses from a 17th-19th century crypt in Germany. Forensic Sci Int Genet 2021; 53:102498. [PMID: 33872864 DOI: 10.1016/j.fsigen.2021.102498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/24/2021] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
Ancient DNA (aDNA) analysis is a powerful tool in multidisciplinary research on human remains, potentially leading to kinship scenarios and historical identifications. In this study, we present a genetic investigation of three noble families from the 17th to 19th centuries AD entombed in burial crypts at the cloister church of Riesa (Germany). Tests were aimed at identifying anticipated and incidental genetic relationships in our sample and the implications thereof for the assumed identity of the deceased. A total of 17 individuals were investigated via morphological, radiographic and aDNA analysis, yielding complete and partial autosomal and Y-STR profiles and reliable mtDNA sequences. Biostatistics and lineage markers revealed the presence of first to third degree relationships within the cohort. The pedigrees of the families Hanisch/von Odeleben and von Welck were thereby successfully reproduced, while four previously unknown individuals could be linked to the von Felgenhauer family. However, limitations of biostatistical kinship analysis became evident when the kinship scenario went beyond simple relationships. A combined analysis with archaeological data and historical records resulted in (almost) unambiguous identification of 14 of the 17 individuals.
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Affiliation(s)
- Amelie Alterauge
- Department of Prehistoric Archaeology, Institute of Archaeological Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland; Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland
| | - Andrea Sulzer
- Department of Forensic Genetics, Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zürich, Switzerland
| | - Mario Gysi
- Department of Forensic Genetics, Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zürich, Switzerland
| | - Cordula Haas
- Department of Forensic Genetics, Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, 8057 Zürich, Switzerland.
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60
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Patterns of genetic diversity in Colombia for 38 indels used in human identification. Forensic Sci Int Genet 2021; 53:102495. [PMID: 33743518 DOI: 10.1016/j.fsigen.2021.102495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/06/2021] [Indexed: 01/15/2023]
Abstract
The current population of Colombia has a genetic heterogeneity resulting from different migrations from other continents and within the country. In addition, there are small groups in their territory that have remained isolated and therefore have a different genetic pool in relation to that of the neighbouring urban populations. This population stratification must be considered in forensic analysis, being more complex for markers with marked intercontinental differentiation. In this study, population differentiation in Colombian admixed, native, and Afro-descendant populations was evaluated for a group of 38 indels described for forensic use. Allelic frequencies and parameters of forensic relevance were determined in each of the groups defined based on population differentiation analyses. In addition to the differences found between population groups, the results show that the set of 38 indels analysed could be useful in studies of individual identification in Colombia. The exclusion power presented by this set of markers suggests the need for joint use with other markers, being able to complement the STRs in paternity cases. High levels of both power of discrimination and exclusion were found when complementing the 38 HID-indels with a second multiplex, for a total of 83 indels.
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61
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Wen D, Sun S, Liu Y, Li J, Yang Z, Kureshi A, Fu Y, Li H, Jiang B, Jin C, Cai J, Zha L. Considering the flanking region variants of nonbinary SNP and phenotype-informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications. Electrophoresis 2021; 42:1115-1126. [PMID: 33483973 DOI: 10.1002/elps.202000341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/22/2020] [Accepted: 01/15/2021] [Indexed: 12/15/2022]
Abstract
The flanking region variants of nonbinary SNPs and phenotype-informative SNPs (piSNPs) have been observed, which may greatly improve the discriminative ability after constituting microhaplotype. In this study, 30 microhaplotype loci based on the nonbinary SNPs and piSNPs (shown to be related to phenotypes such as hair and eye color) were selected. Genotyping were conducted on 100 unrelated northern Han Chinese, and the 26 populations from the 1000 Genome Project were also included for comparison of populations differentiation. The simulated study was conducted for evaluating the efficiency of kinship testing. These 30 microhaplotype loci we selected had good polymorphism, with a mean effective number of alleles (Ae) of 3.46. The average Ae increase was 1.27 compared with the target SNPs. The populations from the five regions worldwide could also be distinguished using these loci. The results of kinship testing showed that these microhaplotype loci had the similar ability as 15 STR loci of AmpFlSTRR IdentifilerR PCR Amplification Kit to identify the biological parent and a stronger ability to exclude the nonbiological parents. So, these 30 microhaplotype loci may be multifunctional for forensic application, including the ability of personal identification and kinship testing equivalent to 15 STR loci, and the power of ancestry inference for distinguishing the main intercontinental population. Moreover, our selected phenotypic microhaplotype loci may theoretically have phenotype prediction capabilities. But the phenotype prediction efficiency of these phenotypic microhaplotype loci may be worse than that of piSNPs and the detailed prediction accuracy of different populations needs to be further studied.
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Affiliation(s)
- Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Shule Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Ying Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Jienan Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Zedeng Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Aliye Kureshi
- School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, P. R. China
| | - Yan Fu
- Huazhi Biotech Co., Ltd, Changsha, P. R. China
| | - Henan Li
- Microanaly Gene Technologies Co., Ltd, Hefei, P. R. China
| | - Bowei Jiang
- The First Research Institute of the Ministry of Public Security P.R.C, Beijing, P. R. China
| | - Chuan Jin
- The First Research Institute of the Ministry of Public Security P.R.C, Beijing, P. R. China
| | - Jifeng Cai
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, P. R. China
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62
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Karamanlidis AA, Kopatz A, de Gabriel Hernando M. Dispersal patterns of a recovering brown bear (Ursus arctos) population in a human-dominated landscape. J Mammal 2021. [DOI: 10.1093/jmammal/gyaa173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Despite increasing habitat fragmentation, large carnivore populations in parts of Europe have been recovering and expanding into human-dominated areas. Knowledge of animal dispersal patterns in such areas is important for their conservation, management, and coexistence with humans. We used genetic data based on 15 microsatellite markers from 312 individuals (98 females, 214 males) to assess kinship and dispersal patterns during the recovery and spatial expansion of a wild brown bear (Ursus arctos) population (2003–2010) in the human-dominated landscape of Greece. We hypothesized that bear dispersal in Greece was sex-biased, with females being more philopatric and males dispersing more frequently and over greater distances. Dispersal indeed was sex-biased, with males dispersing more frequently and farther than females. Overall, females were found to be philopatric; males also appeared to be philopatric, but to a lesser degree. However, a high proportion of females displayed dispersal behavior, which may be indicative of a pre-saturation stage of the population in that part of the country. Our results indicate that dispersal may be due to evading competition and avoiding inbreeding. We also documented long-distance dispersal of bears, which is considered to be indicative of a spatially expanding population. Our results highlight the value of using noninvasive genetic monitoring data to assess kinship among individuals and study dispersal patterns in human-dominated landscapes. Brown bears remain threatened in Greece; we therefore recommend systematic genetic monitoring of the species in combination with careful habitat management to protect suitable habitat (i.e., dispersal corridors) and ultimately ensure co-existence with humans and survival of brown bears in the country.
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Affiliation(s)
- Alexandros A Karamanlidis
- ARCTUROS, Civil Society for the Protection and Management of Wildlife and the Natural Environment, Aetos, Florina, Greece
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Alexander Kopatz
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Miguel de Gabriel Hernando
- ARCTUROS, Civil Society for the Protection and Management of Wildlife and the Natural Environment, Aetos, Florina, Greece
- Department of Biodiversity and Environmental Management, Faculty of Biological and Environmental Sciences, Universidad de León, León, Spain
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63
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Staadig A, Tillmar A. Evaluation of microhaplotypes in forensic kinship analysis from a Swedish population perspective. Int J Legal Med 2021; 135:1151-1160. [PMID: 33506298 PMCID: PMC8205927 DOI: 10.1007/s00414-021-02509-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/08/2021] [Indexed: 11/28/2022]
Abstract
The development of massively parallel sequencing (MPS) technology has enabled the discovery of several new types of forensic markers where microhaplotypes are one of these promising novel genetic markers. Microhaplotypes are, commonly, less than 300 nucleotides in length and consist of two or more closely linked single-nucleotide polymorphisms (SNPs). In this study, we have examined a custom-made QIAseq Microhaplotype panel (Qiagen), including 45 different microhaplotype loci. DNA libraries were prepared according to the GeneRead DNAseq Targeted Panels V2 library preparation workflow (Qiagen) and sequenced on a MiSeq FGx instrument (Verogen). We evaluated the performance of the panel based on 75 samples of Swedish origin and haplotype frequencies were established. We performed sensitivity studies and could detect haplotypes at input amounts down to 0.8 ng. We also studied mixture samples with two contributors for which haplotypes, for the minor contributor, were detectable down to the level of 1:100. Furthermore, we executed kinship simulations to evaluate the usefulness of this panel in kinship analysis. The results showed that both paternity and full sibling cases can clearly be solved. When simulating a half sibling versus unrelated case scenario, there were, however, some overlap of the likelihood ratio distributions potentially resulting in inconclusiveness. To conclude, the results of this initial study are promising for further implementation of this microhaplotype assay into the forensic field, although we noticed some primer design issues that could be optimized, which possibly would increase the power of the assay.
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Affiliation(s)
- Adam Staadig
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden. .,Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.,Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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64
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Norscia I, Coco E, Robino C, Chierto E, Cordoni G. Yawn contagion in domestic pigs (Sus scrofa). Sci Rep 2021; 11:1851. [PMID: 33473157 PMCID: PMC7817675 DOI: 10.1038/s41598-020-80545-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
Contrary to spontaneous yawning—an ancient phenomenon common to vertebrates—contagious yawning (elicited by others’ yawns) has been found only in highly social species and may reflect an emotional inter-individual connection. We investigated yawn contagion in the domestic pig, Sus scrofa. Owing to the complex socio-emotional and cognitive abilities of Sus scrofa, we posited that yawn contagion could be present in this species (Prediction 1) and influenced by individual/social factors (Prediction 2). In June-November 2018, on 104 semi-free ranging adolescent/adult pigs, 224 videos were recorded for video analysis on yawning. Kinship information was refined via genetic analyses. Statistical elaboration was conducted via GLMMs and non-parametric/randomization/cross-tabulation tests. We found yawn contagion in Sus scrofa, as it was more likely that pigs yawned when perceiving rather than not perceiving (yawning/control condition) others’ yawns (response peak in the first out of three minutes). Yawn contagion was more likely: (1) in response to males’ yawns; (2) as the age increased; (3) within short distance (1 m); (4) between full siblings, with no significant association between kinship and distance. The influence of kinship suggests that—as also hypothesized for Homo sapiens—yawn contagion might be linked with emotional communication and possibly contagion.
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Affiliation(s)
- Ivan Norscia
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy.
| | - Elisabetta Coco
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Torino, Turin, Italy
| | - Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Torino, Turin, Italy
| | - Giada Cordoni
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy.
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Taylor CR, Kiesler KM, Sturk-Andreaggi K, Ring JD, Parson W, Schanfield M, Vallone PM, Marshall C. Platinum-Quality Mitogenome Haplotypes from United States Populations. Genes (Basel) 2020; 11:genes11111290. [PMID: 33138247 PMCID: PMC7716222 DOI: 10.3390/genes11111290] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
A total of 1327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC). The laboratory workflow involved long-range PCR to minimize the co-amplification of nuclear mitochondrial DNA segments (NUMTs), PCR-free library preparation to reduce amplification bias, and high-coverage Illumina MiSeq sequencing to produce an average per-sample read depth of 1000 × for low-frequency (5%) variant detection. Point heteroplasmies below 10% frequency were confirmed through replicate amplification, and length heteroplasmy was quantitatively assessed using a custom read count analysis tool. Data analysis involved a redundant, dual-analyst review to minimize errors in haplotype reporting with additional QC checks performed by EMPOP. Applying these methods, eight sample sets were processed from five U.S. metapopulations (African American, Caucasian, Hispanic, Asian American, and Native American) corresponding to self-reported identity at the time of sample collection. Population analyses (e.g., haplotype frequencies, random match probabilities, and genetic distance estimates) were performed to evaluate the eight datasets, with over 95% of haplotypes unique per dataset. The platinum-quality mitogenome haplotypes presented in this study will enable forensic statistical calculations and thereby support the usage of mitogenome sequencing in forensic laboratories.
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Affiliation(s)
- Cassandra R. Taylor
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
| | - Kevin M. Kiesler
- National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA; (K.M.K.); (P.M.V.)
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
| | - Joseph D. Ring
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria;
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
| | - Moses Schanfield
- Department of Forensic Sciences, The George Washington University, Washington, DC 20007, USA;
| | - Peter M. Vallone
- National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA; (K.M.K.); (P.M.V.)
| | - Charla Marshall
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
- Correspondence: ; Tel.: +1-302-346-8519
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66
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Aguiar VRC, de Castro AM, Pinto LM, Ferreira ACS, Dos Santos EVW, Louro ID. Assessing false paternity risk in simulated motherless cases from more than 20 000 real exclusion trios. Transfusion 2020; 61:678-681. [PMID: 33084042 DOI: 10.1111/trf.16153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND When the mother's DNA profile is not available for paternity testing, there is a smaller probability that a locus will exclude an alleged father. This study aims to evaluate the risk of potential false paternity inclusions in motherless cases. STUDY DESIGN AND METHODS More than 20 000 duos were generated by removing the maternal genotypes from exclusion trios. After recalculating paternity in these duos, any found inclusions would be false. RESULTS The use of an appropriate number of loci, mutation model, and mutation rates to analyze motherless paternity cases was robust against false inclusions. A single potential false inclusion was observed in a case wherein kinship plays a role. This result highlights the importance of testing the mother when available and of obtaining information on family circumstances for the proper handling of cases involving related individuals. CONCLUSION The guidelines we used here were sufficient to avoid false inclusions in a data set of more than 20 000 motherless cases.
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Affiliation(s)
- Vitor R C Aguiar
- Departamento de Ciências Biológicas, Núcleo de Genética Humana e Molecular, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Amanda M de Castro
- Departamento de Genética Molecular, Laboratório Hermes Pardini, Vespasiano, Brazil
| | - Laélia M Pinto
- Departamento de Genética Molecular, Laboratório Hermes Pardini, Vespasiano, Brazil
| | | | - Eldamária V W Dos Santos
- Departamento de Ciências Biológicas, Núcleo de Genética Humana e Molecular, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Iuri D Louro
- Departamento de Ciências Biológicas, Núcleo de Genética Humana e Molecular, Universidade Federal do Espírito Santo, Vitória, Brazil
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67
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The genetic legacy of legendary and historical Siberian chieftains. Commun Biol 2020; 3:581. [PMID: 33067556 PMCID: PMC7567834 DOI: 10.1038/s42003-020-01307-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 09/15/2020] [Indexed: 02/02/2023] Open
Abstract
Seventeen years of archaeological and anthropological expeditions in North-Eastern Siberia (in the Sakha Republic, Yakutia) have permitted the genetic analysis of 150 ancient (15th-19th century) and 510 modern individuals. Almost all males were successfully analysed (Y-STR) and this allowed us to identify paternal lineages and their geographical expansion through time. This genetic data was confronted with mythological, historical and material evidence to establish the sequence of events that built the modern Yakut genetic diversity. We show that the ancient Yakuts recovered from this large collection of graves are not representative of an ancient population. Uncommonly, we were also able to demonstrate that the funerary preference observed here involved three specific male lineages, especially in the 18th century. Moreover, this dominance was likely caused by the Russian conquest of Siberia which allowed some male clans to rise to new levels of power. Finally, we give indications that some mythical and historical figures might have been the actors of those genetic changes. These results help us reconsider the genetic dynamics of colonization in some regions, question the distinction between fact and myth in national histories and provide a rare insight into a funerary ensemble by revealing the biased process of its composition.
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Biological kinship in 750 year old human remains from Central Argentina with signs of interpersonal violence. Forensic Sci Med Pathol 2020; 16:649-658. [PMID: 32915387 DOI: 10.1007/s12024-020-00296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2020] [Indexed: 10/23/2022]
Abstract
Human skeletal remains of an adult male (20-24 years old) and a juvenile (4-8 years old), dated to 750 ± 85 14C years BP, were found on the southern margin of Mar Chiquita Lagoon (Córdoba, Argentina). Both individuals show signs of being victims of interpersonal violence, with arrowheads associated with the remains and perimortem lesions on the juvenile, as well as an unusual form of burial, with the juvenile partially overlapped with the adult. The aim of this work is to study a possible kin relationship between these two individuals through ancient DNA analysis. Biological kinship was evaluated by autosomal and Y-chromosome STR (short tandem repeat) typing, PCR-APLP for SNP determination and hypervariable region I sequencing of the mitochondrial DNA. Genetic analyses indicated that these individuals shared the same Y-chromosomal haplotype but different mitochondrial lineages. The likelihood ratio based on autosomal loci indicates that the genetic profiles of the human remains would be more likely to be that indicating a father-son bond. The paleogenetic approach combined with forensic genetic methods applied to this study allowed us to confirm a hypothesis that originated in bioarchaeological evidence. This study constitutes a unique case in Argentina of kinship determination based on DNA profiles of human remains in an archaeological context of interpersonal violence. It is important to highlight the contribution made by these studies to address topics usually hidden in bioarchaeological studies, such as community organization, cultural customs and mortuary practices.
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Cavalheiro CP, Avila E, Gastaldo AZ, Graebin P, Motta CHA, Rodenbusch R, Alho CS. Uniparental disomy of chromosome 21: A statistical approach and application in paternity tests. Forensic Sci Int Genet 2020; 49:102368. [PMID: 32911454 DOI: 10.1016/j.fsigen.2020.102368] [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: 02/05/2020] [Revised: 06/30/2020] [Accepted: 07/31/2020] [Indexed: 11/24/2022]
Abstract
Considering the overall frequency of paternity investigation cases including mutational events, there is a real possibility that at least a fraction of all inconsistencies reported in paternity cases are caused not by polymerase slippage mutations, but to chromosomic abnormalities, as Uniparental Disomy (UPD). We report here the investigation of a trio paternity case (mother, child and alleged father), with observed inconsistencies that can alternatively be explained by occurrence of maternal uniparental isodisomy of chromosome 21 (miUPD21). A total of 350 short tandem repeat (STR) and single nucleotide polymorphism (SNP) markers were tested, statistically suggesting true biological linkage within the trio. Additionally, we propose miUPD21 explains, with significantly greater probability, the occurrence of detected inconsistencies, when compared to alternative hypothesis of multiple and simultaneous slippage mutations. Similar cases could have their statistical conclusions improved or even altered by including unusual chromosomal segregation patterns in the hypothesis formulation, as well as in mathematical calculations. Such reports of allelic inconsistencies being explained by chromosomal alterations are common in clinical genetics, and such situations might have impact on forensic investigation.
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Affiliation(s)
- C P Cavalheiro
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil.
| | - E Avila
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil; Polícia Federal, Setor Técnico Científico, Porto Alegre, RS, Brazil
| | - A Z Gastaldo
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil
| | - P Graebin
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil
| | - C H A Motta
- Instituto de Medicina Social e Criminalística de São Paulo, São Paulo, SP, Brazil
| | - R Rodenbusch
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - C S Alho
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil
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70
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Marshall C, Sturk-Andreaggi K, Gorden EM, Daniels-Higginbotham J, Sanchez SG, Bašić Ž, Kružić I, Anđelinović Š, Bosnar A, Čoklo M, Petaros A, McMahon TP, Primorac D, Holland MM. A Forensic Genomics Approach for the Identification of Sister Marija Crucifiksa Kozulić. Genes (Basel) 2020; 11:genes11080938. [PMID: 32823826 PMCID: PMC7464340 DOI: 10.3390/genes11080938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022] Open
Abstract
Sister Marija Krucifiksa Kozulić (1852–1922) was a Croatian nun who is in consideration for beatification by the Vatican, which is facilitated by the identification of her 20th-century remains. Sister Marija was buried in a tomb in Rijeka, Croatia, along with other nuns including her biological sister, Tereza Kozulić (1861–1933). When the remains were exhumed in 2011, they were found in a deteriorated state and commingled with several other sets of remains. Thus, mitochondrial genome sequencing of the long bones was performed to sort the remains by mitochondrial haplotype. Two similar but unique haplotypes belonging to haplogroup H1bu were identified, and samples from these bones were subjected to autosomal short tandem repeat (STR) and single nucleotide polymorphism (SNP) sequencing. Although only partial profiles were obtained, the data were sufficient for kinship analysis with the profile of a paternal niece of Sister Marija (Fides Kozulić). The data indicate that it is 574,195-fold more likely that the two sets of skeletal remains represent 2nd-degree relatives of Fides than sisters who are unrelated to Fides. Although it is impossible to discern which set of remains belongs to Marija and which belongs to Tereza, forensic genomics methods have enabled identification of the sisters.
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Affiliation(s)
- Charla Marshall
- Armed Forces Medical Examiner System (AFMES), Dover Air Force Base, Dover, DE 19902, USA; (K.S.-A.); (E.M.G.); (J.D.-H.); (S.G.S.); (T.P.M.)
- SNA International, Contractor Supporting the AFMES, Alexandria, VA 22314, USA
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA;
- Correspondence: (C.M.); (M.M.H.); Tel.: +1-302-346-8519 (C.M.); +1-814-865-5286 (M.M.H.)
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System (AFMES), Dover Air Force Base, Dover, DE 19902, USA; (K.S.-A.); (E.M.G.); (J.D.-H.); (S.G.S.); (T.P.M.)
- SNA International, Contractor Supporting the AFMES, Alexandria, VA 22314, USA
| | - Erin M. Gorden
- Armed Forces Medical Examiner System (AFMES), Dover Air Force Base, Dover, DE 19902, USA; (K.S.-A.); (E.M.G.); (J.D.-H.); (S.G.S.); (T.P.M.)
- SNA International, Contractor Supporting the AFMES, Alexandria, VA 22314, USA
| | - Jennifer Daniels-Higginbotham
- Armed Forces Medical Examiner System (AFMES), Dover Air Force Base, Dover, DE 19902, USA; (K.S.-A.); (E.M.G.); (J.D.-H.); (S.G.S.); (T.P.M.)
- SNA International, Contractor Supporting the AFMES, Alexandria, VA 22314, USA
| | - Sidney Gaston Sanchez
- Armed Forces Medical Examiner System (AFMES), Dover Air Force Base, Dover, DE 19902, USA; (K.S.-A.); (E.M.G.); (J.D.-H.); (S.G.S.); (T.P.M.)
- SNA International, Contractor Supporting the AFMES, Alexandria, VA 22314, USA
| | - Željana Bašić
- Department of Forensic Sciences, University of Split, 21000 Split, Croatia; (Ž.B.); (I.K.)
| | - Ivana Kružić
- Department of Forensic Sciences, University of Split, 21000 Split, Croatia; (Ž.B.); (I.K.)
| | - Šimun Anđelinović
- Medical School, University of Split, 21000 Split, Croatia;
- Clinical Department for Pathology, Legal Medicine and Cytology, Clinical Hospital Center Split, 21000 Split, Croatia
| | - Alan Bosnar
- Department of Forensic Medicine and Criminalistics, University of Rijeka School of Medicine, 51000 Rijeka, Croatia;
| | - Miran Čoklo
- Institute for Anthropological Research, Center for Applied Bioanthropology, 10000 Zagreb, Croatia;
| | - Anja Petaros
- National Board of Forensic Medicine, Department of Forensic Medicine, 58758 Linköping, Sweden;
| | - Timothy P. McMahon
- Armed Forces Medical Examiner System (AFMES), Dover Air Force Base, Dover, DE 19902, USA; (K.S.-A.); (E.M.G.); (J.D.-H.); (S.G.S.); (T.P.M.)
| | - Dragan Primorac
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA;
- Medical School, University of Split, 21000 Split, Croatia;
- St. Catherine Specialty Hospital, 49210 Zabok/10000 Zagreb, Croatia
- School of Medicine, University of Osijek, 31000 Osijek, Croatia
- Faculty of Dental Medicine and Health, University of Osijek, 31000 Osijek, Croatia
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, New Haven, CT 06516, USA
- School of Medicine, University of Rijeka, 51000 Rijeka, Croatia
- Medical School REGIOMED, 96450 Coburg, Germany
| | - Mitchell M. Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA;
- Correspondence: (C.M.); (M.M.H.); Tel.: +1-302-346-8519 (C.M.); +1-814-865-5286 (M.M.H.)
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Genetic evidence suggests a sense of family, parity and conquest in the Xiongnu Iron Age nomads of Mongolia. Hum Genet 2020; 140:349-359. [PMID: 32734383 DOI: 10.1007/s00439-020-02209-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
In an effort to characterize the people who composed the groups known as the Xiongnu, nuclear and whole mitochondrial DNA data were generated from the skeletal remains of 52 individuals excavated from the Tamir Ulaan Khoshuu (TUK) cemetery in Central Mongolia. This burial site, attributed to the Xiongnu period, was used from the first century BC to the first century AD. Kinship analyses were conducted using autosomal and Y-chromosomal DNA markers along with complete sequences of the mitochondrial genome. These analyses suggested close kin relationships between many individuals. Nineteen such individuals composed a large family spanning five generations. Within this family, we determined that a woman was of especially high status; this is a novel insight into the structure and hierarchy of societies from the Xiongnu period. Moreover, our findings confirmed that the Xiongnu had a strongly admixed mitochondrial and Y-chromosome gene pools and revealed a significant western component in the Xiongnu group studied. Using a fine-scale approach (haplotype instead of haplogroup-level information), we propose Scytho-Siberians as ancestors of the Xiongnu and Huns as their descendants.
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72
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Simoes Dutra Correa H, Cortellini V, Brescia G, Verzeletti A. Human identification through DNA analysis of restored postmortem teeth. Forensic Sci Int Genet 2020; 47:102302. [DOI: 10.1016/j.fsigen.2020.102302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/30/2022]
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73
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Development of a software for kinship analysis considering linkage and mutation based on a Bayesian network. Forensic Sci Int Genet 2020; 47:102279. [DOI: 10.1016/j.fsigen.2020.102279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 02/08/2020] [Accepted: 03/17/2020] [Indexed: 12/11/2022]
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74
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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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75
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González-Herrera LJ, García-Aceves ME, Domínguez-Cruz MD, López-González PN, Sosa-Escalante JE, Rangel-Villalobos H. A four-step mutation at D22S1045 in one complex paternity case when the brother of the alleged father hypothesis is evaluated. Int J Legal Med 2020; 134:1647-1652. [PMID: 32417977 DOI: 10.1007/s00414-020-02312-1] [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: 02/03/2020] [Accepted: 04/28/2020] [Indexed: 10/24/2022]
Abstract
We report one complex paternity case presenting a presumable paternal four-step STR mutation between the alleged father (AF) and child; the complexity of the case required the AF-brother hypothesis to be discarded without including this DNA sample. A total of 23 autosomal STR loci included in the Powerplex Fusion® and Globalfiler™ kits confirmed one isolated mismatch for D22S1045 between the AF (17/17) and the male child (13/15) in the presence of the mother (15/15). In this case, the STR structure and father's age do not seem to have contributed to promote the observed multistep mutation. The Paternity Index (PI) based on 23 autosomal STRs did not favor the AF paternity over the AF-brother hypothesis based on a flat prior (PI = 0.1217; W = 10.85%). For that reason, we included 38 autosomal human identification (HID) insertions-deletions (indels) and 20 retrotransposon insertion polymorphisms (RIPs) contained in the InnoTyper® 21 kit. Although these biallelic markers favored the AF paternity rather than the AF-brother hypothesis (LR = 110.3; W = 99.1%), the global PI based on 81 autosomal markers supported moderately the AF paternity hypothesis (LR = 13.4; W = 93.1%). The application of different mutation models showed a consistent support to the AF paternity hypothesis (PI = 93.1-99.95%), which could be useful for interpretation in these multistep STR mutation cases. In brief, we showed the impact of a four-step mutation at D22S1045 to obtain definitive paternity conclusions, particularly under a complex scenario when the AF-brother hypothesis is assessed. Forensic genomics arises as the next option for similar complex paternity cases.
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Affiliation(s)
| | - Mayra E García-Aceves
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Av. Universidad #1115, Col. Paso Blanco, CP 47810, Ocotlán, Jalisco, Mexico
| | - Martin D Domínguez-Cruz
- Laboratorio de Genética del Instituto Jalisciense de Ciencias Forenses (IJCF), Guadalajara, Jalisco, Mexico
| | | | | | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Av. Universidad #1115, Col. Paso Blanco, CP 47810, Ocotlán, Jalisco, Mexico.
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76
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Pairwise kinship testing with a combination of STR and SNP loci. Forensic Sci Int Genet 2020; 46:102265. [DOI: 10.1016/j.fsigen.2020.102265] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 12/22/2019] [Accepted: 02/23/2020] [Indexed: 11/22/2022]
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77
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Vai S, Amorim CEG, Lari M, Caramelli D. Kinship Determination in Archeological Contexts Through DNA Analysis. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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78
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Letter to the editor: the successful identification of a scuba diver's corpse after 26 years of submersion. Int J Legal Med 2020; 134:1973-1976. [PMID: 32206870 DOI: 10.1007/s00414-020-02282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/13/2020] [Indexed: 10/24/2022]
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79
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Bertoglio B, Grignani P, Di Simone P, Polizzi N, De Angelis D, Cattaneo C, Iadicicco A, Fattorini P, Presciuttini S, Previderè C. Disaster victim identification by kinship analysis: the Lampedusa October 3rd, 2013 shipwreck. Forensic Sci Int Genet 2020; 44:102156. [DOI: 10.1016/j.fsigen.2019.102156] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 12/30/2022]
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80
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Della Rocca C, Alladio E, Barni F, Cannone F, D’Atanasio E, Trombetta B, Berti A, Cruciani F. LOW DISCRIMINATION POWER OF THE YFILER™ PLUS PCR AMPLIFICATION KIT IN AFRICAN POPULATIONS. DO WE NEED MORE RM Y-STRs? FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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81
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X-chromosome analysis in an unusual deficiency maternity case. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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82
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Genetic characterization of 12 STRs (Investigator® HDplex kit) in the Ecuadorian population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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83
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DNA identification of skeletal remains by investigator’s intuition. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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84
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X-InDels efficacy evaluation in a critical samples paternity case: A Spanish Civil War case from the memorial of the camposines (Tarragona, Spain). FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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85
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Zavarin V, Ilina V, Krassotkin Y, Makarova T, Sutiagina D, Semikhodskii A. Evaluation of sensitivity and specificity of sibship determination in the Caucasian population of the Russian Federation using the 23 STR loci VeriFiler panel. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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86
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Genetic polymorphisms of 12 X-STRs in the Ecuadorian population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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87
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Palomo-Díez S, Gomes C, López-Parra A, Baeza-Richer C, Cuscó I, Raffone C, García-Arumí E, Vinueza-Espinosa D, Santos C, Montes N, Rasal R, Escala O, Cuellar J, Subirá E, Casals F, Malgosa A, Tizzano E, Tartera E, Domenech G, Arroyo-Pardo E. Genetic identification of Spanish civil war victims. The state of the art in Catalonia (Northeastern Spain). FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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88
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Martínez JJ, Tula Molina MF, Sánchez LA, Deus MI, Ramella MI, Maurín GB, Martínez G, Chernomoretz A, Escobar MS, Sibilla G, Miozzo MC. First-degree familial relationships coincidences in a population database of Jujuy (Argentina) compared with simulated populations. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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89
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Castillo A, Pico A, Gil A, Gusmão L, Vargas C. Genetic variation of 23 STR loci in a Northeast Colombian population (department of Santander). FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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90
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Building a custom large-scale panel of novel microhaplotypes for forensic identification using MiSeq and Ion S5 massively parallel sequencing systems. Forensic Sci Int Genet 2019; 45:102213. [PMID: 31835179 DOI: 10.1016/j.fsigen.2019.102213] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
A large number of new microhaplotype loci were identified in the human genome by applying a directed search with selection criteria emphasizing short haplotype length (<120 nucleotides) and maximum levels of polymorphism in the composite SNPs. From these searches, 107 autosomal microhaplotypes and 11 X chromosome microhaplotypes were selected, with well-spaced autosomal positions to ensure their independence in relationship tests. The 118 microhaplotypes were assembled into a single multiplex assay for the analysis of forensic DNA with massively parallel sequencing (MPS). A single AmpliSeq-adapted primer set was made for Illumina MiSeq and Thermo Fisher Ion S5 MPS platforms and the performance of the assay was comprehensively evaluated in both systems. Five microhaplotypes showed critical sequencing failures in both MPS platforms and were removed, while a further 13 required manual checks and the application of sequence quality thresholds in one or both systems to ensure the successful analysis of low-level DNA in these loci. The targeting of short microhaplotype spans during marker selection, with an average length of 51 nucleotides in the 118 loci, led to a high level of sensitivity for the panel when sequencing the very degraded DNA typically encountered in forensic casework and the identification of missing persons.
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91
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Mitochondrial DNA variation in Sub-Saharan Africa: Forensic data from a mixed West African sample, Côte d'Ivoire (Ivory Coast), and Rwanda. Forensic Sci Int Genet 2019; 44:102202. [PMID: 31775077 DOI: 10.1016/j.fsigen.2019.102202] [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] [Received: 06/04/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 11/23/2022]
Abstract
This study provides 398 novel complete mitochondrial control region sequences that augment the still underrepresented data from Africa by three datasets: a mixed West African sample set deriving from 12 countries (n = 145) and datasets from Côte d'Ivoire (Ivory Coast) (n = 100) as well as Rwanda (n = 153). The analysis of mtDNA variation and genetic comparisons with published data revealed low random match probabilities in all three datasets and typical West African and East African diversity, respectively. Genetic parameters indicate that the presented mixed West African dataset may serve as first forensic mtDNA control region database for West Africa in general. In addition, a strategy for responsible forensic application of precious mtDNA population samples potentially containing close maternal relatives is outlined. The datasets will be uploaded to the forensic mtDNA database EMPOP (https://empop.online) upon publication.
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92
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Siino V, Sears C. Artificially intelligent scoring and classification engine for forensic identification. Forensic Sci Int Genet 2019; 44:102162. [PMID: 31604203 DOI: 10.1016/j.fsigen.2019.102162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 11/16/2022]
Abstract
Despite advances in genotyping technologies, traditional kinship analysis tools utilized in forensic identification have seen limited evolution and lack measures of accuracy. Here, we leverage artificial intelligence (AI) and extend the Elston-Stewart algorithm to deliver a method that provides an unprecedented level of flexibility to matching individuals with pedigrees by likelihood ratio. We designed an AI that utilizes a prediction cascade based on gradient descent logistic regression which allows for iterative solution of multi missing person scenarios. Furthermore, the AI can quantify the confidence underlying likelihood ratios across the spectrum of pedigrees, regardless of the amount of genetic information available and the number of missing persons. The algorithm accommodates an arbitrary number of generations and ancestral relationships, including multiple marriages, mutations, and consanguinity. We demonstrate that a properly trained AI significantly and reproducibly outperforms a human interpreter. We discuss published limitations of existing tools and demonstrate that they are not amenable to the size and complexity of this study. This novel method significantly improves the trade-off between sensitivity and specificity beyond the limits of traditional kinship analysis tools and introduces opportunities beyond the field of forensic genetics.
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Affiliation(s)
- Viviane Siino
- Ananomouse Corporation, Newton, MA 02459, United States.
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93
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Brazilian forensic casework analysis through MPS applications: Statistical weight-of-evidence and biological nature of criminal samples as an influence factor in quality metrics. Forensic Sci Int 2019; 303:109938. [DOI: 10.1016/j.forsciint.2019.109938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/22/2019] [Indexed: 12/18/2022]
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94
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Optimizing the information increase through the addition of relatives and genetic markers in identification and kinship cases. Forensic Sci Int Genet 2019; 40:210-218. [DOI: 10.1016/j.fsigen.2019.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/23/2019] [Accepted: 02/20/2019] [Indexed: 11/18/2022]
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95
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Genetic kinship and admixture in Iron Age Scytho-Siberians. Hum Genet 2019; 138:411-423. [DOI: 10.1007/s00439-019-02002-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/15/2019] [Indexed: 01/08/2023]
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96
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Living with the dead: A case report and review of the literature. J Forensic Leg Med 2019; 62:107-111. [DOI: 10.1016/j.jflm.2019.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/31/2019] [Accepted: 02/04/2019] [Indexed: 11/19/2022]
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97
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Courts C, Preuß-Wössner J. All mixed up?-genotype change after stem cell transplantation impeded verification of 21-year-old semen sample-a case report. Int J Legal Med 2019; 133:767-770. [PMID: 30617846 DOI: 10.1007/s00414-018-01995-x] [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: 11/08/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
Abstract
We report a case of identity testing in which a patient charged us with the verification of a semen sample that he had donated and cryopreserved more than 20 years ago and now was suspecting of having been inadvertently interchanged. We found a non-match of the DNA profiles of the patient's blood and the semen samples but could show that this was due to the patient having received a stem cell transplantation of his full brother as part of a cancer therapy in 1997 which was not known to us when the samples were first tested. Also, the blood and semen samples exhibited a low probability of full sibship at first supporting the patient's suspicion that his semen sample might indeed have been interchanged. By also testing Y-STRs and including hair roots in the DNA analysis, we could show that the transplant did indeed originate from the patient's brother and that the semen sample did indeed originate from the patient.
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Affiliation(s)
- Cornelius Courts
- Institute of Forensic Medicine, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 12, Kiel, Germany.
| | - Johanna Preuß-Wössner
- Institute of Forensic Medicine, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 12, Kiel, Germany
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98
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Liu QL, Chen YF, Zang Y, Liu KY, Zhao H, Lu DJ. Two loci concurrent mutations in non-exclusion parentage cases using 19 STR profiles. Leg Med (Tokyo) 2018; 35:73-76. [DOI: 10.1016/j.legalmed.2018.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 08/19/2018] [Accepted: 09/22/2018] [Indexed: 11/29/2022]
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99
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Holmala K, Herrero A, Kopatz A, Schregel J, Eiken HG, Hagen SB. Genetic evidence of female kin clusters in a continuous population of a solitary carnivore, the Eurasian lynx. Ecol Evol 2018; 8:10964-10975. [PMID: 30519420 PMCID: PMC6262933 DOI: 10.1002/ece3.4562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/16/2018] [Accepted: 08/29/2018] [Indexed: 11/11/2022] Open
Abstract
Large terrestrial carnivores can sometimes display strong family bonds affecting the spatial distribution of related individuals. We studied the spatial genetic relatedness and family structure of female Eurasian lynx, continuously distributed in southern Finland. We hypothesized that closely related females form matrilineal assemblages, clustering together with relatives living in the neighboring areas. We evaluated this hypothesis using tissue samples of 133 legally harvested female lynx (from year 2007 to 2015), genotyped with 23 microsatellite markers, and tested for possible spatial genetic family structure using a combination of Bayesian clustering, spatial autocorrelation, and forensic genetic parentage analysis. The study population had three potential family genetic clusters, with a high degree of admixture and geographic overlap, and showed a weak but significant negative relationship between pairwise genetic and geographic distance. Moreover, parentage analysis indicated that 64% of the females had one or more close relatives (sister, mother, or daughter) within the study population. Individuals identified as close kin consistently assigned to the same putative family genetic cluster. They also were sampled closer geographically than females on average, although variation was large. Our results support the possibility that Eurasian lynx forms matrilineal assemblages, and comparisons with males are now required to further assess this hypothesis.
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Affiliation(s)
- Katja Holmala
- Natural Resources Institute Finland (Luke)HelsinkiFinland
| | - Annika Herrero
- Natural Resources Institute Finland (Luke)HelsinkiFinland
| | - Alexander Kopatz
- NIBIO – SvanhovdNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Julia Schregel
- NIBIO – SvanhovdNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Hans G. Eiken
- NIBIO – SvanhovdNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Snorre B. Hagen
- NIBIO – SvanhovdNorwegian Institute of Bioeconomy ResearchSvanvikNorway
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100
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Tillmar A, Grandell I, Montelius K. DNA identification of compromised samples with massive parallel sequencing. Forensic Sci Res 2018; 4:331-336. [PMID: 32002491 PMCID: PMC6968675 DOI: 10.1080/20961790.2018.1509186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 11/04/2022] Open
Abstract
Genetic profiling is a standard procedure for human identification, i.e. in criminal cases and mass disasters, and has been proven to be an important part in the process in the repatriation of victims to their relatives. In the event of a catastrophe whether it be a natural disaster, terror attack or accident, fatalities of many nationalities may be a consequence and international collaboration becomes necessary. Current DNA techniques used on a routine basis at forensic laboratories world-wide are very useful, and results reported from different labs are compared, making it possible to be matched in order to declare the identification of a victim. Statistical calculations of possibilities of a random match are achievable since population data from many parts of the world are available. However, decomposition and degradation of the remains are not uncommon in the aftermath of a catastrophe and hence it may be difficult to retrieve detailed DNA profiles from such samples. Massive parallel sequencing (MPS) is a technique capable of producing a vast amount of DNA sequence data in a high-through put manner, and panels of single nucleotide polymorphism (SNP) markers allow the amplification of small DNA fragments, often seen in compromised samples. Here, we report the results from a set of 10 samples from missing person identification cases, analyzed with an MPS based method comprising 131 SNP markers and compared with direct reference material or buccal swab samples collected from relatives of the deceased. We assess the weight of evidence of a match by statistical calculation. Furthermore, we compare results reported on different platforms using different SNP panels, and conclude that more work has to be done if results from missing person identification cases analyzed on MPS with SNP panels at different laboratories are to be fully reliable and thus comparable.
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Affiliation(s)
- Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.,Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden
| | - Ida Grandell
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Kerstin Montelius
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
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