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Iyavoo S, Perry J, Knights S, Mavrommatis M, Petrova T, Bevan A, Cummings S, Pedroza Matute S, Song D, Haizel T. Unveiling genetic diversity and forensic utility of SureID® human DNA identification kits: a comprehensive analysis of 44 autosomal STR loci in English and Irish populations. Ann Hum Biol 2023; 50:399-406. [PMID: 37815229 DOI: 10.1080/03014460.2023.2265814] [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: 03/14/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023]
Abstract
Background: Human identification and kinship testing in forensic science rely on Short Tandem Repeat (STR) multiplex kits, typically containing loci recommended by standard sets. However, complementary kits with additional STR loci can be valuable in complex cases. Allele frequency databases specific to the population are essential for accurate forensic analysis.Aim: This study aimed to generate allele frequencies and population genetic data for 44 autosomal STR loci from SureID® PanGlobal and 27comp kits in English and Irish populations for forensic casework, human identification, and kinship testing.Subjects and methods: Buccal swab samples from 645 White Caucasians (365 English, 280 Irish) were collected. DNA was extracted and amplified using the mentioned kits. Quality control, statistical analysis, and genetic distance calculations were performed.Results: Both kits demonstrated robustness with no significant deviations from Hardy-Weinberg Equilibrium (HWE). Variant alleles and minor discordances between kits were observed. Syntenic STR pairs were identified but showed no significant linkage. A close genetic relationship was found between English and Irish populations, allowing for combined databases.Conclusions: The SureID® PanGlobal and 27comp kits showed high discriminatory power and reliability in the English and Irish populations. Care is needed when handling variant alleles, discordances, and syntenic loci. Combining data from both populations is feasible for a comprehensive database. Further studies are required to explore their effectiveness in diverse populations.
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Affiliation(s)
- Sasitaran Iyavoo
- IDna Genetics Limited, Norfolk, UK
- School of Chemistry, College of Health and Science, University of Lincoln, Lincolnshire, UK
| | - Jessica Perry
- School of Chemistry, College of Health and Science, University of Lincoln, Lincolnshire, UK
| | | | | | | | | | | | | | - Danlu Song
- Ningbo Health Gene Technologies Co. Ltd, Ningbo, China
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2
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Forensic Applications of Markers Present on the X Chromosome. Genes (Basel) 2022; 13:genes13091597. [PMID: 36140765 PMCID: PMC9498577 DOI: 10.3390/genes13091597] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Microsatellite genetic markers are the gold standard for human genetic identification. Forensic analyses around the world are carried out through protocols using the analysis of STR markers in autosomal chromosomes and in the Y chromosome to solve crimes. However, these analyses do not allow for the resolution of all cases, such as rape situations with suspicion of incest, paternity without a maternal sample for comparison, and biological traces with DNA mixture where the profile sought is female, among other situations. In these complex cases, the study of X-chromosome STR markers significantly increases the probability of identification by complementing the data obtained for autosomal and Y-chromosome markers, due to the unique structure of the X chromosome and its exclusive method of inheritance. However, there are currently no validated Brazilian protocols for this purpose, nor are there any population data necessary for statistical analyses that must be included in the issuance of expert reports. Thus, the aim of this article is to provide a literary review of the applications of X-chromosomal markers in population genetics.
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3
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Zhang Q, Wang X, Cheng P, Yang S, Li W, Zhou Z, Wang S. Complex kinship analysis with a combination of STRs, SNPs, and indels. Forensic Sci Int Genet 2022; 61:102749. [DOI: 10.1016/j.fsigen.2022.102749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/26/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022]
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4
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Xu Q, Wang Z, Kong Q, Wang X, Huang A, Li C, Liu X. Improving the System Power of Complex Kinship Analysis by Combining Multiple Systems. Forensic Sci Int Genet 2022; 60:102741. [DOI: 10.1016/j.fsigen.2022.102741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/04/2022] [Accepted: 06/12/2022] [Indexed: 11/04/2022]
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5
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Zieger M, Gouy A, Utz S. Expanding the Swiss autosomal marker set to 32 STRs. Int J Legal Med 2021; 135:2309-2310. [PMID: 34143274 PMCID: PMC8523451 DOI: 10.1007/s00414-021-02624-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/24/2021] [Indexed: 12/03/2022]
Abstract
By genotyping 1198 individuals with the Qiagen Investigator® HDplex Kit, we expand the Swiss autosomal STR dataset to 32 loci, providing additional resources for complex kinship cases. We present the first high-quality allele frequency dataset for loci D2S1360, D5S2500, D7S1517, and D10S2325 that will be accessible through the ENFSI reference database STRidER. For loci D3S1744, D4S2366, D6S474, D8S1132, and D21S2055, we provide a first European STRidER dataset.
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Affiliation(s)
- Martin Zieger
- Institute of Forensic Medicine, Forensic Molecular Biology Department, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland
| | - Alexandre Gouy
- Gouy Data Consulting, Sentier de Renges 4A, 1026 Denges, Switzerland
| | - Silvia Utz
- Institute of Forensic Medicine, Forensic Molecular Biology Department, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland
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6
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Li R, Budowle B, Sun H, Ge J. Linkage and linkage disequilibrium among the markers in the forensic MPS panels. J Forensic Sci 2021; 66:1637-1646. [PMID: 33885147 DOI: 10.1111/1556-4029.14724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 11/28/2022]
Abstract
For the past two to three decades, forensic DNA evidence has been analyzed with a limited number of short tandem repeats (STRs), and these STRs are usually assumed to be independent for statistical calculations. With the development and implementation of the MPS technologies, more autosomal markers, both single nucleotide polymorphisms (SNPs) and STRs, can be analyzed. A number of these markers are physically very close to each other, and it may not be appropriate to assume all these markers are genetically unlinked or in linkage equilibrium. In this study, publicly accessible genomic data from five representative populations were used to evaluate the genetic linkage and linkage disequilibrium (LD) between autosomal markers represented in six major commercial panels (in total, 362 markers). Among the 3041 syntenic marker pairs, 1524 pairs had sex-average genetic distances <50 cM, and thus, these marker pairs can be considered as genetically linked. Among the 143 marker pairs with physical distances <1 Mb, 19 LD haplotype blocks (comprising 39 SNPs in total) were detected for at least one of the tested populations. Statistical methods for interpreting linked markers and/or markers in LD were suggested for various case scenarios.
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Affiliation(s)
- Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.,Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.,Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
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7
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Zhang Y, Yu Z, Mo X, Zhao X, Li W, Liu H, Liu C, Wu R, Sun H. Comparative evaluation of autosomal STRs and X-chromosome STRs as a complement of autosomal STRs in kinship testing in Southern Han Chinese. Ann Hum Biol 2020; 48:66-69. [PMID: 33256486 DOI: 10.1080/03014460.2020.1856926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Nowadays, kinship testing is very common in forensic caseworks, but the power of autosomal short tandem repeats (A-STRs) may be limited in complex cases. X-Chromosome short tandem repeats (X-STRs), having a unique heritage mode, should be of special use in some deficient cases. To evaluate and compare the potential of A-STR and X-STR as supplement genetic markers in deficient kinship testing, we simulated 10,000 duos for each of 18 kinds of relationships involving full sibling, half-sibling, grandparent-grandchild, and uncle/aunt-nephew/niece. Loci from STRTyper10, PowerPlex 16, and Investigator Argus X-12 were studied in Southern Han Chinese and the distribution of likelihood ratio (LR) values was analysed. With the addition of the X-12 system, the distribution of LR values for the full sisters, paternal half-sisters, paternal grandmother-granddaughters, maternal aunt-nieces, and maternal aunt-nephews separated much more obviously from those of unrelated duos, and the effectiveness was 1.0000, 0.99865, 0.9991, 0.8996 and 0.9634, respectively, which was more efficient than A-STRs. For the individual duos with other relationships, the effects of adding X-STRs and A-STRs were similar. Therefore, for the Southern Han Chinese, X-STRs can be very useful in kinship testing involving full sisters, paternal half-sisters, paternal grandmother-granddaughters, and maternal aunt-nieces/nephews.
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Affiliation(s)
- Yinming Zhang
- Institute of Forensic Science, Ministry of Public Security, Beijing, P.R. China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zhengliang Yu
- Institute of Forensic Science, Ministry of Public Security, Beijing, P.R. China
| | - Xiaoting Mo
- Institute of Forensic Science, Ministry of Public Security, Beijing, P.R. China
| | - Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing, P.R. China
| | - Wanshui Li
- Institute of Forensic Science, Ministry of Public Security, Beijing, P.R. China
| | - Hong Liu
- Guangzhou Forensic Institute, Guangzhou, P.R. China
| | - Chao Liu
- Guangzhou Forensic Institute, Guangzhou, P.R. China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P.R. China
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8
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Brustad HK, Vigeland MD, Egeland T. Pairwise relatedness testing in the context of inbreeding: expectation and variance of the likelihood ratio. Int J Legal Med 2020; 135:117-129. [PMID: 32989564 PMCID: PMC7782430 DOI: 10.1007/s00414-020-02426-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 09/10/2020] [Indexed: 12/01/2022]
Abstract
In this paper we investigate various effects of inbreeding on the likelihood ratio (LR) in forensic kinship testing. The basic setup of such testing involves formulating two competing hypotheses, in the form of pedigrees, describing the relationship between the individuals. The likelihood of each hypothesis is computed given the available genetic data, and a conclusion is reached if the ratio of these exceeds some pre-determined threshold. An important aspect of this approach is that the hypotheses are usually not exhaustive: The true relationship may differ from both of the stated pedigrees. It is well known that this may introduce bias in the test results. Previous work has established formulas for the expected value and variance of the LR, given the two competing hypotheses and the true relationship. However, the proposed method only handles cases without inbreeding. In this paper we extend these results to all possible pairwise relationships. The key ingredient is formulating the hypotheses in terms of Jacquard coefficients instead of the more restricted Cotterman coefficients. While the latter describe the relatedness between outbred individuals, the more general Jacquard coefficients allow any level of inbreeding. Our approach also enables scrutiny of another frequently overlooked source of LR bias, namely background inbreeding. This ubiquitous phenomenon is usually ignored in forensic kinship computations, due to lack of adequate methods and software. By leveraging recent work on pedigrees with inbred founders, we show how background inbreeding can be modeled as a continuous variable, providing easy-to-interpret results in specific cases. For example, we show that if true siblings are subjected to a test for parent-offspring, moderate levels of background inbreeding are expected to inflate the LR by more than 50%.
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Affiliation(s)
| | - Magnus Dehli Vigeland
- Department of Medical Genetics, University of Oslo, PB 4956 Nydalen, 0424, Oslo, Norway
| | - Thore Egeland
- Norwegian University of Life Sciences, 1432, Aas, Norway
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9
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Pairwise kinship testing with a combination of STR and SNP loci. Forensic Sci Int Genet 2020; 46:102265. [DOI: 10.1016/j.fsigen.2020.102265] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 12/22/2019] [Accepted: 02/23/2020] [Indexed: 11/22/2022]
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10
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Hirata S, Kojima K, Misawa K, Gervais O, Kawai Y, Nagasaki M. Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population. Heliyon 2018; 4:e00625. [PMID: 29872759 PMCID: PMC5986539 DOI: 10.1016/j.heliyon.2018.e00625] [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: 12/05/2017] [Revised: 03/22/2018] [Accepted: 05/08/2018] [Indexed: 11/29/2022] Open
Abstract
Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.
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Affiliation(s)
- Satoshi Hirata
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Kaname Kojima
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Kazuharu Misawa
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Olivier Gervais
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Yosuke Kawai
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Masao Nagasaki
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
- Corresponding author.
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11
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Liu QL, Xue L, Wu WW, He X, liu KY, Zhao H, Lu DJ. Potential of 13 linked autosomal short tandem repeat loci in pairwise kinship analysis. Electrophoresis 2016; 37:2800-2806. [DOI: 10.1002/elps.201600238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/02/2016] [Accepted: 08/23/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Qiu-Ling Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
| | - Li Xue
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
| | - Wei-Wei Wu
- Department of Criminal Investigation of Zhejiang Provincial Public Security Bureau; Hangzhou P. R. China
| | - Xin He
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
| | - Kai-Yan liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
| | - Hu Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
| | - De-Jian Lu
- Faculty of Forensic Medicine, Zhongshan School of Medicine; Sun Yat-Sen University; Guangzhou P. R. China
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12
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Liu QL, Chen ZX, Chen CG, Lu DJ. Genetic polymorphism of 22 autosomal STR markers in a Han population of Southern China. Forensic Sci Int Genet 2016; 24:e14-e16. [DOI: 10.1016/j.fsigen.2016.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/21/2016] [Accepted: 06/22/2016] [Indexed: 11/16/2022]
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13
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The likelihood ratio as a random variable for linked markers in kinship analysis. Int J Legal Med 2016; 130:1445-1456. [DOI: 10.1007/s00414-016-1416-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
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14
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Grandell I, Samara R, Tillmar AO. A SNP panel for identity and kinship testing using massive parallel sequencing. Int J Legal Med 2016; 130:905-914. [DOI: 10.1007/s00414-016-1341-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/16/2016] [Indexed: 01/03/2023]
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15
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Turrina S, Ferrian M, Caratti S, Cosentino E, De Leo D. Kinship analysis: assessment of related vs unrelated based on defined pedigrees. Int J Legal Med 2015; 130:113-9. [DOI: 10.1007/s00414-015-1290-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/09/2015] [Indexed: 10/22/2022]
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16
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Tamura T, Osawa M, Ochiai E, Suzuki T, Nakamura T. Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis. Leg Med (Tokyo) 2015; 17:320-5. [DOI: 10.1016/j.legalmed.2015.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 03/23/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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17
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Slooten KJ, Egeland T. Exclusion probabilities and likelihood ratios with applications to mixtures. Int J Legal Med 2015; 130:39-57. [DOI: 10.1007/s00414-015-1217-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/23/2015] [Indexed: 12/17/2022]
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18
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Efficient computations with the likelihood ratio distribution. Forensic Sci Int Genet 2015; 14:116-24. [DOI: 10.1016/j.fsigen.2014.09.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 08/04/2014] [Accepted: 09/23/2014] [Indexed: 12/15/2022]
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19
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Kruijver M, Meester R, Slooten K. Optimal strategies for familial searching. Forensic Sci Int Genet 2014; 13:90-103. [DOI: 10.1016/j.fsigen.2014.06.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 06/11/2014] [Indexed: 11/28/2022]
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20
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Wu W, Hao H, Liu Q, Han X, Wu Y, Cheng J, Lu D. Analysis of linkage and linkage disequilibrium for syntenic STRs on 12 chromosomes. Int J Legal Med 2014; 128:735-9. [PMID: 24929640 DOI: 10.1007/s00414-014-1032-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 06/02/2014] [Indexed: 11/30/2022]
Abstract
The purpose of this study is to evaluate allelic association and linkage of 18 adjacent syntenic short tandem repeat (STR) pairs form out of 30 markers located on 12 different autosomes. Linkage disequilibrium was tested by using the unknown gametic phase genotypes and phased haplotypes from 290 unrelated individuals from Chinese Han population. Genetic linkage analysis between syntenic STRs was performed based on 145 two-generation families which involved 628 meioses. The results showed no significant linkage disequilibrium at any STR pairs and independent inheritance between syntenic STR pairs was indicated. Significant linkage (maximum logarithm of odd (LOD) scores >3.0) was found in 6 out of the 18 adjacent syntenic STR pairs (D1S1627-D1S1677, CSF1PO-D5S818, D6S1017-D6S1043, D6S1043-D6S474, D12S391-vWA, and D19S253-D19S433). These significant linkage marker pairs had a genetic distance ranged from 11.94 to 41.33 cM deduced from HapMap. When recombination fractions determined in families were compared to those derived from Kosambi mapping function based on HapMap data, the latter may have an overestimation. In summary, our results demonstrated that product rule included syntenic STRs can be used for unrelated individual profile probability and the recombination fraction based on family data was superior to the estimation from HapMap for kinship analysis.
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Affiliation(s)
- Weiwei Wu
- Department of Criminal Investigation of Zhejiang Provincial Public Security Bureau, 66#, Minsheng Road, 310009, Hangzhou, People's Republic of China
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Basgalupp SP, Rodenbusch R, Schumacher S, Gastaldo AZ, Santos Silva DSB, Alho CS. Investigation of paternity with alleged father deceased or missing: analysis of success at the end of the report. Forensic Sci Int Genet 2014; 12:120-1. [PMID: 24929954 DOI: 10.1016/j.fsigen.2014.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/02/2014] [Accepted: 05/20/2014] [Indexed: 10/25/2022]
Abstract
In this work we present a retrospective study of 858 cases of paternity investigation performed in Rio Grande do Sul, Southern Brazil, from 2007 to 2012, where the alleged father was deceased or missing. These cases represent 3.3% (858/26187) of paternity tests performed in that period. Considering the analysis of 17 DNA short tandem repeat loci, we present here the proportion of cases with conclusive results according to the number of relatives of the unavailable alleged father investigated and their kinship. The results show 81.0% (695/858) of cases with conclusive results and their characteristics.
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Affiliation(s)
- Suelen Porto Basgalupp
- Laboratório de Genética Humana e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 90619-900 Porto Alegre, RS, Brazil; Laboratório de Investigação de Paternidade, Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), 90610-000 Porto Alegre, RS, Brazil
| | - Rodrigo Rodenbusch
- Laboratório de Genética Humana e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 90619-900 Porto Alegre, RS, Brazil; Laboratório de Investigação de Paternidade, Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), 90610-000 Porto Alegre, RS, Brazil
| | - Simone Schumacher
- Laboratório de Investigação de Paternidade, Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), 90610-000 Porto Alegre, RS, Brazil
| | - André Zoratto Gastaldo
- Laboratório de Genética Humana e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 90619-900 Porto Alegre, RS, Brazil; Laboratório de Investigação de Paternidade, Centro de Desenvolvimento Científico e Tecnológico (CDCT), Fundação Estadual de Produção e Pesquisa em Saúde (FEPPS), 90610-000 Porto Alegre, RS, Brazil
| | - Deborah Soares Bispo Santos Silva
- Laboratório de Genética Humana e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 90619-900 Porto Alegre, RS, Brazil
| | - Clarice Sampaio Alho
- Laboratório de Genética Humana e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 90619-900 Porto Alegre, RS, Brazil.
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22
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Egeland T, Pinto N, Vigeland MD. A general approach to power calculation for relationship testing. Forensic Sci Int Genet 2014; 9:186-90. [DOI: 10.1016/j.fsigen.2013.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 04/02/2013] [Accepted: 05/03/2013] [Indexed: 11/30/2022]
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23
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Dørum G, Bleka Ø, Gill P, Haned H, Snipen L, Sæbø S, Egeland T. Exact computation of the distribution of likelihood ratios with forensic applications. Forensic Sci Int Genet 2013; 9:93-101. [PMID: 24528587 DOI: 10.1016/j.fsigen.2013.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 10/25/2013] [Accepted: 11/30/2013] [Indexed: 10/25/2022]
Abstract
If complex DNA profiles, conditioned on multiple individuals are evaluated, it may be difficult to assess the strength of the evidence based on the likelihood ratio. A likelihood ratio does not give information about the relative weights that are provided by separate contributors. Alternatively, the observed likelihood ratio can be evaluated with respect to the distribution of the likelihood ratio under the defense hypothesis. We present an efficient algorithm to compute an exact distribution of likelihood ratios that can be applied to any LR-based model. The distribution may have several applications, but is used here to compute a p-value that corresponds to the observed likelihood ratio. The p-value is the probability that a profile under the defense hypothesis, substituted for a questioned contributor e.g. suspect, would attain a likelihood ratio which is at least the same magnitude as that observed. The p-value can be thought of as a scaled version of the likelihood ratio, giving a quantitative measure of the strength of the evidence relative to the specified hypotheses and the model used for the analysis. The algorithm is demonstrated on examples based on real data. R code for the algorithm is freely available in the R package euroMix.
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Affiliation(s)
- Guro Dørum
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (UMB), Norway.
| | - Øyvind Bleka
- Department of Forensic Genetics, Norwegian Institute of Public Health, Oslo, Norway
| | - Peter Gill
- Department of Forensic Genetics, Norwegian Institute of Public Health, Oslo, Norway; Rikshospitalet, University of Oslo, Oslo, Norway
| | - Hinda Haned
- Netherlands Forensic Institute, Department of Human Biological Traces, The Hague, The Netherlands
| | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (UMB), Norway
| | - Solve Sæbø
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (UMB), Norway
| | - Thore Egeland
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (UMB), Norway; Department of Forensic Genetics, Norwegian Institute of Public Health, Oslo, Norway
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24
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Liu QL, Luo H, Zhao H, Huang XL, Cheng JD, Lu DJ. Recombination analysis of autosomal short tandem repeats in Chinese Han families. Electrophoresis 2013; 35:883-7. [PMID: 24323827 DOI: 10.1002/elps.201300417] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 10/26/2013] [Accepted: 10/28/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Qiu-Ling Liu
- Faculty of Forensic Medicine; Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Hong Luo
- Clinical Institute for Transfusion Medicine; Guangzhou Blood Center; Guangzhou P. R. China
| | - Hu Zhao
- Faculty of Forensic Medicine; Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Xiao-Ling Huang
- Faculty of Forensic Medicine; Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - Jian-Ding Cheng
- Faculty of Forensic Medicine; Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
| | - De-Jian Lu
- Faculty of Forensic Medicine; Zhongshan School of Medicine; Sun Yat-sen University; Guangzhou P. R. China
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25
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Exclusion probabilities and likelihood ratios with applications to kinship problems. Int J Legal Med 2013; 128:415-25. [DOI: 10.1007/s00414-013-0938-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 10/29/2013] [Indexed: 11/27/2022]
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26
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Schumm JW, Gutierrez-Mateo C, Tan E, Selden R. A 27-locus STR assay to meet all United States and European law enforcement agency standards. J Forensic Sci 2013; 58:1584-92. [PMID: 23822765 DOI: 10.1111/1556-4029.12214] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 08/15/2012] [Accepted: 08/19/2012] [Indexed: 11/27/2022]
Abstract
Different national and international agencies have selected specific STR sets for forensic database use. To enhance database comparison across national and international borders, a 27-locus multiplex system was developed comprising all 15 STR loci of the European standard set, the current 13 STR loci of the CODIS core, the proposed 22 STR loci of the expanded CODIS core, 4 additional commonly used STR loci, and the amelogenin locus. Development required iterative primer design to resolve primer-related artifacts, amplicon sizing, and locus-to-locus balance issues. The 19.5-min assay incorporated newly developed six-dye chemistry analyzed using a novel microfluidic electrophoresis instrument capable of simultaneous detection and discrimination of 8 or more fluorescent dyes. The 27-locus multiplex offers the potential for a new international STR standard permitting laboratories in any jurisdiction to use a single reaction to determine profiles for loci they typically generate plus an expanded common STR profiling set of global interest.
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27
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Phillips C, Fernandez-Formoso L, Gelabert-Besada M, Garcia-Magariños M, Santos C, Fondevila M, Carracedo Á, Lareu MV. Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing. Electrophoresis 2013; 34:1151-62. [DOI: 10.1002/elps.201200621] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 12/13/2012] [Accepted: 12/17/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Chris Phillips
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
| | - Luis Fernandez-Formoso
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
| | - Miguel Gelabert-Besada
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
| | | | - Carla Santos
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
| | - Manuel Fondevila
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
| | | | - Maria Victoria Lareu
- Forensic Genetics Unit; Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela; Spain
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28
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Huang YM, Wang J, Jiao Z, Yang L, Zhang X, Tang H, Liu Y. Assessment of application value of 19 autosomal short tandem repeat loci of GoldenEyeTM 20A kit in forensic paternity testing. Int J Legal Med 2013; 127:587-90. [DOI: 10.1007/s00414-013-0842-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 02/25/2013] [Indexed: 11/24/2022]
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29
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Nothnagel M, Szibor R, Vollrath O, Augustin C, Edelmann J, Geppert M, Alves C, Gusmão L, Vennemann M, Hou Y, Immel UD, Inturri S, Luo H, Lutz-Bonengel S, Robino C, Roewer L, Rolf B, Sanft J, Shin KJ, Sim JE, Wiegand P, Winkler C, Krawczak M, Hering S. Collaborative genetic mapping of 12 forensic short tandem repeat (STR) loci on the human X chromosome. Forensic Sci Int Genet 2012; 6:778-84. [DOI: 10.1016/j.fsigen.2012.02.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 02/01/2012] [Accepted: 02/29/2012] [Indexed: 10/28/2022]
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30
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FamLink – A user friendly software for linkage calculations in family genetics. Forensic Sci Int Genet 2012; 6:616-20. [PMID: 22390853 DOI: 10.1016/j.fsigen.2012.01.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 01/23/2012] [Accepted: 01/30/2012] [Indexed: 11/23/2022]
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31
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Comparative evaluation of alternative batteries of genetic markers to complement autosomal STRs in kinship investigations: autosomal indels vs. X-chromosome STRs. Int J Legal Med 2012; 126:917-21. [PMID: 22940765 DOI: 10.1007/s00414-012-0768-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/21/2012] [Indexed: 10/27/2022]
Abstract
Kinship investigations such as paternity are currently solved using sets of (commercially available) highly polymorphic autosomal short tandem repeats (STRs), which lead to powerful likelihood ratios (LR). Still, some difficult cases arise whenever the kinship is much more remote or if the alternative hypotheses are not correctly formulated due to the lack of information (for e.g. there is an unknown relationship between the alleged and the true fathers). In these situations, beyond the routinely used marker set, laboratories usually enlarge the number and/or the type of markers analysed. Among these, autosomal indels and X-chromosome STRs have gained popularity. The aim of this study was to compare the results obtained after complementing an initial set of autosomal STRs with indels or with X-chromosome-specific STRs in simulated paternity cases where the alleged father is a close relative of the real one. Results show that in paternity cases where a low number of incompatibilities are observed, the best strategy is to increase the number of autosomal STRs under analysis. Nevertheless, if these are not available, our study globally shows that in father-daughter duos, a set of 12 X-STRs is more advantageous than 38 highly diverse autosomal biallelic markers. Additionally, the usefulness of X-STRs was also evaluated in cases where only a close relative of the alleged parent (father or mother) is available for testing. For those situations where these markers have the power to exclude, strong LR values are obtained. In the remaining cases, LRs are usually weak and sometimes the results are more likely under the wrong kinship hypothesis.
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32
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Westen AA, Haned H, Grol LJW, Harteveld J, van der Gaag KJ, de Knijff P, Sijen T. Combining results of forensic STR kits: HDplex validation including allelic association and linkage testing with NGM and Identifiler loci. Int J Legal Med 2012; 126:781-9. [DOI: 10.1007/s00414-012-0724-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/12/2012] [Indexed: 10/28/2022]
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33
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Tamura T, Osawa M, Kimura R, Inaoka Y, Tanaka S, Satoh F, Sato I. Evaluation of the allele-sharing approach, known as the IBS method, in kinship analysis. J Forensic Leg Med 2012; 20:112-6. [PMID: 23357397 DOI: 10.1016/j.jflm.2012.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 02/10/2011] [Accepted: 05/30/2012] [Indexed: 11/25/2022]
Abstract
To infer relatedness from genetic data based on short tandem repeats, the exact method, in which shared allele frequencies are applied to relevant equations, has been conventionally used. An alternative approach is the IBS method that is based on the number of shared alleles between individuals. In the present study, the performance of the IBS method in pairwise kinship analysis was compared with the exact method using simulated data of 10,000 genotype pairs for 15 loci in the ABI Identifiler system. The likelihood ratio in allele-sharing of zero, one and two was calculated from joint probabilities based on allele frequencies of the Japanese population. Whereas the IBS method generally produced lower values of combined indices, smaller deviations of the distributions were evident. The threshold for identification of full siblings relative to non-relatives was comparable with that of the exact method, indicating that both inference powers were almost identical. The likelihood ratio in the IBS method depends on the heterozygosity at a locus, and heterozygosities of the 15 loci were consistent across various population groups, particularly in East Asians. The convenience of fixed LR values in the IBS method is beneficial for cases with uncertain allele frequencies and rare alleles.
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Affiliation(s)
- Tomonori Tamura
- Scientific Crime Laboratory, Kanagawa Prefectural Police, Yamashitacho 155, Naka-ku, Yokohama 231-0023, Japan
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34
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Børsting C, Mikkelsen M, Morling N. Kinship Analysis with Diallelic SNPs - Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory. ACTA ACUST UNITED AC 2012; 39:195-201. [PMID: 22851935 DOI: 10.1159/000338957] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 01/27/2012] [Indexed: 11/19/2022]
Abstract
BACKGROUND: The mutation rate of single nucleotide polymorphisms (SNPs) is estimated to be 100,000 times lower than that of short tandem repeats (STRs), which makes SNPs very suitable for relationship testing. The SNPforID multiplex assay was the first SNP typing assay that was a real alternative to the commonly used STR kits in kinship and crime case work and the first SNP assay to be validated in a forensic laboratory accredited according to the ISO17025 standard. METHODS: A total of 54 crime case samples were typed with the SNPforID multiplex assay. 30 samples from relationship cases were sequenced in selected SNP loci. RESULTS: It was demonstrated that mixtures were easily detected with the SNPforID assay by analyzing the signal strengths of the detected alleles. Unusual imbalances in signal strengths that were observed in a few individuals could be explained by unexpected SNPs in one of the primer binding sites. A complicated relationship case with four closely related individuals is presented. CONCLUSION: Mixtures can be detected with bi-allelic SNPs. The SNPforID assay is a very useful supplement to the STR kits in relationship testing.
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Affiliation(s)
- Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Denmark
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35
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Phillips C, García-Magariños M, Salas A, Carracedo A, Lareu MV. SNPs as Supplements in Simple Kinship Analysis or as Core Markers in Distant Pairwise Relationship Tests: When Do SNPs Add Value or Replace Well-Established and Powerful STR Tests? Transfus Med Hemother 2012; 39:202-210. [PMID: 22851936 DOI: 10.1159/000338857] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/03/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND: Genetic tests for kinship testing routinely reach likelihoods that provide virtual proof of the claimed relationship by typing microsatellites-commonly consisting of 12-15 standard forensic short tandem repeats (STRs). Single nucleotide polymorphisms (SNPs) have also been applied to kinship testing but these binary markers are required in greater numbers than multiple-allele STRs. However SNPs offer certain advantageous characteristics not found in STRs, including, much higher mutational stability, good performance typing highly degraded DNA, and the ability to be readily up-scaled to very high marker numbers reaching over a million loci. This article outlines kinship testing applications where SNPs markedly improve the genetic data obtained. In particular we explore the minimum number of SNPs that will be required to confirm pairwise relationship claims in deficient pedigrees that typify missing persons' identification or war grave investigations where commonly few surviving relatives are available for comparison and the DNA is highly degraded. METHODS: We describe the application of SNPs alongside STRs when incomplete profiles or allelic instability in STRs create ambiguous results, we review the use of high density SNP arrays when the relationship claim is very distant, and we outline simulations of kinship analyses with STRs supplemented with SNPs in order to estimate the practical limit of pairwise relationships that can be differentiated from random unrelated pairs from the same population. RESULTS: The minimum number of SNPs for robust statistical inference of parent-offspring relationships through to those of second cousins (S-3-3) is estimated for both simple, single multiplex SNP sets and for subsets of million-SNP arrays. CONCLUSIONS: There is considerable scope for resolving ambiguous STR results and for improving the statistical power of kinship analysis by adding small-scale SNP sets but where the pedigree is deficient the pairwise relationships must be relatively close. For more distant relationships it is possible to reduce chip-based SNP arrays from the million+ markers down to ∼7,000. However, such numbers indicate that current genotyping approaches will not be able to deliver sufficient data to resolve distant pairwise relationships from the limited DNA typical of the most challenging identification cases.
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Affiliation(s)
- Christopher Phillips
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Galicia, Spain
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36
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DNA microarray as a tool in establishing genetic relatedness—Current status and future prospects. Forensic Sci Int Genet 2012; 6:322-9. [PMID: 21813350 DOI: 10.1016/j.fsigen.2011.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 06/12/2011] [Accepted: 07/05/2011] [Indexed: 11/21/2022]
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37
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O’Connor KL, Hill CR, Vallone PM, Butler JM. Corrigendum to “Linkage disequilibrium analysis of D12S391 and vWA in U.S. population and paternity samples” [Forensic Sci. Int.: Genet. (in press), doi:10.1016/j.fsigen.2010.09.003]. Forensic Sci Int Genet 2011. [DOI: 10.1016/j.fsigen.2011.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Lu D, Liu Q, Wu W, Zhao H. Mutation analysis of 24 short tandem repeats in Chinese Han population. Int J Legal Med 2011; 126:331-5. [DOI: 10.1007/s00414-011-0630-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 10/04/2011] [Indexed: 10/16/2022]
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39
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Phillips C, Ballard D, Gill P, Court DS, Carracedo A, Lareu MV. The recombination landscape around forensic STRs: Accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP data. Forensic Sci Int Genet 2011; 6:354-65. [PMID: 21871851 DOI: 10.1016/j.fsigen.2011.07.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 07/09/2011] [Accepted: 07/24/2011] [Indexed: 11/30/2022]
Abstract
Family studies can be used to measure the genetic distance between same-chromosome (syntenic) STRs in order to detect physical linkage or linkage disequilibrium. However, family studies are expensive and time consuming, in many cases uninformative, and lack a reliable means to infer the phase of the diplotypes obtained. HapMap provides a more comprehensive and fine-scale estimation of recombination rates using high density multi-point SNP data (average inter-SNP distance: 900 nucleotides). Data at this fine scale detects sub-kilobase genetic distances across the whole recombining human genome. We have used the most recent HapMap SNP data release 22 to measure and compare genetic distances, and by inference fine-scale recombination rates, between 29 syntenic STR pairs identified from 39 validated STRs currently available for forensic use. The 39 STRs comprise 23 core loci: SE33, Penta D & E, 13 CODIS and 7 non-CODIS European Standard Set STRs, plus supplementary STRs in the recently released Promega CS-7™ and Qiagen Investigator HDplex™ kits. Also included were D9S1120, a marker we developed for forensic use unique to chromosome 9, and the novel D6S1043 component STR of SinoFiler™ (Applied Biosystems). The data collated provides reliable estimates of recombination rates between each STR pair, that can then be placed into haplotype frequency calculators for short pedigrees with multiple meiotic inputs and which just requires the addition of allele frequencies. This allows all current STR sets or their combinations to be used in supplemented paternity analyses without the need for further adjustment for physical linkage. The detailed analysis of recombination rates made for autosomal forensic STRs was extended to the more than 50 X chromosome STRs established or in development for complex kinship analyses.
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Affiliation(s)
- C Phillips
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain.
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40
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Børsting C, Morling N. Reinvestigations of six unusual paternity cases by typing of autosomal single-nucleotide polymorphisms. Transfusion 2011; 52:425-30. [PMID: 21790631 DOI: 10.1111/j.1537-2995.2011.03260.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND In some relationship cases, the initial investigations of autosomal short tandem repeats (STRs) lead to an ambiguous conclusion and supplementary investigations become necessary. STUDY DESIGN AND METHODS Six unusual paternity cases were previously investigated by other researchers and published as case work examples in forensic journals. Here, the cases were reinvestigated by typing the samples for 49 autosomal single-nucleotide polymorphisms (SNPs) using the SNPforID multiplex assay. RESULTS Three cases were solved by the SNP investigation without the need for any additional testing. In two cases, the SNP results supported the conclusions based on STRs. In the last case, the SNP results spoke in favor of paternity, and the combined paternity index based on autosomal STRs and SNPs was 12.3 billion. Nevertheless, the alleged father was excluded by X-chromosome typing. CONCLUSION The case work examples underline the importance of performing supplementary investigations, and they advocate for the implementation of several panels that may be used in the highly unusual cases. Panels with SNPs or other markers with low mutation probabilities are preferable as supplementary markers, because the risk of detecting (additional) mutations is very low.
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Affiliation(s)
- Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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41
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Pinto N, Silva PV, Amorim A. A general method to assess the utility of the X-chromosomal markers in kinship testing. Forensic Sci Int Genet 2011; 6:198-207. [PMID: 21592877 DOI: 10.1016/j.fsigen.2011.04.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 03/25/2011] [Accepted: 04/01/2011] [Indexed: 11/29/2022]
Abstract
In studies involving pedigree reconstruction and kinship estimation, it is acknowledged that some pedigrees have the same algebraic expressions for the joint genotypic probabilities and are, therefore, indistinguishable when considering only genetic information, no matter what the mode of transmission considered. Indeed, although standard forensic practice considers solely unlinked autosomal markers, the existence of pedigrees with the referred theoretical property (that are then said to belong to the same kinship class) is possible when considering any kind of genetic transmission. The research on genetic relatedness has always been linked to the root concept of identity-by-descent (IBD). However, although the basic theoretical core for autosomal transmission has been long formalised, a general method allowing the decision if two pedigrees linking two non-inbred individuals are distinguishable using unlinked autosomal markers along with the respective IBD partitions (and consequently the algebraic expressions for the joint genotypic probabilities) was only recently published. In this work X-chromosomal transmission will be at stake, considering that the analytical framework for X-chromosomal markers has been recently established and the importance of X-chromosome markers for these questions has been steadily growing, particularly in forensics, as a tool both to complement the information given by autosomes in complex kinship testing cases and to differentiate pedigrees belonging to the same autosomal kinship class. Therefore, here it will be presented a formal and mathematically well supported framework where a general counting rule is given, allowing a secure and expeditious decision on the usefulness of typing (unlinked) X-chromosomal markers on pairwise kinship testing involving two non-inbred individuals. Moreover the counting rule now presented allows the derivation of algebraic expressions for the joint genotypic probabilities associated with any pedigree.
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Affiliation(s)
- Nádia Pinto
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Portugal.
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