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Tan Y, Tian H, Xiao Y, Xu B, Wang H, Yang M, Liu S. Screening a new set of microhaplotypes in exonic regions for sample identity testing and paternity testing during whole exome sequencing analysis. Int J Legal Med 2024:10.1007/s00414-024-03326-9. [PMID: 39325160 DOI: 10.1007/s00414-024-03326-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 08/31/2024] [Indexed: 09/27/2024]
Abstract
Whole exome sequencing (WES) is widely used in clinical diagnosis. Before obtaining an accurate diagnosis, it is essential to conduct sample identity testing and paternity testing on trio samples. Currently, there is a lack of optimal genetic markers for these purposes, with limited literature available in this area. Microhaplotypes (MHs) are promising genetic markers due to their high polymorphism, low mutation rate, short amplified fragments, absence of stutter and amplification bias. These characteristics make them suitable for sample tracking and paternity testing during WES analysis. In this study, we screened out a set of polymorphic MHs in exonic regions for the above purposes. The results showed that the power of discrimination (PD) and probability of exclusion (PE) of this set of markers ranged from 0.2682 to 0.8878 and 0.0178 to 0.4583, respectively. Both the cumulative power of discrimination (CPD) and cumulative probability of exclusion (CPE) exceeded 0.999999, indicating the great value of these markers in paternity testing and individual identification in the study population. However, these markers had the effective number of alleles (Ae) values ranging from 1.1784 to 3.8727 (average 2.1805) and informativeness (In) values ranging from 0.0151 to 0.2209 (average 0.0766), showing limited value in DNA mixture analysis and biogeographical ancestry inference.
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Affiliation(s)
- Yu Tan
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Huan Tian
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Yuanyuan Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Bocheng Xu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - Mei Yang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China.
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China.
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2
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Zhang Q, Liu L, Wang Y, Liu Q, Zhang M, Zhang X, Tang Z, Ding X, Zhang X, Shao L, Zhou Z, Wang S. Genetic identification of human remains from the Korean War. Electrophoresis 2024; 45:1356-1369. [PMID: 38549469 DOI: 10.1002/elps.202200197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/15/2024] [Accepted: 01/27/2024] [Indexed: 08/22/2024]
Abstract
The genetic identification of skeletal remains from Chinese People's Volunteers (CPVs) of the Korean War has been challenging because of the degraded DNA samples and the lack of living close relatives. This study established a workflow for identifying CPVs by combining Y-chromosome short tandem repeats (Y-STRs), mitochondrial DNA (mtDNA) hypervariable regions I and II, autosomal STRs (aSTRs), and identity-informative SNPs (iiSNPs). A total of 20 skeletal remains of CPVs and 46 samples from their alleged relatives were collected. The success rate of DNA extraction from human remains was 100%. Based on Y-STRs, six remains shared the same male lineages with their alleged relatives. Meanwhile, mtDNA genotyping supports two remains sharing the same maternal lineages with their alleged relatives. Likelihood ratios (LRs) were further obtained from 27 aSTRs and 94 iiSNPs or 1936 iiSNPs to confirm their relationship. All joint pedigree LRs were >100. Finally, six remains were successfully identified. This pilot study for the systematic genetic identification of CPVs from the Korean War can be applied for the large-scale identification of CPVs in the future.
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Affiliation(s)
- Qingzhen Zhang
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Liyan Liu
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Yu Wang
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Qiqi Liu
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Minli Zhang
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Xiaochang Zhang
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Zhaobing Tang
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Xiaoran Ding
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - XiuJuan Zhang
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Liting Shao
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Zhe Zhou
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing, P. R. China
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Haarkötter C, Saiz M, Gálvez X, Vinueza-Espinosa DC, Medina-Lozano MI, Álvarez JC, Lorente JA. Evaluation of the usefulness of insertion-null markers in critical skeletal remains. Int J Legal Med 2024; 138:1287-1293. [PMID: 38509248 PMCID: PMC11164766 DOI: 10.1007/s00414-024-03205-3] [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: 10/20/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Forensic DNA analysis in compromised skeletal remains may pose challenges due to DNA degradation, often resulting in partial or negative autosomal STRs profiles. To address this issue, alternative approaches such as mitochondrial DNA or SNPs typing may be employed; however, they are labour-intensive and costly. Insertion-null alleles (INNULs), short interspersed nuclear elements, have been suggested as a valuable tool for human identification in challenging samples due to their small amplicon size. A commercial kit including 20 INNULs markers along with amelogenin (InnoTyper® 21) has been developed. This study assesses its utility using degraded skeletal remains, comparing the results obtained (the number of detected alleles, RFU values, PHR, and the number of reportable markers) to those obtained using GlobalFiler™. Subsequently, the random match probability of the two profiles for each sample was determined using Familias version 3 to evaluate the power of discrimination of the results obtained from each kit. In every sample, InnoTyper® 21 yielded more alleles, higher RFU values, and a greater number of reportable loci. However, in most cases, both profiles were similarly informative. In conclusion, InnoTyper® 21 serves as a valuable complement to the analysis of challenging samples in cases where a poor or negative profile was obtained.
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Affiliation(s)
- Christian Haarkötter
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - María Saiz
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - Xiomara Gálvez
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - Diana C Vinueza-Espinosa
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - María Isabel Medina-Lozano
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - Juan Carlos Álvarez
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain.
| | - Jose Antonio Lorente
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
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Agudo MM, Aanes H, Albert M, Janssen K, Gill P, Bleka Ø. An overview of autosomal STRs and identity SNPs in a Norwegian population using massively parallel sequencing. Forensic Sci Int Genet 2024; 71:103057. [PMID: 38733649 DOI: 10.1016/j.fsigen.2024.103057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024]
Abstract
In recent years, probabilistic genotyping software has been adapted for the analysis of massively parallel sequencing (MPS) forensic data. Likelihood ratios (LR) are based on allele frequencies selected from populations of interest. This study provides an outline of sequence-based (SB) allele frequencies for autosomal short tandem repeats (aSTRs) and identity single nucleotide polymorphisms (iSNPs) in 371 individuals from Southern Norway. 27 aSTRs and 94 iSNPs were previously analysed with the ForenSeq™ DNA Signature Prep Kit (Verogen). The number of alleles with frequencies less than 0.05 for sequenced-based alleles was 4.6 times higher than for length-based alleles. Consistent with previous studies, it was observed that sequence-based data (both with and without flanks) exhibited higher allele diversity compared to length-based (LB) data; random match probabilities were lower for SB alleles confirming their advantage to discriminate between individuals. Two alleles in markers D22S1045 and Penta D were observed with SNPs in the 3´ flanking region, which have not been reported before. Also, a novel SNP with a minor allele frequency (MAF) of 0.001, was found in marker TH01. The impact of the sample size on minor allele frequency (MAF) values was studied in 88 iSNPs from Southern Norway (n = 371). The findings were then compared to a larger Norwegian population dataset (n = 15,769). The results showed that the smaller Southern Norway dataset provided similar results, and it was a representative sample. Population structure was analyzed for regions within Southern Norway; FST estimates for aSTR and iSNPs did not indicate any genetic structure. Finally, we investigated the genetic differences between Southern Norway and two other populations: Northern Norway and Denmark. Allele frequencies between these populations were compared, and we found no significant frequency differences (p-values > 0.0001). We also calculated the pairwise FST values per marker and comparisons between Southern and Northern Norway showed small differences. In contrast, the comparisons between Southern Norway and Denmark showed higher FST values for some markers, possibly driven by distinct alleles that were present in only one of the populations. In summary, we propose that allele frequencies from each population considered in this study could be used interchangeably to calculate genotype probabilities.
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Affiliation(s)
- Maria Martin Agudo
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway; Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Håvard Aanes
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
| | - Michel Albert
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
| | - Kirstin Janssen
- Centre for Forensic Genetics, UiT The Arctic University of Norway, Norway
| | - Peter Gill
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway; Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Øyvind Bleka
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway.
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Yang D, Ma SX, Zhao GL, Gao A, Xu ZK. Determining the effects of genetic linkage when using a combination of STR and SNP loci for kinship testing. Leg Med (Tokyo) 2024; 69:102441. [PMID: 38599008 DOI: 10.1016/j.legalmed.2024.102441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/19/2024] [Accepted: 03/30/2024] [Indexed: 04/12/2024]
Abstract
The pedigree likelihood ratio (LR) can be used for determining kinship in the forensic kinship testing. LR can be obtained by analyzing the DNA data of Short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci. With the advancement of biotechnology, increasing number of genetic markers have been identified, thereby expanding the pedigree range of kinship testing. Moreover, some of the loci are physically closer to each other and genetic linkage between loci is inevitable. LRs can be calculated by accounting for linkage or ignoring linkage (LRlinkage and LRignore, respectively). GeneVisa is a software for kinship testing (www.genevisa.net) and adopts the Lander-Green algorithm to deal with genetic linkage. Herein, we used the simulation program of the software GeneVisa to investigate the effects of genetic linkage on 1st-degree, 2nd-degree, and 3rd-degree kinship testing. We used this software to simulate LRlinkage and LRignore values based on 43 STRs and 134 SNPs in commercial kits by using the allele frequency rate and genetic distance data of the European population. The effects of linkage on LR distribution and LRs of routine cases were investigated by comparing the LRlinkage values with the LRignore values. Our results revealed that the linkage effect on LR distributions is small, but the effect on LRs of routine cases may be large. Moreover, the results indicated that the discriminatory power of genetic markers for kinship testing can be improved by accounting for linkage.
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Affiliation(s)
- Da Yang
- Institute of Forensic Medicine And Laboratory Medicine, Jining Medical University, Shandong province, P. R. China; Forensic Science Center of Jining Medical University, Shandong province, P. R. China.
| | - Sheng Xuan Ma
- Institute of Forensic Medicine And Laboratory Medicine, Jining Medical University, Shandong province, P. R. China
| | - Guo Liang Zhao
- Institute of Forensic Medicine And Laboratory Medicine, Jining Medical University, Shandong province, P. R. China
| | - Ao Gao
- Institute of Forensic Medicine And Laboratory Medicine, Jining Medical University, Shandong province, P. R. China
| | - Zhao Kun Xu
- Institute of Forensic Medicine And Laboratory Medicine, Jining Medical University, Shandong province, P. R. China
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Della Rocca C, Chighine A, Piras G, Vecchio C, Mameli A. Nails as optimal source of DNA for molecular identification of 5 decomposed bodies recovered from seawater: from Y-ancestry to personal identification. Int J Legal Med 2024; 138:787-792. [PMID: 38282084 DOI: 10.1007/s00414-024-03170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/18/2024] [Indexed: 01/30/2024]
Abstract
Molecular identification of extremely compromised human remains in forensic field is usually performed from DNA typing of bones, which are a difficult sample to work with. Moreover, autosomal STR profiles do not always result in the identification of the donor due to lack of comparisons or non-hit throughout database searching. An attempt to overcome these issues is represented by fingernails as an alternative DNA source and Y-STRs typing to infer both geographical and familial ancestry of the unknown donor. In this study, we analyzed both 24 autosomal and 27 Y-chromosome STRs from unidentified human remains (UHRs) of five males recovered from the water near the southwestern coast of Sardinia by the Italian Harbor Master's Office. Nail clippings provided an optimal source of autologous DNA for molecular identification in a very short time, producing complete autosomal and Y-STR profiles even under conditions of high body degradation. Unfortunately, no match neither compatibility occurred using autosomal STRs (aSTRs), initially. Upon analyzing the Y-haplotypes, we found out they had already been observed in northern Africa, providing us important investigative leads. This prompted the International Criminal Police Organization (INTERPOL) to provide us with references of alleged relatives that were then confirmed to be related. The use of fingernails represents an excellent DNA source especially for genetic identification of decomposed bodies recovered in seawater environment. Notably, DNA extracted from nails gave high-quality Y-STR haplotypes by which predicting paternal ancestry of the unidentified donors may result fundamental in the forensic investigative context.
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Affiliation(s)
- Chiara Della Rocca
- Reparto Carabinieri Investigazioni Scientifiche di Cagliari-Sezione di Biologia, Cagliari, Italy.
| | - Alberto Chighine
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cagliari, Italy
| | - Gavino Piras
- Reparto Carabinieri Investigazioni Scientifiche di Cagliari-Sezione di Biologia, Cagliari, Italy
| | - Cesare Vecchio
- Reparto Carabinieri Investigazioni Scientifiche di Cagliari-Sezione di Biologia, Cagliari, Italy
| | - Alessandro Mameli
- Reparto Carabinieri Investigazioni Scientifiche di Cagliari-Sezione di Biologia, Cagliari, Italy
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Cai M, Lei F, Liu Y, Wang X, Wang H, Xie W, Yang Z, Yang S, Zhu B. Joint application of A-InDels and miniSTRs for forensic personal, full and half sibling identifications, and genetic differentiation analyses in two populations from China. BMC Genomics 2024; 25:329. [PMID: 38566035 PMCID: PMC10986087 DOI: 10.1186/s12864-024-10187-4] [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: 04/29/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Previously, a novel multiplex system of 64 loci was constructed based on capillary electrophoresis platform, including 59 autosomal insertion/deletions (A-InDels), two Y-chromosome InDels, two mini short tandem repeats (miniSTRs), and an Amelogenin gene. The aim of this study is to evaluate the efficiencies of this multiplex system for individual identification, paternity testing and biogeographic ancestry inference in Chinese Hezhou Han (CHH) and Hubei Tujia (CTH) groups, providing valuable insights for forensic anthropology and population genetics research. RESULTS The cumulative values of power of discrimination (CDP) and probability of exclusion (CPE) for the 59 A-InDels and two miniSTRs were 0.99999999999999999999999999754, 0.99999905; and 0.99999999999999999999999999998, 0.99999898 in CTH and CHH groups, respectively. When the likelihood ratio thresholds were set to 1 or 10, more than 95% of the full sibling pairs could be identified from unrelated individual pairs, and the false positive rates were less than 1.2% in both CTH and CHH groups. Biogeographic ancestry inference models based on 35 populations were constructed with three algorithms: random forest, adaptive boosting and extreme gradient boosting, and then 10-fold cross-validation analyses were applied to test these three models with the average accuracies of 86.59%, 84.22% and 87.80%, respectively. In addition, we also investigated the genetic relationships between the two studied groups with 33 reference populations using population statistical methods of FST, DA, phylogenetic tree, PCA, STRUCTURE and TreeMix analyses. The present results showed that compared to other continental populations, the CTH and CHH groups had closer genetic affinities to East Asian populations. CONCLUSIONS This novel multiplex system has high CDP and CPE in CTH and CHH groups, which can be used as a powerful tool for individual identification and paternity testing. According to various genetic analysis methods, the genetic structures of CTH and CHH groups are relatively similar to the reference East Asian populations.
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Affiliation(s)
- Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Yanfang Liu
- Laboratory of Fundamental Nursing Research, School of Nursing, Guangdong Medical University, Dongguan, Guangdong, China
| | - Xi Wang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Hongdan Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Weibing Xie
- School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Zi Yang
- School of Business, Macau University of Science and Technology, Macao, China
| | - Shangwu Yang
- The people's hospital of Hezhou, Guangxi, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China.
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Norscia I, Collarini E, Robino C, Chierto E, Cordoni G. Witness for resolution: post-conflict quadratic affiliation in semi-free ranging pigs. Curr Zool 2024; 70:233-243. [PMID: 38726243 PMCID: PMC11078055 DOI: 10.1093/cz/zoad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/21/2023] [Indexed: 05/12/2024] Open
Abstract
In social mammals, post-conflict resolution can involve the reunion of former opponents (reconciliation), spontaneous/solicited post-conflict affiliation of a third party with either opponent (triadic contacts), and affiliation between other individuals (hereafter bystanders; quadratic contacts). Quadratic contacts-possibly informing complex cognitive abilities-have been neglected in post-conflict studies. We investigated quadratic affiliation in semi-free ranging pigs Sus scrofa, at the ethical farm Parva-Domus (Cavagnolo, Italy). Kinship was known. We collected behavioral data on adult pigs (n = 104) via video recordings (43 h) followed by video analyses. Affiliative and anxiety behaviors between bystanders were collected under post-conflict (PC; following a conflict between non-bystanders) and matched-control (MC; no conflict) conditions. Quadratic affiliation was present in pigs, as bystanders affiliated more in PC than MC, and such affiliation was followed by a decrease in the anxiety behaviors of both the interacting bystanders. Thus, quadratic contacts may be partly aimed at reducing one's own anxiety (intrinsic regulation). Quadratic affiliation was highest between closely related bystanders, which suggests that such affiliation may be most effective when close kin is involved. Quadratic affiliation was lowest after reconciliation and spontaneous triadic contacts. This suggests that direct peacemaking between opponents and spontaneous triadic contacts with close kin may most likely replace quadratic affiliation. Hence, pigs can be influenced by the negative events that affect other pigs-but not themselves-and their response may be modulated by social factors. Such non-random quadratic affiliation may point toward the presence of elements of social appraisal abilities in pigs.
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Affiliation(s)
- Ivan Norscia
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Edoardo Collarini
- Department of Public Health Sciences and Pediatrics, University of Torino, C.So Galileo Galilei 22, 10126 Torino, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Torino, C.So Galileo Galilei 22, 10126 Torino, Italy
| | - Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Torino, C.So Galileo Galilei 22, 10126 Torino, Italy
| | - Giada Cordoni
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
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Yuan X, Wang X, Lan Q, Li S, Lin Y, Zhao M, Xu H, Lei F, Shen C, Zhu B. Using two self-developed InDel panels to explore forensic traits and ancestral components in the Hui group. Genomics 2024; 116:110756. [PMID: 38061479 DOI: 10.1016/j.ygeno.2023.110756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/05/2023] [Accepted: 12/03/2023] [Indexed: 12/30/2023]
Abstract
To address the challenges faced by forensic examiners in degraded DNA analysis, we have developed two different panels for various forensic applications, encompassing an AIM-InDel panel for ancestry inference and a Multi-InDel panel for individual identification, respectively. Herein, the efficiencies of these two panels were tested in the Chinese Hui group. By calculating forensic parameters and simulating family relationships, we verified that the Multi-InDel panel could be an effective tool for individual identification, paternity testing, and could assist in kinship identification in the Hui group. For full siblings, the true positive rate of kinship discrimination was 96.553%, when the threshold of log10LR was 1. The cumulative probability of matching as well as cumulative probability of exclusion were 3.8117 × 10-26 and 0.999999722, respectively. Meanwhile, we found that the AIM-InDel panel was effective for bio-geographic ancestry inference, with the vast majority of loci contributing significantly to distinguish East Asian, African, and European populations. By studying the population structure of the Hui ethnic minority, the genetic distance to the Beijing Han population was the closest among the 26 reference populations, which was similar to previous reports. In summary, we have developed two panels which can be effectively applied to the Hui group for individual identification, parentage testing and bio-geographic ancestry inference.
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Affiliation(s)
- Xi Yuan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Xi Wang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shuanglin Li
- Department of Anatomy and Histology, School of Basic Medical Sciences, Shenzhen University, Shenzhen 518060, China
| | - Yifeng Lin
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Ming Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Chunmei Shen
- Department of Clinical Laboratory, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China; Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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Lan Q, Lin Y, Wang X, Yuan X, Shen C, Zhu B. Targeted sequencing of high-density SNPs provides an enhanced tool for forensic applications and genetic landscape exploration in Chinese Korean ethnic group. Hum Genomics 2023; 17:107. [PMID: 38008719 PMCID: PMC10680316 DOI: 10.1186/s40246-023-00541-0] [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: 06/16/2023] [Accepted: 10/05/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND In this study, we present a NGS-based panel designed for sequencing 1993 SNP loci for forensic DNA investigation. This panel addresses unique challenges encountered in forensic practice and allows for a comprehensive population genetic study of the Chinese Korean ethnic group. To achieve this, we combine our results with datasets from the 1000 Genomes Project and the Human Genome Diversity Panel. RESULTS We demonstrate that this panel is a reliable tool for individual identification and parentage testing, even when dealing with degraded DNA samples featuring exceedingly low SNP detection rates. The performance of this panel for complex kinship determinations, such as half-sibling and grandparent-grandchild scenarios, is also validated by various kinship simulations. Population genetic studies indicate that this panel can uncover population substructures on both global and regional scales. Notably, the Han population can be distinguished from the ethnic minorities in the northern and southern regions of East Asia, suggesting its potential for regional ancestry inference. Furthermore, we highlight that the Chinese Korean ethnic group, along with various Han populations from different regional areas and certain northern ethnic minorities (Daur, Tujia, Japanese, Mongolian, Xibo), exhibit a higher degree of genetic affinities when examined from a genomic perspective. CONCLUSION This study provides convincing evidence that the NGS-based panel can serve as a reliable tool for various forensic applications. Moreover, it has helped to enhance our knowledge about the genetic landscape of the Chinese Korean ethnic group.
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Affiliation(s)
- Qiong Lan
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yifeng Lin
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xi Wang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xi Yuan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chunmei Shen
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Bofeng Zhu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.
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11
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Childebayeva A, Zavala EI. Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics. iScience 2023; 26:108066. [PMID: 37927550 PMCID: PMC10622734 DOI: 10.1016/j.isci.2023.108066] [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] [Indexed: 11/07/2023] Open
Abstract
Degraded DNA is used to answer questions in the fields of ancient DNA (aDNA) and forensic genetics. While aDNA studies typically center around human evolution and past history, and forensic genetics is often more concerned with identifying a specific individual, scientists in both fields face similar challenges. The overlap in source material has prompted periodic discussions and studies on the advantages of collaboration between fields toward mutually beneficial methodological advancements. However, most have been centered around wet laboratory methods (sampling, DNA extraction, library preparation, etc.). In this review, we focus on the computational side of the analytical workflow. We discuss limitations and considerations to consider when working with degraded DNA. We hope this review provides a framework to researchers new to computational workflows for how to think about analyzing highly degraded DNA and prompts an increase of collaboration between the forensic genetics and aDNA fields.
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Affiliation(s)
- Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Kansas, Lawrence, KS, USA
| | - Elena I. Zavala
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, University of Oregon, Eugene, OR, USA
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12
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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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13
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Casanova-Adán L, Mosquera-Miguel A, González-Bao J, Ambroa-Conde A, Ruiz-Ramírez J, Cabrejas-Olalla A, González-Martín E, Freire-Aradas A, Rodríguez-López A, Phillips C, Lareu MV, de la Puente M. Adapting an established Ampliseq microhaplotype panel to nanopore sequencing through direct PCR. Forensic Sci Int Genet 2023; 67:102937. [PMID: 37812882 DOI: 10.1016/j.fsigen.2023.102937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
We have adapted an established Ampliseq microhaplotype panel for nanopore sequencing with the Oxford Nanopore Technologies (ONT) system, as a cost-effective and highly scalable solution for forensic genetics applications. For this purpose, we designed a protocol combining direct PCR amplification from unextracted DNA with ONT library construction and sequencing using the MinION device and workflow. The analysis of reference samples at input amounts of 5-10 ng of DNA demonstrates stable coverage patterns, allele balance, and strand bias, reaching profile completeness and concordance rates of ∼95%. Similar levels were achieved when using direct-PCR from blood, buccal and semen swabs. Dilution series results indicate sensitivity is maintained down to 250 pg of input DNA, and informative profiles are produced down to 62.5 pg. Finally, we demonstrated the forensic utility of the nanopore workflow by analyzing two third degree pedigrees that showed low likelihood ratio values after the analysis of an extended panel of 38 STRs, achieving likelihood ratios 2-3 orders of magnitude higher when testing with the MinION-based haplotype data.
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Affiliation(s)
- L Casanova-Adán
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - J González-Bao
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - J Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Cabrejas-Olalla
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - E González-Martín
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Rodríguez-López
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain.
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14
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Gabriele A, Chierto E, Gino S, Inturri S, Aneli S, Robino C. Privacy and ethical challenges of the Amelogenin sex test in forensic paternity/kinship analysis: Insights from a 13-year case history. Forensic Sci Int Synerg 2023; 7:100440. [PMID: 37840559 PMCID: PMC10568343 DOI: 10.1016/j.fsisyn.2023.100440] [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: 10/28/2022] [Revised: 09/07/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
The Amelogenin sex test included in forensic DNA typing kits has the potential to identify congenital conditions such as differences/disorders of sex development (DSD). It can also reveal mismatches between genotypic sex and gender marker in identity documents of transgender persons who obtained legal gender recognition. In a 13-year case history of paternity/kinship tests, involving n = 962 females and n = 1001 males, two mismatches between Amelogenin sex test (male) and gender marker (female), and three cases of chromosomal DSD (Klinefelter syndrome) were observed. The concrete risk of observing Amelogenin anomalies, their potential causes, and the context in which they occur (forensic, i.e. non-medical) mean that laboratory operators are called to strike a complex balance between privacy interests and individual health rights when providing preliminary information and reporting Amelogenin incidental findings. This case history argues for the need of a more responsible approach towards the Amelogenin sex test in the forensic community.
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Affiliation(s)
- Alessandro Gabriele
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Sarah Gino
- Department of Health Sciences, University of Eastern Piedmont, Via Solaroli 17, 28100, Novara, Italy
| | - Serena Inturri
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
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15
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Cui W, Chen M, Yang Y, Cai M, Lan Q, Xie T, Zhu B. Applications of 1993 single nucleotide polymorphism loci in forensic pairwise kinship identifications and inferences. Forensic Sci Int Genet 2023; 65:102889. [PMID: 37247510 DOI: 10.1016/j.fsigen.2023.102889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/19/2023] [Accepted: 05/11/2023] [Indexed: 05/31/2023]
Abstract
Kinship testing plays critical roles in criminal investigations, missing person searches, civil disputes, as well as identifying disaster victims. The existing commonly used short tandem repeat (STR) loci have limited effectiveness in the identification of second-degree and more distant kinships. In this study, a total of 1993 SNP loci of 119 Chinese Han individuals from eight families were sequenced on the MGISEQ-2000RS platform. The system powers of this panel for kinship identifications were evaluated based on both the likelihood ratio (LR) and identical by state (IBS) methods. The results indicated that this panel could be used as an effective tool to kinship analyses including paternity testing, full sibling testing, second-degree kinships, and first cousin kinship analyses. Both the LR and IBS methods could be applied in distinguishing first-degree and second-degree pairs from unrelated individuals. Based on the 1993 SNP loci, LR>1000 and LR<0.001 are recommended as the thresholds of identifying first-cousin kinships from unrelated individuals, and the system power of such thresholds was 0.9470. Besides, kinship coefficients for different kinship pairs were estimated and then were used to predict the kinships for pairwise individuals. This panel performs an effective kinship inference power for the predictions of first-degree, second-degree kinships and unrelated individual pairs, while presenting low sensitivity in the prediction of first-cousin kinships.
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Affiliation(s)
- Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yan Yang
- Golden Bridge Big Data Technology Co., LTD, Beijing, China
| | - Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Tong Xie
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China; Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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16
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Antão-Sousa S, Pinto N, Rende P, Amorim A, Gusmão L. The sequence of the repetitive motif influences the frequency of multistep mutations in Short Tandem Repeats. Sci Rep 2023; 13:10251. [PMID: 37355683 PMCID: PMC10290632 DOI: 10.1038/s41598-023-32137-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/23/2023] [Indexed: 06/26/2023] Open
Abstract
Microsatellites, or Short Tandem Repeats (STRs), are subject to frequent length mutations that involve the loss or gain of an integer number of repeats. This work aimed to investigate the correlation between STRs' specific repetitive motif composition and mutational dynamics, specifically the occurrence of single- or multistep mutations. Allelic transmission data, comprising 323,818 allele transfers and 1,297 mutations, were gathered for 35 Y-chromosomal STRs with simple structure. Six structure groups were established: ATT, CTT, TCTA/GATA, GAAA/CTTT, CTTTT, and AGAGAT, according to the repetitive motif present in the DNA leading strand of the markers. Results show that the occurrence of multistep mutations varies significantly among groups of markers defined by the repetitive motif. The group of markers with the highest frequency of multistep mutations was the one with repetitive motif CTTTT (25% of the detected mutations) and the lowest frequency corresponding to the group with repetitive motifs TCTA/GATA (0.93%). Statistically significant differences (α = 0.05) were found between groups with repetitive motifs with different lengths, as is the case of TCTA/GATA and ATT (p = 0.0168), CTT (p < 0.0001) and CTTTT (p < 0.0001), as well as between GAAA/CTTT and CTTTT (p = 0.0102). The same occurred between the two tetrameric groups GAAA/CTTT and TCTA/GATA (p < 0.0001) - the first showing 5.7 times more multistep mutations than the second. When considering the number of repeats of the mutated paternal alleles, statistically significant differences were found for alleles with 10 or 12 repeats, between GATA and ATT structure groups. These results, which demonstrate the heterogeneity of mutational dynamics across repeat motifs, have implications in the fields of population genetics, epidemiology, or phylogeography, and whenever STR mutation models are used in evolutionary studies in general.
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Affiliation(s)
- Sofia Antão-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
- Department of Biology, Faculty of Sciences of University of Porto (FCUP), Porto, Portugal.
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.
| | - Nádia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Center of Mathematics of University of Porto (CMUP), Porto, Portugal
| | - Pablo Rende
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences of University of Porto (FCUP), Porto, Portugal
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Department of Biology, Faculty of Sciences of University of Porto (FCUP), Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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Marsico FL, Caridi I. Incorporating non-genetic evidence in large scale missing person searches: A general approach beyond filtering. Forensic Sci Int Genet 2023; 66:102891. [PMID: 37523799 DOI: 10.1016/j.fsigen.2023.102891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 08/02/2023]
Abstract
The search for missing persons implies several steps, from the preliminary investigation that involves collecting background data related to the case to the genetic kinship testing. Despite its crucial importance in identifications, only some approaches mathematically formalize the possibility of using preliminary investigation data. In some cases, a filtering strategy is applied, which implies selecting a subset of possible victims where some non-genetic variables perfectly match those of the missing. Through a Bayesian approach, we propose a mathematical model for computing the prior odds based on non-genetic variables usually collected during the preliminary investigation, such as biological sex, hair colour, and age. We use computational simulations to show how to incorporate these prior odds in DNA-database searches. Importantly, our results suggest that applying the proposed model leads to better search performance in underpowered cases from the genetic point of view, where few or distant relatives of the missing person are available for genotyping. Furthermore, the results are also helpful when using non-genetic data for prior odds in well-powered cases, where genetic data are enough to reach a reliable conclusion. It performs better than other approaches, such as using non-genetic data for filtering. The software mispitools, freely available on CRAN, implements all described methods (https://CRAN.R-project.org/package=mispitools).
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Affiliation(s)
- Franco L Marsico
- Calculus Institute, University of Buenos Aires, Argentina; IDEPI, National University of Jose Clemente Paz, Argentina.
| | - Inés Caridi
- Calculus Institute, University of Buenos Aires, Argentina.
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18
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Semikhodskii A, Makarova T, Sutyagina D. Paternity pseudo-exclusion caused by tetragametic chimerism in a gestational surrogacy case. Eur J Med Genet 2023:104799. [PMID: 37276934 DOI: 10.1016/j.ejmg.2023.104799] [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: 01/15/2023] [Revised: 05/22/2023] [Accepted: 06/03/2023] [Indexed: 06/07/2023]
Abstract
Chimerism is a condition when an organism is composed of two or more populations of genetically distinct cells. Chimerism often produces curious results of medical and genetic investigations and could be a major cause of false negative conclusions in parentage testing. Here we describe a paternity pseudo-exclusion due to tetragametic chimerism in a gestational surrogacy case originated in a fertility clinic. Initial analysis using a buccal swab from the child and a peripheral blood sample from the father showed paternity exclusion at 6 STR loci. To find out the reason for observed paternal discrepancy father's semen sample used for IVF and samples from other tissues were genotyped. Buccal swabs, semen, hair follicles, nail clippings and cerumen showed identical mixed autosomal STR profiles originated from two genetically different cell lines and for all the 24 informative loci contain paternal obligate alleles. Results of Y-STR profiling of all paternal sample types showed a DNA profile originated from a single man. The mixed profiles obtained for different tissue types suggest that two genetically different cell lines contributed to formation of both the endoderm and the ectoderm of the father. The mesoderm seems to be monoclonal having originated from a genetically homogenous cell line as evidenced by the STR profile of peripheral blood. Such allelic pattern for various tissues suggests that the clonal origin happened at the very early stage of embryonic development. Approaches to minimise the rate of false exclusions in DNA parentage tests due to chimerism are discussed.
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Affiliation(s)
| | - Tatiana Makarova
- Medical Genomics LLC, 48 Zhelyabov Str, Tver, 170100, Russian Federation
| | - Daria Sutyagina
- Medical Genomics LLC, 48 Zhelyabov Str, Tver, 170100, Russian Federation
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19
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Xue J, Tan M, Zhang R, Chen D, Liu G, Zheng Y, Wu Q, Xiao Y, Liao M, Qu S, Liang W. Evaluation of microhaplotype panels for complex kinship analysis using massively parallel sequencing. Forensic Sci Int Genet 2023; 65:102887. [PMID: 37209601 DOI: 10.1016/j.fsigen.2023.102887] [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: 11/28/2022] [Revised: 04/27/2023] [Accepted: 04/29/2023] [Indexed: 05/22/2023]
Abstract
In recent years, microhaplotypes (MHs) have become a research hotspot within the field of forensic genetics. Traditional MHs contain only SNPs that are closely linked within short fragments. Herein, we broaden the concept of general MHs to include short InDels. Complex kinship identification plays an important role in disaster victim identification and criminal investigations. For distant relatives (e.g., 3rd-degree), many genetic markers are required to enhance power of kinship testing. We performed genome-wide screening for new MH markers composed of two or more variants (InDel or SNP) within 220 bp based on the Chinese Southern Han from the 1000 Genomes Project. An NGS-based 67plex MH panel (Panel B) was successfully developed, and 124 unrelated individual samples were sequenced to obtain population genetic data, including alleles and allele frequencies. Of the 67 genetic markers, 65 MHs were, as far as we know, newly discovered, and 32 MHs had effective number of allele (Ae) values greater than 5.0. The average Ae and heterozygosity of the panel were 5.34 and 0.7352, respectively. Next, 53 MHs from a previous study were collected as Panel A (average Ae of 7.43), and Panel C with 87 MHs (average Ae of 7.02) was formed by combining Panels A and B. We investigated the utility of these three panels in kinship analysis (parent-child, full siblings, 2nd-degree, 3rd-degree, 4th-degree, and 5th-degree relatives), with Panel C exhibiting better performance than the two other panels. Panel C was able to separate parent-child, full-sibling, and 2nd-degree relative duos from unrelated controls in real pedigree data, with a small false testing level (FTL) of 0.11% in simulated 2nd-degree duos. For more distant relationships, the FTL was much higher: 8.99% for 3rd-degree, 35.46% for 4th-degree, and 61.55% for 5th-degree. When a carefully chosen extra relative was known, this may enhance the testing power for distant kinship analysis. Two twins from the Q family (2-5 and 2-7) and W family (3-18 and 3-19) shared the same genotypes in all tested MHs, which led to the incorrect conclusion that an uncle-nephew duo was classified as a parent-child duo. In addition, Panel C showed great capacity for excluding close relatives (2nd-degree and 3rd-degree relatives) during paternity tests. Among 18,246 real and 10,000 simulated unrelated pairs, none were misinterpreted as a relative within 2nd-degree at a log10(LR) cutoff of 4. The panels presented herein could provide supplementary power for the analysis of complex kinship.
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Affiliation(s)
- Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China.
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Zhalsanova IZ, Postrigan AE, Valiakhmetov NR, Kolesnikov NA, Zhigalina DI, Zarubin AA, Petrova VV, Minaycheva LI, Seitova GN, Skryabin NA, Stepanov VA. Case Report: A Novel Homozygous Variant of the SERPINF1 Gene in Rare Osteogenesis Imperfecta Type VI. Int J Mol Sci 2023; 24:ijms24076672. [PMID: 37047644 PMCID: PMC10095092 DOI: 10.3390/ijms24076672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
Osteogenesis imperfecta (OI) is a group of connective tissue disorders with different types of inheritance. OI is characterized by bone fragility and deformities, frequent fractures, low bone-mineral density, and impaired bone micro-architectonics. We described here a case of a one-year-old Tuvan patient with multiple fractures. The disease manifestation occurred first at 12 weeks of age as a shoulder joint bruise, and during the year, the patient sustained 27 fractures. Genetic testing revealed a novel homozygous mutation, c.259_260insCGGCC (p.T87fs), in the SERPINF1 gene. This insertion leads to an open-reading frameshift, and the mutation is not represented in the databases. Mutations in SERPINF1 lead to type VI OI, the clinical picture of which is similar to the disease phenotype manifestation of the patient. Thus, the patient’s diagnosis was established by finding a novel pathogenic variant in the SERPINF1 gene.
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Affiliation(s)
- Irina Zh. Zhalsanova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk 634050, Russia
| | - Anna Evgenievna Postrigan
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk 634050, Russia
| | | | | | - Daria Ivanovna Zhigalina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk 634050, Russia
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21
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Staadig A, Hedman J, Tillmar A. Applying Unique Molecular Indices with an Extensive All-in-One Forensic SNP Panel for Improved Genotype Accuracy and Sensitivity. Genes (Basel) 2023; 14:genes14040818. [PMID: 37107576 PMCID: PMC10137749 DOI: 10.3390/genes14040818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
One of the major challenges in forensic genetics is being able to detect very small amounts of DNA. Massively parallel sequencing (MPS) enables sensitive detection; however, genotype errors may exist and could interfere with the interpretation. Common errors in MPS-based analysis are often induced during PCR or sequencing. Unique molecular indices (UMIs) are short random nucleotide sequences ligated to each template molecule prior to amplification. Applying UMIs can improve the limit of detection by enabling accurate counting of initial template molecules and removal of erroneous data. In this study, we applied the FORCE panel, which includes ~5500 SNPs, with a QIAseq Targeted DNA Custom Panel (Qiagen), including UMIs. Our main objective was to investigate whether UMIs can enhance the sensitivity and accuracy of forensic genotyping and to evaluate the overall assay performance. We analyzed the data both with and without the UMI information, and the results showed that both genotype accuracy and sensitivity were improved when applying UMIs. The results showed very high genotype accuracies (>99%) for both reference DNA and challenging samples, down to 125 pg. To conclude, we show successful assay performance for several forensic applications and improvements in forensic genotyping when applying UMIs.
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22
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Chen M, Cui W, Bai X, Fang Y, Yao H, Zhang X, Lei F, Zhu B. Comprehensive evaluations of individual discrimination, kinship analysis, genetic relationship exploration and biogeographic origin prediction in Chinese Dongxiang group by a 60-plex DIP panel. Hereditas 2023; 160:14. [PMID: 36978173 PMCID: PMC10052841 DOI: 10.1186/s41065-023-00271-2] [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: 11/23/2022] [Accepted: 02/22/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Dongxiang group, as an important minority, resides in Gansu province which is located at the northwest China, forensic detection system with more loci needed to be studied to improve the application efficiency of forensic case investigation in this group. METHODS A 60-plex system including 57 autosomal deletion/insertion polymorphisms (A-DIPs), 2 Y chromosome DIPs (Y-DIPs) and the sex determination locus (Amelogenin) was explored to evaluate the forensic application efficiencies of individual discrimination, kinship analysis and biogeographic origin prediction in Gansu Dongxiang group based on the 60-plex genotype results of 233 unrelated Dongxiang individuals. The 60-plex genotype results of 4582 unrelated individuals from 33 reference populations in five different continents were also collected to analyze the genetic background of Dongxiang group and its genetic relationships with other continental populations. RESULTS The system showed high individual discrimination power, as the cumulative power of discrimination (CPD), cumulative power of exclusion (CPE) for trio and cumulative match probability (CMP) values were 0.99999999999999999999997297, 0.999980 and 2.7029E- 24, respectively. The system could distinguish 98.12%, 93.78%, 82.18%, 62.35% and 39.32% of full sibling pairs from unrelated individual pairs, when the likelihood ratio (LR) limits were set as 1, 10, 100, 1000 and 10,000 based on the simulated family samples, respectively. Additionally, Dongxiang group had the close genetic distances with populations in East Asia, especially showed the intimate genetic relationships with Chinese Han populations, which were concluded from the genetic affinities and genetic background analyses of Dongxiang group and 33 reference populations. In terms of the effectiveness of biogeographic origin inference, different artificial intelligent algorithms possessed different efficacies. Among them, the random forest (RF) and extreme gradient boosting (XGBoost) algorithm models could accurately predict the biogeographic origins of 99.7% and 90.59% of three and five continental individuals, respectively. CONCLUSION This 60-plex system had good performance for individual discrimination, kinship analysis and biogeographic origin prediction in Dongxiang group, which could be used as a powerful tool for case investigation.
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Affiliation(s)
- Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xiaole Bai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yating Fang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, 230031, Anhui, China
| | - Hongbin Yao
- Belt and Road Research Center for Forensic Molecular Anthropology, Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, 730070, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, China.
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23
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Mostad P, Tillmar A, Kling D. Improved computations for relationship inference using low-coverage sequencing data. BMC Bioinformatics 2023; 24:90. [PMID: 36894920 PMCID: PMC9999603 DOI: 10.1186/s12859-023-05217-z] [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: 10/06/2022] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
Pedigree inference, for example determining whether two persons are second cousins or unrelated, can be done by comparing their genotypes at a selection of genetic markers. When the data for one or more of the persons is from low-coverage next generation sequencing (lcNGS), currently available computational methods either ignore genetic linkage or do not take advantage of the probabilistic nature of lcNGS data, relying instead on first estimating the genotype. We provide a method and software (see familias.name/lcNGS) bridging the above gap. Simulations indicate how our results are considerably more accurate compared to some previously available alternatives. Our method, utilizing a version of the Lander-Green algorithm, uses a group of symmetries to speed up calculations. This group may be of further interest in other calculations involving linked loci.
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Affiliation(s)
- Petter Mostad
- Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Göteborg, Sweden.
| | - Andreas Tillmar
- Department of Forensic Genetics and Toxicology, National Board of Forensic Medicine, Linköping, Sweden.,Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Daniel Kling
- Department of Forensic Genetics and Toxicology, National Board of Forensic Medicine, Linköping, Sweden.,Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway.,Biostatistics (BIAS), Norwegian University of Life Sciences, Ås, Norway
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24
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Chen M, Lan Q, Nie S, Hu L, Fang Y, Cui W, Bai X, Liu L, Zhu B. Forensic efficiencies of individual identification, kinship testing and ancestral inference in three Yunnan groups based on a self-developed multiple DIP panel. Front Genet 2023; 13:1057231. [PMID: 36685924 PMCID: PMC9845582 DOI: 10.3389/fgene.2022.1057231] [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: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 01/06/2023] Open
Abstract
Deletion/insertion polymorphism (DIP), as a short insertion/deletion sequence polymorphic genetic marker, has attracted the attention of forensic genetic scientist due to its lack of stutter, short amplicon and abundant ancestral information. In this study, based on a self-developed 43 autosomal deletion/insertion polymorphism (A-DIP) loci panel which could meet the forensic application purposes of individual identification, kinship testing and ancestral inference to some extent, we evaluated the forensic efficiencies of the above three forensic objectives in Chinese Yi, Hani and Miao groups of Yunnan province. The cumulative match probability (CPM) and combined probability of exclusion (CPE) of these three groups were 1.11433E-18, 8.24299E-19, 4.21721E-18; 0.999610217, 0.999629285 and 0.999582084, respectively. Average 96.65% full sibling pairs could be identified from unrelated individual pairs (as likelihood ratios > 1) using this DIP panel, whereas the average false positive rate was 3.69% in three target Yunnan groups. With the biogeographical ancestor prediction models constructed by extreme gradient boosting (XGBoost) and support vector machine (SVM) algorithms, 0.8239 (95% CI 0.7984, 0.8474) of the unrelated individuals could be correctly divided according to the continental origins based on the 43 A-DIPs which were large frequency distribution differentiations among different continental populations. The present results of principal component analysis (PCA), multidimensional scaling (MDS), neighbor joining (NJ) and maximum likelihood (ML) phylogenetic trees and STRUCTURE analyses indicated that these three Yunnan groups had relatively close genetic distances with East Asian populations.
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Affiliation(s)
- Man Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qiong Lan
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Yating Fang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaole Bai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Liu Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China,Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China,*Correspondence: Bofeng Zhu,
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25
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Cordoni G, Comin M, Collarini E, Robino C, Chierto E, Norscia I. Domestic pigs (Sus scrofa) engage in non-random post-conflict affiliation with third parties: cognitive and functional implications. Anim Cogn 2023; 26:687-701. [PMID: 36344830 PMCID: PMC9950185 DOI: 10.1007/s10071-022-01688-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/09/2022]
Abstract
In social mammals, conflict resolution involves the reunion of former opponents (aggressor and victim) after an aggressive event (reconciliation) or post-conflict triadic contacts with a third party, started by either opponent (solicited-TSC) or spontaneously offered by the third party (unsolicited-TUC). These post-conflict strategies can serve different functions, including consolation (specifically when TUCs reduce the victim's anxiety). We investigated the possible presence and modulating factors of such strategies on semi-free ranging pigs (Sus scrofa; N = 104), housed at the ethical farm Parva Domus (Cavagnolo, Italy). Kinship was known. Reconciliation was present and mainly occurred between weakly related pigs to possibly improve tolerant cohabitation. Triadic contacts (all present except aggressor TSCs) mostly occurred between close kin. TSCs enacted by victims reduced neither their post-conflict anxiety behaviors nor further attacks by the previous aggressor, possibly because TSCs remained largely unreciprocated. TUCs towards aggressors did not reduce aggressor post-conflict anxiety but limited aggression redirection towards third parties. TUCs towards the victim reduced the victim but not the third-party's anxiety. However, TUCs may also provide inclusive fitness benefits to third parties by benefiting close kin. In sum, pigs engaged in non-random solicited/unsolicited triadic contacts, which suggests that pigs might possess socio-emotional regulation abilities to change their own or others' experience and elements of social appraisal, necessary to detect the emotional arousal of relevant others and (in case of TUCs) take the agency to restore homeostasis.
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Affiliation(s)
- Giada Cordoni
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy.
| | - Marta Comin
- grid.7605.40000 0001 2336 6580Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Edoardo Collarini
- grid.7605.40000 0001 2336 6580Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy
| | - Carlo Robino
- grid.7605.40000 0001 2336 6580Department of Public Health Sciences and Pediatrics, University of Torino, Turin, Italy
| | - Elena Chierto
- grid.7605.40000 0001 2336 6580Department of Public Health Sciences and Pediatrics, University of Torino, Turin, Italy
| | - Ivan Norscia
- Department of Life Sciences and Systems Biology, University of Torino, Turin, Italy.
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26
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Tao R, Yang Q, Xia R, Zhang X, Chen A, Li C, Zhang S. A sequence-based 163plex microhaplotype assay for forensic DNA analysis. Front Genet 2022; 13:988223. [PMID: 36276985 PMCID: PMC9579316 DOI: 10.3389/fgene.2022.988223] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Novel genetic marker microhaplotype has led to an upsurge in forensic genetic research. This study established a 163 microhaplotype (MH) multiplex assay based on next-generation sequencing (NGS) and evaluated the assay's performance and applicability. Our results showed that the 163 MH assay was accurate, repeatable and reliable, and could distinguish between African, European-American, Southern Asia and Eastern Asia populations. Among the 163 MH makers, 48 MHs with Ae > 3.0 in China Eastern Han were selected and confirmed to be highly polymorphic, with a combined power of discrimination of 1-8.26 × 10-44 and the combined power of exclusion in duos and trios of 1-1.26 × 10-8 and 1-8.27 × 10-16, respectively. Moreover, the mixture study demonstrated the realizability of the MHs in deconvoluting mixtures with different proportions of two to five-person. In conclusion, our findings support the use of this MH assay for ancestry inference, human identification, paternity testing and mixture deconvolution in forensic research.
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Affiliation(s)
| | | | | | | | | | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
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27
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Di Nunzio C, Maione G, Di Nunzio A, Scalise C, Ricci P, Tinto N. Deconvolution rules a tool to solve a complex paternity case where child was chimeric. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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How frequently are Autosomal and X-STRs multistep mutations perceived as single-step? FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Wen D, Xing H, Liu Y, Li J, Qu W, He W, Wang C, Xu R, Liu Y, Jia H, Zha L. The application of short and highly polymorphic microhaplotype loci in paternity testing and sibling testing of temperature-dependent degraded samples. Front Genet 2022; 13:983811. [PMID: 36226179 PMCID: PMC9549137 DOI: 10.3389/fgene.2022.983811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Paternity testing and sibling testing become more complex and difficult when samples degrade. But the commonly used genetic markers (STR and SNP) cannot completely solve this problem due to some disadvantages. The novel genetic marker microhaplotype proposed by Kidd’s research group combines the advantages of STR and SNP and is expected to become a promising genetic marker for kinship testing in degraded samples. Therefore, in this study, we intended to select an appropriate number of highly polymorphic SNP-based microhaplotype loci, detect them by the next-generation sequencing technology, analyze their ability to detect degraded samples, calculate their forensic parameters based on the collected 96 unrelated individuals, and evaluate their effectiveness in paternity testing and sibling testing by simulating kinship relationship pairs, which were also compared to 15 STR loci. Finally, a short and highly polymorphic microhaplotype panel was developed, containing 36 highly polymorphic SNP-based microhaplotype loci with lengths smaller than 100 bp and Ae greater than 3.00, of which 29 microhaplotype loci could not reject the Hardy-Weinberg equilibrium and linkage equilibrium after the Bonferroni correction. The CPD and CPE of these 29 microhaplotype loci were 1-2.96E-26 and 1-5.45E-09, respectively. No allele dropout was observed in degraded samples incubated with 100°C hot water for 40min and 60min. According to the simulated kinship analysis, the effectiveness at the threshold of 4/−4 reached 98.39% for relationship parent-child vs. unrelated individuals, and the effectiveness at the threshold of 2/−2 for relationship full-sibling vs. unrelated individuals was 93.01%, which was greater than that of 15 STR loci (86.75% for relationship parent-child vs. unrelated individuals and 81.73% for relationship full-sibling vs. unrelated individuals). After combining our 29 microhaplotype loci with other 50 short and highly polymorphic microhaplotype loci, the effectiveness values at the threshold of 2/−2 were 82.42% and 90.89% for relationship half-sibling vs. unrelated individuals and full-sibling vs. half-sibling. The short and highly polymorphic microhaplotype panel we developed may be very useful for paternity testing and full sibling testing in degraded samples, and in combination with short and highly polymorphic microhaplotype loci reported by other researchers, may be helpful to analyze more distant kinship relationships.
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Affiliation(s)
- Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Hao Xing
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Ying Liu
- Xiangya Stomatological Collage, Central South University, Changsha, China
| | - Jienan Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Weifeng Qu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Wei He
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Chudong Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Ruyi Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yi Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Hongtao Jia
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, China
- *Correspondence: Lagabaiyila Zha,
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30
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Flores-Espinoza R, Angulo-Pozo AN, Garzón-Salazar A, Cabrera-Andrade A, Paz-Cruz E, Burgos G, Gusmão L. EVALUATING POPULATION STRUCTURE OF ECUADOR FOR FORENSIC STR MARKERS. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.09.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Simões Dutra Corrêa H, Cortellini V, Franceschetti L, Verzeletti A. Forensic DNA Typing From Femurs and Bones of the Foot: A Study of 3 Cases. Am J Forensic Med Pathol 2022; 43:269-272. [PMID: 34935696 DOI: 10.1097/paf.0000000000000741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
ABSTRACT Evidence has been accumulating in the sense that femur may not always be the best option for DNA typing of skeletal remains. Recent studies have shown that bones of the hands and feet appear to be a superior source of preserved DNA. The current study reanalyzed DNA quantitation, degradation, and short tandem repeat typing in femurs, lateral cuneiforms, and distal foot phalanges. Data from 3 human identification cases involving corpses in an advanced decomposition state were collected. We found that in the studied cases, the femur provided equal or inferior results, recovering 84.9% of true alleles. Lateral cuneiforms (99.2%) and distal foot phalanges (96.8%) yielded higher percentages. In addition, more drop-ins and drop-outs were detected in femurs than cuneiforms and phalanges. This study adds to current findings that advocate for further investigation into bone selection for use in forensic practice. The impacts of our findings are limited by the small number of individuals studied and may not apply to old and degraded bones.
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Affiliation(s)
| | - Venusia Cortellini
- From the Forensic Medicine Unit, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Lorenzo Franceschetti
- From the Forensic Medicine Unit, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Andrea Verzeletti
- From the Forensic Medicine Unit, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
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32
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Oldoni F, Della Rocca C, Podini D. Investigation of 74 microhaplotypes for kinship testing in US populations. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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33
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Della Rocca C, Trombetta B, Barni F, D’Atanasio E, Hajiesmaeil M, Berti A, Hadi S, Cruciani F. Improving discrimination capacity through rapidly mutating Y-STRs in structured populations from the African continent. Forensic Sci Int Genet 2022; 61:102755. [DOI: 10.1016/j.fsigen.2022.102755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/21/2022] [Accepted: 07/31/2022] [Indexed: 11/16/2022]
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34
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Antão-Sousa S, Conde-Sousa E, Gusmão L, Amorim A, Pinto N. Estimations of Mutation Rates Depend on Population Allele Frequency Distribution: The Case of Autosomal Microsatellites. Genes (Basel) 2022; 13:genes13071248. [PMID: 35886031 PMCID: PMC9323320 DOI: 10.3390/genes13071248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/28/2022] [Accepted: 07/11/2022] [Indexed: 01/27/2023] Open
Abstract
Microsatellites (or short-tandem repeats (STRs)) are widely used in anthropology and evolutionary studies. Their extensive polymorphism and rapid evolution make them the ideal genetic marker for dating events, such as the age of a gene or a population. This usage requires the estimation of mutation rates, which are usually estimated by counting the observed Mendelian incompatibilities in one-generation familial configurations (typically parent(s)–child duos or trios). Underestimations are inevitable when using this approach, due to the occurrence of mutational events that do not lead to incompatibilities with the parental genotypes (‘hidden’ or ‘covert’ mutations). It is known that the likelihood that one mutation event leads to a Mendelian incompatibility depends on the mode of genetic transmission considered, the type of familial configuration (duos or trios) considered, and the genotype(s) of the progenitor(s). In this work, we show how the magnitude of the underestimation of autosomal microsatellite mutation rates varies with the populations’ allele frequency distribution spectrum. The Mendelian incompatibilities approach (MIA) was applied to simulated parent(s)/offspring duos and trios in different populational scenarios. The results showed that the magnitude and type of biases depend on the population allele frequency distribution, whatever the type of familial data considered, and are greater when duos, instead of trios, are used to obtain the estimates. The implications for molecular anthropology are discussed and a simple framework is presented to correct the naïf estimates, along with an informatics tool for the correction of incompatibility rates obtained through the MIA.
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Affiliation(s)
- Sofia Antão-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), 4200-465 Porto, Portugal
- Faculty of Sciences, University of Porto (FCUP), 4169-007 Porto, Portugal
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro 20550-013, Brazil;
- Correspondence:
| | - Eduardo Conde-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Instituto de Engenharia Biomédica (INEB), 4200-135 Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro 20550-013, Brazil;
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), 4200-465 Porto, Portugal
- Faculty of Sciences, University of Porto (FCUP), 4169-007 Porto, Portugal
| | - Nádia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), 4200-135 Porto, Portugal; (E.C.-S.); (A.A.); (N.P.)
- Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), 4200-465 Porto, Portugal
- Center of Mathematics, University of Porto (CMUP), 4169-007 Porto, Portugal
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Extended population genetic analysis of 12 X-STRs - Exemplified using a Norwegian population sample. Forensic Sci Int Genet 2022; 60:102745. [PMID: 35870434 DOI: 10.1016/j.fsigen.2022.102745] [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: 10/21/2021] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022]
Abstract
The use of X-chromosomal markers to resolve questions of relatedness has experienced a significant increase during the last years in forensic genetics. Perhaps primarily due to the emergence of commercial kits, but equally important due to an increased awareness of the utility of those markers. The X-chromosomal inheritance pattern entails that some cases, for instance paternal half-sisters, can potentially be resolved using a few X-chromosomal markers alone. For the statistical assessment in kinship cases it is of importance to have relevant population frequency data. In the present study 631 unrelated males from a Norwegian population sample are analyzed. The resulting haplotypes are compared to previously studied population samples and a deeper analysis of the linkage disequilibrium (LD) structure is conducted. We demonstrate that the power to detect LD will be low when few males, say below 300, are analyzed. We use entropy to describe the degree of LD between multiallelic loci and describe how this measure varies between different studied populations. Large population frequency databases have been recommended when using X-chromosomal markers, and we show that by combining reference databases from genetically similar populations, more precise haplotype frequency estimates can be obtained for rare haplotypes which improves the statistical assessment of the weight of evidence. In addition, we promote the use of simulations to assess the utility of STR markers in contrast to standard forensic parameters. Specifically we perform extensive simulations on cases where X-chromosomal markers are important and illustrate how the results can be used to infer the information gained from these markers.
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Lan Q, Zhao C, Chen C, Xu H, Fang Y, Yao H, Zhu B. Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set. Front Genet 2022; 13:816737. [PMID: 35601485 PMCID: PMC9121381 DOI: 10.3389/fgene.2022.816737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
The MPS technology has expanded the potential applications of DNA markers and increased the discrimination power of the targeted loci by taking variations in their flanking regions into consideration. Here, a collection of nuclear and extranuclear DNA markers (totally six kinds of nuclear genetic markers and mtDNA hypervariable region variations) were comprehensively and systematically assessed for polymorphism detections, further employed to dissect the population backgrounds in the Yugu ethnic group from Gansu province (Yugu) and Han population from the Inner Mongolia Autonomous Region (NMH) of China. The elevated efficiencies of the marker set in separating full sibling and challenging half sibling determination cases in parentage tests (iiSNPs), as well as predicting ancestry origins of unknown individuals from at least four continental populations (aiSNPs) and providing informative characteristic-related clues for Chinese populations (piSNPs) are highlighted in the present study. To sum up, different sets of DNA markers revealed sufficient effciencies to serve as promising tools in forensic applications. Genetic insights from the perspectives of autosomal DNA, Y chromosomal DNA, and mtDNA variations yielded that the Yugu ethnic group was genetically close related to the Han populations of the northern region. But we admit that more reference populations (like Mongolian, Tibetan, Hui, and Tu) should be incorporated to gain a refined genetic background landscape of the Yugu group in future studies.
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Affiliation(s)
- Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Congying Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chong Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yating Fang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Hongbing Yao
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Bofeng Zhu,
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A multi-dimensional evaluation of the 'NIST 1032' sample set across four forensic Y-STR multiplexes. Forensic Sci Int Genet 2022; 57:102655. [PMID: 35007854 PMCID: PMC9901497 DOI: 10.1016/j.fsigen.2021.102655] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 02/08/2023]
Abstract
This manuscript reports Y-chromosomal short tandem repeat (Y-STR) haplotypes for 1032 male U.S. population samples across 30 Y-STR loci characterized by three capillary electrophoresis (CE) length-based kits (PowerPlex Y23 System, Yfiler Plus PCR Amplification Kit, and Investigator Argus Y-28 QS Kit) and one sequence-based kit (ForenSeq DNA Signature Prep Kit): DYF387S1, DYS19, DYS385 a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS505, DYS518, DYS522, DYS533, DYS549, DYS570, DYS576, DYS612, DYS627, DYS635, DYS643, and Y-GATA-H4. The length-based Y-STR haplotypes include six loci that are not reported in the sequence-based kit (DYS393, DYS449, DYS456, DYS458, DYS518, and DYS627), whereas three loci included in the sequence-based kit are not present in length-based kits (DYS505, DYS522, and DYS612). For the latter, a custom multiplex was used to generate CE length-based data, allowing 1032 samples to be evaluated for concordance across the 30 Y-STR loci included in these four commercial Y-STR typing kits. Discordances between typing methods were analyzed further to assess underlying causes such as primer binding site mutations and flanking region insertions/deletions. Allele-level frequency and statistical information is provided for sequenced loci, excluding the multi-copy loci DYF387S1 and DYS385 a/b, for which locus-specific haplotype-level frequencies are provided instead. The resulting data reveals the degree of information gained through sequencing: 88% of sequenced Y-STR loci contain additional sequence-based alleles compared to length-based data, with the DYS389II locus containing the most additional alleles (51) observed by sequencing. Despite these allelic increases, only minimal improvement was observed in haplotype resolution by sequence, with all four commercial kits providing a similar ability to differentiate length-based haplotypes in this sample set. Finally, a subset of 369 male samples were compared to their corresponding additionally sequenced father samples, revealing the sequence basis for the 50 length-based changes observed, and no additional sequence-based mutations. GenBank accession numbers are reported for each unique sequence, and associated records are available in the STRSeq Y-Chromosomal STR Loci National Center for Biotechnology Information (NCBI) BioProject, accession PRJNA380347. Haplotype data is updated in the Y-STR Haplotype Reference Database (YHRD) for the 'NIST 1032' data set to now achieve the level of maximal haplotype of YHRD. All supplementary files including revisions to previously published Y-STR data are available in the NIST Public Data Repository: U.S. population data for human identification markers, DOI 10.18434/t4/1500024.
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Kasu M, Cloete K, Pitere R, Tsiana K, D’Amato M. The Genetic Landscape of South African males: A Y-STR Perspective. Forensic Sci Int Genet 2022; 58:102677. [DOI: 10.1016/j.fsigen.2022.102677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/04/2022]
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Pilli E, Tarallo R, Riccia PL, Berti A, Novelletto A. Kinship assignment with the ForenSeq™ DNA Signature Prep Kit: Sources of error in simulated and real cases. Sci Justice 2022; 62:1-9. [PMID: 35033321 DOI: 10.1016/j.scijus.2021.10.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 08/31/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022]
Abstract
Kinship recognition between anonymous DNA samples is becoming a relevant issue in forensics, more so with the increasing number of DNA profiles in databanks. Also, NGS-based genotyping is being increasingly used in routine personal identification, to simultaneously type large numbers of markers of different kind. In the present work, we explored computationally and experimentally the performance of the ForenSeq™ DNA Signature Prep Kit in identifying the true relationship between two anonymous samples, distinguishing it from other possible relationships. We analyzed with Familias R series of 10,000 pairs with 9 different simulated relationships, corresponding to different degrees of autosomal sharing. For each pair we obtained likelihood ratios for five kinship hypotheses vs. unrelatedness, and used their ranking to identify the preferred relationship. We also typed 21 subjects from two pedigrees, representing from parent-child to 4th cousins relationships. As expected, the power for identifying the true relationship decays in the order of autosomal sharing. Parent-child and full siblings can be robustly identified against other relationships. For half-siblings the chance of reaching a significant conclusion is already small. For more distant relationships the proportion of cases correctly and significantly identified is 10% or less. Bidirectional errors in kinship attribution include the suggestion of relatedness when this does not exist (10-50%), and the suggestion of independence in pairs of individuals more than 4 generations apart (25-60%). The real cases revealed a relevant effect of genotype miscalling at some loci, which could only be partly avoided by modulating the analysis parameters. In conclusion, with the exception of first degree relatives, the kit can be useful to inform additional investigations, but does not usually provide probatory results.
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Affiliation(s)
- Elena Pilli
- Department of Biology, University of Florence, Florence, Italy.
| | - Roberta Tarallo
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Pietro La Riccia
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche, Sezione di Biologia, Roma, Italy
| | - Andrea Novelletto
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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Watahiki H, Fujii K, Fukagawa T, Mita Y, Kitayama T, Mizuno N. Frequencies of D19S433 silent alleles in a Japanese population of 1501 individuals and their effect on likelihood ratios calculated in kinship tests. Leg Med (Tokyo) 2022; 54:102008. [PMID: 34974234 DOI: 10.1016/j.legalmed.2021.102008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/02/2021] [Accepted: 12/23/2021] [Indexed: 11/15/2022]
Abstract
Although silent alleles in D19S433 typing using the GlobalFiler PCR Amplification Kit have been reported, the exact frequency of the D19S433 silent alleles in population data of 1501 Japanese individuals, which are widely used for the assessment of Japanese STR typing results, is unclear. In this study, we examined the exact D19S433 silent allele frequency in this population data. We newly observed the G32A variant causing silent alleles at D19S433 in five samples. Combining them with data including 30 samples with the variant reported previously, we determined that the total frequency of the silent alleles (i.e. the frequency of the G32A variant) in the 1501 Japanese samples was 0.0117 (35/3002). Using the D19S433 allele frequency data, we evaluated the effect of presence/absence information for the D19S433 silent allele on kinship tests. Likelihood ratios (LRs) were calculated for both simulated parent-child and full sibling cases, revealing that the LR may change by approximately 10-2 to 103 fold when the presence/absence of the D19S433 silent allele is revealed in a kinship test. Therefore, if a sufficiently large or small LR is obtained, there is little need to determine the presence/absence of the D19S433 silent allele in Japanese kinship tests using GlobalFiler. This study will be beneficial for the assessment of Japanese human identification and kinship test results using GlobalFiler.
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Affiliation(s)
- Haruhiko Watahiki
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan.
| | - Koji Fujii
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan
| | - Takashi Fukagawa
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan
| | - Yusuke Mita
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan
| | - Tetsushi Kitayama
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba 277-0882, Japan
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Dash HR, Vajpayee K, Agarwal R, Gang A, Shukla R, Srivastava A. Evaluation of diallelic STR markers with inter-population allelic database for their usefulness in paternity trios in the Central Indian population. Ann Hum Biol 2021; 48:605-613. [PMID: 34866517 DOI: 10.1080/03014460.2021.2014567] [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: 10/19/2022]
Abstract
BACKGROUND Most of the forensic DNA laboratories have migrated to new generation STR kits of 6 dye chemistry with more than 20 autosomal STRs. The population-specific databases of such STR markers are lacking in many regions. AIM To evaluate the effect of the inter-population database in 100 paternity trios with no inconsistencies at 23 STRs. SUBJECTS AND METHODS 100 paternity trios were evaluated considering inter-population allelic frequency values for calculation of Combined Paternity Index (CPI) and Probability of Paternity (POP). RESULTS No significant variation (p < 0.05) among the allele frequencies at the interpopulation level was observed. The number of obligate alleles and the likelihood of transferring obligate alleles from the putative father showed a positive correlation (p < 0.005) with Power of Discrimination (PD), Polymorphic Information Content (PIC), Power of Exclusion (PE), Paternity Index (PI), Observed and Expected Heterozygosity (Ho and He), and a statistically significant negative correlation (p < 0.005) with Matching Probability (Pm). The average Combined Paternity Index (CPI) and Probability of Paternity (POP) did not show any statistically significant difference (p < 0.05) at the interpopulation level. CONCLUSION The allelic database showed no effect on the CPI and POP in 100 paternity trios. This suggests no urgent need for using population-specific databases for statistical evaluation of paternity trios without inconsistencies.
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Affiliation(s)
| | - Kamayani Vajpayee
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, India.,Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Radhika Agarwal
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, India
| | - Anubha Gang
- Regional Forensic Science Laboratory, Indore, India
| | - Ritesh Shukla
- Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Ankit Srivastava
- Institute of Forensic Science and Criminology, Bundelkhand University, Jhansi, India
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Haas C, Körner C, Sulzer A, Kratzer A. 19th century family saga re-told by DNA recovered from postcard stamps. Forensic Sci Int 2021; 330:111129. [PMID: 34883299 DOI: 10.1016/j.forsciint.2021.111129] [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: 09/21/2021] [Revised: 11/05/2021] [Accepted: 11/27/2021] [Indexed: 11/26/2022]
Abstract
Old postcards with stamps might help unravelling historical family stories and relationships. By employing ancient DNA recovered from world war I postage stamps, we disprove a family saga of an illegitimate child born in 1887. We developed a protocol to collect DNA from saliva, trapped and protected on the backside of postage stamps glued on postcards. With replicate STR analyses we were able to assemble almost full autosomal and Y-STR profiles of three male, deceased family members. The illegitimate child turned out to be a legitimate child of a later married couple.
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Affiliation(s)
- Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
| | - Christian Körner
- Department of Environmental Sciences, University of Basel, Switzerland
| | - Andrea Sulzer
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Adelgunde Kratzer
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
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Tao R, Xu Q, Wang S, Xia R, Yang Q, Chen A, Qu Y, Lv Y, Zhang S, Li C. Pairwise kinship analysis of 17 pedigrees using massively parallel sequencing. Forensic Sci Int Genet 2021; 57:102647. [PMID: 34902810 DOI: 10.1016/j.fsigen.2021.102647] [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: 07/12/2021] [Revised: 11/18/2021] [Accepted: 11/28/2021] [Indexed: 01/23/2023]
Abstract
With the tremendous development of massively parallel sequencing (MPS) in the last decade, it has been widely applied in basic science, clinical diagnostics, microbial genomics, as well as forensic genetics. MPS has lots of advantages that may facilitate the kinship analysis. In this study, 243 Chinese Han individuals from 17 families were involved and sequenced using the ForenSeq™ DNA Signature Prep Kit (Verogen, Inc., San Diego, USA), which provided the sequence information of 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative SNPs (iSNPs). A total of 275 pairs of parent-child, 123 pairs of full siblings, 1 pair of twins, 1 pair of half siblings, 158 pairs of grandparent-grandchild, 222 pairs of uncle/aunt-nephew/niece and 121 pairs of first cousins, as well as 701 pairs of unrelated individuals were identified. Using both likelihood ratio (LR) and identical by state (IBS) methods, the kinship analysis was conducted among these relative and non-relative pairs based on the A-STRs and SNPs. As a result, the ForenSeq Signature Kit could solve the analysis of parent-child (t1 = -4, t2 = 4), full siblings (t1 = -2, t2 = 2) and most second-degree kinships (t1 = -1, t2 = 1) using the LR method. When the IBS method was applied, 123 full sibling pairs had a higher average IBS value than other kinship groups in this study. And the IBS method could play a role in the testing of parent-child and full siblings.
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Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Shouyu Wang
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China
| | - Qi Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, PR China
| | - Yehui Lv
- Shanghai University of Medicine & Health Sciences, Shanghai 200237, PR China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, PR China.
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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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Developmental validation of a software implementation of a flexible framework for the assignment of likelihood ratios for forensic investigations. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2021.100231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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46
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Population genetic data of 22 autosomal STR loci from the Dominican Republic. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2021.100228] [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] Open
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Ge J, King JL, Smuts A, Budowle B. Precision DNA Mixture Interpretation with Single-Cell Profiling. Genes (Basel) 2021; 12:1649. [PMID: 34828255 PMCID: PMC8623868 DOI: 10.3390/genes12111649] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
Wet-lab based studies have exploited emerging single-cell technologies to address the challenges of interpreting forensic mixture evidence. However, little effort has been dedicated to developing a systematic approach to interpreting the single-cell profiles derived from the mixtures. This study is the first attempt to develop a comprehensive interpretation workflow in which single-cell profiles from mixtures are interpreted individually and holistically. In this approach, the genotypes from each cell are assessed, the number of contributors (NOC) of the single-cell profiles is estimated, followed by developing a consensus profile of each contributor, and finally the consensus profile(s) can be used for a DNA database search or comparing with known profiles to determine their potential sources. The potential of this single-cell interpretation workflow was assessed by simulation with various mixture scenarios and empirical allele drop-out and drop-in rates, the accuracies of estimating the NOC, the accuracies of recovering the true alleles by consensus, and the capabilities of deconvolving mixtures with related contributors. The results support that the single-cell based mixture interpretation can provide a precision that cannot beachieved with current standard CE-STR analyses. A new paradigm for mixture interpretation is available to enhance the interpretation of forensic genetic casework.
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Affiliation(s)
- Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (J.L.K.); (A.S.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Jonathan L. King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (J.L.K.); (A.S.); (B.B.)
| | - Amy Smuts
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (J.L.K.); (A.S.); (B.B.)
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; (J.L.K.); (A.S.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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Gehrig C, Delémont S, Comte J, Hicks T, Basset P, Grosjean F, Dion D, Cossu C, Bottinelli M, Hecht M, Sulzer A, Voegeli P, Castella V. A Swiss collaborative exercise for Disaster Victim Identification (DVI): Covering situations with different levels of complexity. J Forensic Leg Med 2021; 83:102254. [PMID: 34592483 DOI: 10.1016/j.jflm.2021.102254] [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: 05/26/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 11/27/2022]
Abstract
The identification of victims of a disaster (DVI) requires the collaboration of different specialists. Within a DVI context, DNA analyses often play an important role. Consequently, forensic genetic laboratories should be prepared to cope with DVI situations, as this can involve large-scale DNA profile comparisons. Six forensic genetic laboratories from Switzerland participated in an exercise where supposedly a plane had crashed. The goal of the exercise was to monitor participants use of dedicated software with ground truth cases and to make them aware of the existence of particular situations that may occur in real cases. For assigning the value of the comparison of the DNA profiles, all participating laboratories used the DVI module of Familias v3.2.1 In addition, one of the 6 laboratories used the Pedigree Searcher from CODIS v7.0. The data (AmpFlSTR® NGM SElect™ profiles) were generated to challenge the participating laboratories: cases with first, second degree biological parents, mutation events, as well as non-paternity cases were included. This study shows that the majority of the participants used the software in an appropriate way. However, a few misleading conclusions were detected for the most challenging situations. These errors belonged to one of the following categories: false pedigree, false association using the higher LR, misleading contextual information (false paternity) and not clustering family members. Specific recommendations are provided in order to reduce misuse of the software and the risk of misinterpretations by using all the relevant information.
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Affiliation(s)
- Christian Gehrig
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland.
| | | | - Jennifer Comte
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland
| | - Tacha Hicks
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland; Fondation pour la Formation Continue Universitaire Lausannoise (UNIL-EPFL), Switzerland
| | - Patrick Basset
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland
| | | | - Daniel Dion
- Institut für Rechtsmedizin, Basel, Switzerland
| | | | | | - Mirco Hecht
- Institut für Rechtsmedizin, Bern, Switzerland
| | | | | | - Vincent Castella
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland
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49
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Interpretation of DNA data within the context of UK forensic science - investigation. Emerg Top Life Sci 2021; 5:395-404. [PMID: 34151948 PMCID: PMC8457768 DOI: 10.1042/etls20210165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/08/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022]
Abstract
This article is the second part of a review of the interpretation of DNA data in forensic science. The first part describes the evaluation of autosomal profile for criminal trials where an evidential weight is assigned to the profile of a person of interest (POI) and a crime-scene profile. This part describes the state of the art and future advances in the interpretation of forensic DNA data for providing intelligence information during an investigation. Forensic DNA is crucial in the investigative phase of an undetected crime where a POI needs to be identified. A sample taken from a crime scene is profiled using a range of forensic DNA tests. This review covers investigation using autosomal profiles including searching national and international crime and reference DNA databases. Other investigative methodologies described are kinship analysis; familial searching; Y chromosome (Y-STR) and mitochondrial (mtDNA) profiles; appearance prediction and geographic ancestry; forensic genetic genealogy; and body identification. For completeness, the evaluation of Y-STRs, mtDNA and kinship analysis are briefly described. Taken together, parts I and II, cover the range of interpretation of DNA data in a forensic context.
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50
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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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