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Li R, Wang N, Zang Y, Liu J, Wu E, Wu R, Sun H. Easykin: a flexible and user-friendly online tool for forensic kinship testing and missing person identification. Int J Legal Med 2023; 137:1671-1681. [PMID: 37747571 DOI: 10.1007/s00414-023-03083-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/05/2023] [Indexed: 09/26/2023]
Abstract
In forensic kinship testing and missing person identification, it is a fundamental question to choose the most informative reference relatives, select appropriate genotyping systems, and evaluate the weight of evidence comprehensively. Despite that several useful tools have been developed, they have not addressed these questions satisfactorily. In this paper, we develop a flexible and user-friendly online tool, Easykin, to address the aforementioned issues. It has some promising features: (i) Pedigrees can be constructed easily and presented intuitively with just a few mouse clicks. (ii) System power can be estimated before testing based on certain set of markers and reference relatives. (iii) The pruning function of EasyKin enables users to choose appropriate subsets of available references. (iv) Parameters at a specific LR for a single case may ease evidence interpretation. (v) The user interface (UI) is an HTML-based dashboard, which is friendly to both professional and non-professional users and can be used anytime and anywhere. Here, we presented three common cases as examples to demonstrate how kinship testing and missing person identification can be improved with EasyKin. In conclusion, this tool provides a one-stop solution for forensic use, that is, instructing users to choose appropriate kits and reference relatives before testing, calculating LR in the testing, and providing parameters for data interpretation after testing. EasyKin is freely available at https://forensicsysu.shinyapps.io/EasyKin/ .
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Affiliation(s)
- Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, 510080, Guangdong, People's Republic of China
- School of Medicine, Jiaying University, Meizhou, 514015, People's Republic of China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510089, Guangdong, People's Republic of China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, 510080, Guangdong, People's Republic of China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510089, Guangdong, People's Republic of China
| | - Yu Zang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, 510080, Guangdong, People's Republic of China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510089, Guangdong, People's Republic of China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, 510080, Guangdong, People's Republic of China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510089, Guangdong, People's Republic of China
| | - Enlin Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, 510080, Guangdong, People's Republic of China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510089, Guangdong, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, 510080, Guangdong, People's Republic of China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510089, Guangdong, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, 510080, Guangdong, People's Republic of China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510089, Guangdong, People's Republic of China.
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2
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Analysis of Family Structure and Paternity Test of Tan Sheep in Yanchi Area, China. Animals (Basel) 2022; 12:ani12223099. [PMID: 36428327 PMCID: PMC9686711 DOI: 10.3390/ani12223099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Tan sheep is a special breed of locally protected sheep in China, one of the best quality meat sheep in the world. Due to the unclear pedigree of the rams on the Ningxia Tan sheep breeding farm, we investigated 74 rams in the field and explored a new method for family division. Genomic DNA was extracted from the blood of breeding rams. Using Plink software, GCTA tools and R language, we analyzed the genetic structure, kinship, and inbreeding coefficient of the breeding sheep, which revealed the genetic relationship between the individuals. The results showed that there was no obvious clustering phenomenon in the PCA, and the genetic background of the samples was similar. The G matrix and IBS distance matrix indicated that most individuals were far away from each other. Paternity testing identified 24 pairs of unknown parent-child pairs, and all the Tan sheep could be divided into 12 families, which provided a reference for sheep breeding. The average inbreeding coefficient based on the ROH of this population was 0.049, so there was a low degree of inbreeding and the rams in the field were able to maintain high genetic diversity. Overall, we explored a more accurate method through paternity and kinship analysis; it provides a scientific basis for pedigree construction, which has an important application value for Tan sheep breeding.
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Xu Q, Wang Z, Kong Q, Wang X, Huang A, Li C, Liu X. Improving the System Power of Complex Kinship Analysis by Combining Multiple Systems. Forensic Sci Int Genet 2022; 60:102741. [DOI: 10.1016/j.fsigen.2022.102741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/04/2022] [Accepted: 06/12/2022] [Indexed: 11/04/2022]
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4
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Laurent FX, Fischer A, Oldt RF, Kanthaswamy S, Buckleton JS, Hitchin S. Streamlining the decision-making process for international DNA kinship matching using Worldwide allele frequencies and tailored cutoff log 10LR thresholds. Forensic Sci Int Genet 2021; 57:102634. [PMID: 34871915 DOI: 10.1016/j.fsigen.2021.102634] [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: 02/16/2021] [Revised: 10/13/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022]
Abstract
The identification of human remains belonging to missing persons is one of the main challenges for forensic genetics. Although other means of identification can be applied to missing person investigations, DNA is often extremely valuable to further support or refute potential associations. When reference DNA samples cannot be collected from personal items belonging to a missing person, a direct DNA identification cannot be carried out. However, identifications can be made indirectly using DNA from the missing person's relatives. The ranking of likelihood ratio (LR) values, which measure the fit of a missing person for any given pedigree, is often the first step in selecting candidates in a DNA database. Although implementing DNA kinship matching in a national environment is feasible, many challenges need to be resolved before applying this method to an international configuration. In this study, we present an innovative and intuitive method to perform international DNA kinship matching and facilitate the comparison of DNA profiles when the ancestry is unknown or unsure and/or when different marker sets are used. This straightforward method, which is based on calculations performed with the DNA matching software BONAPARTE, Worldwide allele frequencies and tailored cutoff log10LR thresholds, allows for the classification of potential candidates according to the strength of the DNA evidence and the predicted proportion of adventitious matches. This is a powerful method for streamlining the decision-making process in missing person investigations and DVI processes, especially when there are low numbers of overlapping typed STRs. Intuitive interpretation tables and a decision tree will help strengthen international data comparison for the identification of reported missing individuals discovered outside their national borders.
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Affiliation(s)
- François-Xavier Laurent
- International Criminal Police Organization - INTERPOL, DNA Unit, 200 quai Charles de Gaulle, 69006 Lyon, France.
| | - Andrea Fischer
- International Criminal Police Organization - INTERPOL, DNA Unit, 200 quai Charles de Gaulle, 69006 Lyon, France; Landeskriminalamt Baden-Württemberg, Taubenheimstr. 85, 70372 Stuttgart, Germany
| | - Robert F Oldt
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - John S Buckleton
- University of Auckland, Department of Statistics, Private Bag, 92019 Auckland, New Zealand
| | - Susan Hitchin
- International Criminal Police Organization - INTERPOL, DNA Unit, 200 quai Charles de Gaulle, 69006 Lyon, France.
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5
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Wu R, Chen H, Li R, Zang Y, Shen X, Hao B, Wang Q, Sun H. Pairwise kinship testing with microhaplotypes: Can advancements be made in kinship inference with these markers? Forensic Sci Int 2021; 325:110875. [PMID: 34166816 DOI: 10.1016/j.forsciint.2021.110875] [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: 04/02/2021] [Revised: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Kinship testing based on genetic relatedness is one of the major tasks in forensic genetics. Although short tandem repeats (STRs) are the "gold standard" biomarkers for relationship testing, microhaplotypes (MHs) have also emerged as viable options for kinship elucidation. In this work, the kinship testing efficiency of 54 highly polymorphic MHs was studied in two extended families consisting of parent-offspring, full siblings, grandparent-grandchildren, uncle/aunt-nephew/nieces, and first cousins. In addition, ten-thousand pairs of different degrees of relationships were simulated using various datasets including 54 MHs, 27 STRs plus 94 single nucleotide polymorphisms (SNPs) that were included in the ForenSeq DNA Signature Prep Kit (ForenSeq), 54 MHs plus loci in ForenSeq, and different subsets of 417-published MHs. The panels' system effectiveness in the kinship analysis were accessed by likelihood ratio distributions. The results showed that 54 MHs could be used in first-degree relationship testing with high reliability. The effectiveness of 54 MHs was slightly lower than ForenSeq but only by a narrow margin. Both 54 MHs and ForenSeq were not sufficient for distant relationship testing, and approximately 200 microhaplotypes with an average expected heterozygosity (He) = 0.79 were enough to determine second-degree relationships, but a panel of 417 MHs with an average He = 0.72 was not sufficient to first cousins testing according to the simulation analysis. In conclusion, 54 MHs could be used to serve as supplement markers for kinship testing; and well-established STR markers plus well-performing microhaplotype markers may become collective tools in forensic applications, though an enlarged pool of forensic markers is needed for distant relationship testing.
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Affiliation(s)
- Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Hui Chen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Yu Zang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Bo Hao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
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6
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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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Zhang Y, Yu Z, Mo X, Zhao X, Li W, Liu H, Liu C, Wu R, Sun H. Comparative evaluation of autosomal STRs and X-chromosome STRs as a complement of autosomal STRs in kinship testing in Southern Han Chinese. Ann Hum Biol 2020; 48:66-69. [PMID: 33256486 DOI: 10.1080/03014460.2020.1856926] [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] [Indexed: 10/22/2022]
Abstract
Nowadays, kinship testing is very common in forensic caseworks, but the power of autosomal short tandem repeats (A-STRs) may be limited in complex cases. X-Chromosome short tandem repeats (X-STRs), having a unique heritage mode, should be of special use in some deficient cases. To evaluate and compare the potential of A-STR and X-STR as supplement genetic markers in deficient kinship testing, we simulated 10,000 duos for each of 18 kinds of relationships involving full sibling, half-sibling, grandparent-grandchild, and uncle/aunt-nephew/niece. Loci from STRTyper10, PowerPlex 16, and Investigator Argus X-12 were studied in Southern Han Chinese and the distribution of likelihood ratio (LR) values was analysed. With the addition of the X-12 system, the distribution of LR values for the full sisters, paternal half-sisters, paternal grandmother-granddaughters, maternal aunt-nieces, and maternal aunt-nephews separated much more obviously from those of unrelated duos, and the effectiveness was 1.0000, 0.99865, 0.9991, 0.8996 and 0.9634, respectively, which was more efficient than A-STRs. For the individual duos with other relationships, the effects of adding X-STRs and A-STRs were similar. Therefore, for the Southern Han Chinese, X-STRs can be very useful in kinship testing involving full sisters, paternal half-sisters, paternal grandmother-granddaughters, and maternal aunt-nieces/nephews.
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Affiliation(s)
- Yinming Zhang
- Institute of Forensic Science, Ministry of Public Security, Beijing, P.R. China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zhengliang Yu
- Institute of Forensic Science, Ministry of Public Security, Beijing, P.R. China
| | - Xiaoting Mo
- Institute of Forensic Science, Ministry of Public Security, Beijing, P.R. China
| | - Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing, P.R. China
| | - Wanshui Li
- Institute of Forensic Science, Ministry of Public Security, Beijing, P.R. China
| | - Hong Liu
- Guangzhou Forensic Institute, Guangzhou, P.R. China
| | - Chao Liu
- Guangzhou Forensic Institute, Guangzhou, P.R. China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
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8
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Delest A, Godfrin D, Chantrel Y, Ulus A, Vannier J, Faivre M, Hollard C, Laurent FX. Sequenced-based French population data from 169 unrelated individuals with Verogen's ForenSeq DNA signature prep kit. Forensic Sci Int Genet 2020; 47:102304. [PMID: 32417726 DOI: 10.1016/j.fsigen.2020.102304] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022]
Abstract
Massively Parallel Sequencing (MPS) applied to forensic genetics allows the simultaneous analysis of hundreds of genetic markers and the access to full amplicon sequences which help to increase available allele diversity. Meanwhile, sequence variation within the repeat regions represents the majority of the allele diversity, flanking regions adjacent to the repeat core provide an additional degree of variation. The forensic genetics community needs access to population data, from relevant parts of the world that contain this new sequence diversity in order to perform statistical calculations. In this study, we report sequence-based Short Tandem Repeat (STR) and identity Single Nucleotide Polymorphism (iSNPs) allele data for 169 French individuals across 58 STRs and 92 SNPs included in the Verogen ForenSeq DNA Signature Prep kit. 42 STRs out of 58 showed an increased number of alleles due to sequence variation in the repeat motif and/or the flanking regions. D9S1122 showed the largest overall gain with an increase of observed heterozygosities of almost 25 %. The combined match probability combining 27 autosomal STRs and 91 identity SNPs was 1.11E-69. Sequence-based allele frequencies included in this publication will help forensic laboratories to increase the power of discrimination for identification, kinship analysis and mixture interpretation.
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Affiliation(s)
- Anna Delest
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France.
| | - Dominique Godfrin
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Yann Chantrel
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Ayhan Ulus
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Julien Vannier
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Magalie Faivre
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Clémence Hollard
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - François-Xavier Laurent
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France.
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Zvénigorosky V, Sabbagh A, Gonzalez A, Fausser JL, Palstra F, Romanov G, Solovyev A, Barashkov N, Fedorova S, Crubézy É, Ludes B, Keyser C. The limitations of kinship determinations using STR data in ill-defined populations. Int J Legal Med 2020; 134:1981-1990. [PMID: 32318826 DOI: 10.1007/s00414-020-02298-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/07/2020] [Indexed: 11/30/2022]
Abstract
The likelihood ratio (LR) method is commonly used to determine kinship in civil, criminal, or forensic cases. For the past 15 years, our research group has also applied LR to ancient STR data and obtained kinship results for collections of graves or necropolises. Although we were able to reconstruct large genealogies, some pairs of individuals showed ambiguous results. Second-degree relationships, half-sibling pairs for example, were often inconsistent with detected first-degree relationships, such as parent/child or brother/sister pairs. We therefore set about providing empirical estimations of the error rates for the LR method in living populations with STR allelic diversities comparable to that of the ancient populations we had previously studied. We collected biological samples in the field in North-Eastern Siberia and West Africa and studied more than 800 pairs of STR profiles from individuals with known relationships. Because commercial STR panels were constructed for specific regions (namely Europe and North America), their allelic makeup showed a significant deficit in diversity when compared to European populations, replicating a situation often faced in ancient DNA studies. We assessed the capacity of the LR method to confirm known relationships (effectiveness) and its capacity to detect those relationships (reliability). Concerns over the effectiveness of LR determinations are mostly an issue in forensic studies, while the reliability of the detection of kinship is an issue for the study of necropolises or other large gatherings of unidentified individuals, such as disaster victims or mass graves. We show that the application of LR to both test populations highlights specific issues (both false positives and false negatives) that prevent the confirmation of second-degree kinship or even full siblingship in small populations. Up to 29% of detected full sibling relationships were either overestimated half-sibling relationships or underestimated parent-offspring relationships. The error rate for detected half-sibling relationships was even higher, reaching 41%. Only parent-offspring pairs were reliably detected or confirmed. This implies that, in populations that are small, ill-defined, or for which the STR loci analyzed are inappropriate, an examiner might not be able to distinguish a pair of full siblings from a pair of half-siblings. Furthermore, half-sibling pairs might be overlooked altogether, an issue that is exacerbated by the common confusion, in many languages and cultures, between half-siblings and full siblings. Consequently, in the study of ancient populations, human remains of unknown origins, or poorly surveyed modern populations, we recommend a conservative approach to kinship determined by LR. Next-generation sequencing data should be used when possible, but the costs and technology involved might be prohibitive. Therefore, in potentially contentious situations or cases lacking sufficient external information, uniparental markers should be analyzed: ideally, complete mitochondrial genomes and Y-chromosome haplotypes (STR, SNP, and/or sequencing).
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Affiliation(s)
- Vincent Zvénigorosky
- CNRS FRE 2029-BABEL,, Paris Descartes University, Paris, France. .,Strasbourg Institute of Legal Medicine, Strasbourg, France.
| | - Audrey Sabbagh
- UMR 261 MERIT, IRD, Paris Descartes University, Paris, France
| | | | | | - Friso Palstra
- UMR 261 MERIT, IRD, Paris Descartes University, Paris, France
| | - Georgii Romanov
- Laboratory of Molecular Biology, North-Eastern Federal University, Yakutsk, Sakha Republic, Russia.,Laboratory of Molecular Genetics, Yakut Science-Centre of Complex Medical Problems, Yakutsk, Sakha Republic, Russia
| | - Aisen Solovyev
- Laboratory of Molecular Biology, North-Eastern Federal University, Yakutsk, Sakha Republic, Russia.,Institute for Humanitarian Studies and Problems of Indigenous Peoples of the North, Yakutsk, Sakha Republic, Russia
| | - Nikolay Barashkov
- Laboratory of Molecular Biology, North-Eastern Federal University, Yakutsk, Sakha Republic, Russia.,Laboratory of Molecular Genetics, Yakut Science-Centre of Complex Medical Problems, Yakutsk, Sakha Republic, Russia
| | - Sardana Fedorova
- Laboratory of Molecular Biology, North-Eastern Federal University, Yakutsk, Sakha Republic, Russia.,Laboratory of Molecular Genetics, Yakut Science-Centre of Complex Medical Problems, Yakutsk, Sakha Republic, Russia
| | - Éric Crubézy
- CNRS UMR 5288 AMIS, Toulouse Paul Sabatier University, Toulouse, France
| | - Bertrand Ludes
- CNRS FRE 2029-BABEL,, Paris Descartes University, Paris, France
| | - Christine Keyser
- CNRS FRE 2029-BABEL,, Paris Descartes University, Paris, France.,Strasbourg Institute of Legal Medicine, Strasbourg, France
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10
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Cho S, Kim MY, Lee JH, Lee HY, Lee SD. Large-scale identification of human bone remains via SNP microarray analysis with reference SNP database. Forensic Sci Int Genet 2020; 47:102293. [PMID: 32276230 DOI: 10.1016/j.fsigen.2020.102293] [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: 05/25/2019] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are valuable markers complementary to conventional forensic short tandem repeat (STR) markers in genetic typing, with potential advantages in challenging forensic casework. With the advent of high-throughput technologies, such as microarrays and massively parallel sequencing, the use of SNP typing has now expanded to large-scale forensic applications. Herein, a forensic case is presented to demonstrate the usefulness of SNP typing in identifying large-scale human bone remains with reference database construction. A total of 402 bone remains were recovered from an island in the Jeju Province of Korea where a massive disaster occurred in 1948. The first phase of the identification process was accomplished via conventional DNA typing methods including autosomal and Y-chromosomal STR typing, and mitochondrial DNA sequencing, which resulted in the identification of 74 of 402 remains. The second phase of the identification involved the remaining 327 unidentified remains using SNP typing as a supplementary tool based on Affymetrix resequencing array. The SNP markers of 782 family members were also analyzed and a reference database was constructed for comparison. An additional 51 bone remains were identified in the second phase. SNP data obtained from the supplementary genotyping yielded additional genetic information as well as contributed to kinship testing to determine the second degrees of relationship. In addition SNPs are useful in discriminating ambiguous relationship when only STR data are available. A software program developed for SNP typing system enabled efficient kinship analysis for large-scale forensic identification. The results and the casework are described and discussed.
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Affiliation(s)
- Sohee Cho
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Moon-Young Kim
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Hwan Young Lee
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea; Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Soong Deok Lee
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea; Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea.
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11
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Hwa HL, Wu MY, Lee JCI, Yin HI, Hsu PM, Li SF, Hwu WL, Su CW. Analysis of nondegraded and degraded DNA mixtures of close relatives using massively parallel sequencing. Leg Med (Tokyo) 2020; 42:101631. [DOI: 10.1016/j.legalmed.2019.101631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/30/2019] [Accepted: 09/21/2019] [Indexed: 10/25/2022]
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12
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Slooten K. Likelihood ratio distributions and the (ir)relevance of error rates. Forensic Sci Int Genet 2020; 44:102173. [DOI: 10.1016/j.fsigen.2019.102173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/29/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022]
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13
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Zhu J, Chen P, Qu S, Wang Y, Jian H, Cao S, Liu Y, Zhang R, Lv M, Liang W, Zhang L. Evaluation of the microhaplotype markers in kinship analysis. Electrophoresis 2019; 40:1091-1095. [DOI: 10.1002/elps.201800351] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 11/02/2018] [Accepted: 12/12/2018] [Indexed: 01/28/2023]
Affiliation(s)
- Jing Zhu
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Peng Chen
- Department of Forensic MedicineNanjing Medical University Nanjing P. R. China
| | - Shengqiu Qu
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Yinji Wang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Hui Jian
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Shuqiang Cao
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Yuqing Liu
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Ranran Zhang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Meili Lv
- Department of ImmunologyWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Weibo Liang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Lin Zhang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
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14
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Li R, Li H, Peng D, Hao B, Wang Z, Huang E, Wu R, Sun H. Improved pairwise kinship analysis using massively parallel sequencing. Forensic Sci Int Genet 2019; 38:77-85. [DOI: 10.1016/j.fsigen.2018.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 09/24/2018] [Accepted: 10/09/2018] [Indexed: 01/16/2023]
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