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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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Haddadan SG, Babaei E, Setareh M. Population-genetic and comparative interpopulation studies of the 15 autosomal STR markers in the population living in the Northwest of Iran. Ann Hum Genet 2024. [PMID: 38895879 DOI: 10.1111/ahg.12564] [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: 08/05/2023] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 06/21/2024]
Abstract
INTRODUCTION Iran, a country in the Middle East, has several ethnic and ethno-religious groups and needs its own ethnic-specific databases for the forensic statistical parameters and allele frequency of STR markers. METHODS We have investigated 600 unrelated Turk individuals from four northwestern provinces of Iran using the Identifiler™ system (TPOX, FGA, vWA, TH01, CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, and D21S11). Furthermore, STR allelic frequencies were compared to previously population-based data. RESULTS AND CONCLUSION After Bonferroni correction, deviation from Hardy-Weinberg equilibrium (HWE) was observed in the FGA, TPOX, VWA, and D19S433 loci (P value < 0.05). The combined power of discrimination (CPD) and exclusion (CPE) values for all 15 STR loci were 0.9999999999999999999984 and 0.9999999, respectively. In comparison with Azerbaijani and Turkish populations, there were no significant differences on all STR markers. However, in the Chinese Han population, differences at 13 STR loci were detected. Additionally, comparisons of Fischer genetic distance indices (FST) P-values did not reveal any statistically significant difference between Northwestern Iran, Azerbaijan and Iran (Fars) populations. PCA and PCoA analyses showed that our population was grouped with different populations in different quarters, showing a positive and negative correlation, respectively. In the NJ and UPGMA phylogenetic trees, Iranian populations were grouped together. These results demonstrated that the given set of STR markers can be confidently used for all identification tests in Northwestern Iran.
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Affiliation(s)
| | - Esmaeil Babaei
- Department of Biology, School of Natural Science, University of Tabriz, Tabriz, Iran
| | - Mehrdad Setareh
- Legal Medicine Research Center, Legal Medicine Organization of East Azerbaijan, Tabriz, Iran
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3
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Bodner M, Ballard D, Borsuk LA, King JL, Parson W, Phillips C, Gettings KB. Harmonizing the forensic nomenclature for STR loci D6S474 and DYS612. Forensic Sci Int Genet 2024; 70:103012. [PMID: 38295652 DOI: 10.1016/j.fsigen.2024.103012] [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: 08/10/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 04/01/2024]
Abstract
The autosomal STR D6S474 and the Y-chromosomal STR DYS612 have been reported in multiple ways in the forensic literature, with differences in both the bracketed repeat structures and counting of numerical length-based capillary electrophoresis (CE) alleles. These issues often come to light when STR loci are introduced in commercial assays and results compared with historical publications of allele frequency data, or multiple assays are characterized with reference materials. We review the forensic literature and other relevant information, and provide suggestions for the future treatment of each STR.
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Affiliation(s)
- Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - David Ballard
- King's Forensics, King's College London, Franklin-Wilkins Building, London, UK
| | - Lisa A Borsuk
- National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, MD, USA
| | - Jonathan L King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Katherine Butler Gettings
- National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, MD, USA.
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4
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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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Alsafiah HM, Goodwin WH. Population genetic data for 17 non-CODIS STR loci for the Saudi Arabian population using the SureID®23comp Human Identification Kit. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.029] [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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Dash HR, Vajpayee K, Srivastava A, Das S. Prevalence and characterisation of size and sequence-based microvariant alleles at nine autosomal STR markers in the Central Indian population. Ann Hum Biol 2021; 48:614-620. [PMID: 34818952 DOI: 10.1080/03014460.2021.2010804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND Though microvariant alleles are widely reported in global populations, they are not well characterised to date. AIM To study the prevalence and characterisation of size and sequence-based microvariant alleles. SUBJECTS AND METHODS Next Generation Sequencing (NGS) was used to sequence microvariant alleles at nine autosomal STR markers in 138 samples. RESULTS After sequencing 31 STR markers using Precision ID GlobalFilerTM NGS STR panel v2, only nine markers, i.e. D12S391, D19S433, D1S1656, D21S11, D2S441, D7S820, FGA, Penta D, and TH01 showed the prevalence of microvariant alleles. Occurrence of microvariant alleles was positively correlated with Total Possible Alleles (p < 0.005), Power of Discrimination (p < 0.01), Polymorphic Information Content (p < 0.01), and Power of Exclusion (p < 0.05) and negatively correlated with the Matching Probability (p < 0.01). The average allele frequency of the microvariant alleles was found to be significantly less than the allele frequency value of the complete alleles (p = 0.88). Further, sequencing of these microvariant alleles reveals the deletion of nucleotides from the start, end, or middle of the repeat unit is responsible for the generation of a microvariant allele. CONCLUSIONS Prevalence of microvariant alleles is rare in nature and is limited to 9 STR loci out of 31 STR loci tested in the central Indian population. The occurrence of microvariant alleles in a locus increases its forensic and paternity application.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| | - Kamayani Vajpayee
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India.,School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Ankit Srivastava
- Institute of Forensic Science and Criminology, Bundelkhand University, Jhansi, UP, India
| | - Surajit Das
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
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Cui W, Jin X, Fang Y, Lan Q, Lan J, Chen M, Mei S, Xie T, Zhu B. An interpretation of the genetic polymorphism and population genetic background of Ankang Han population via a novel InDel panel. Forensic Sci Res 2021; 7:694-701. [PMID: 36817236 PMCID: PMC9930792 DOI: 10.1080/20961790.2021.1997368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
In this research, genotyping data of 43 InDel loci in 311 Han individuals in Ankang City, Shaanxi Province, China were detected using a self-developed five-dye multiplex amplification panel. The allelic frequencies and forensic parameters of all InDel loci were calculated. The combined power of discrimination and probability of exclusion values were 0.999 999 999 999 999 998 827 39 and 0.999 887 424, respectively, which demonstrated that this 43-InDel panel was powerful for individual identifications in Ankang Han population. Moreover, genetic distances, pairwise FST values, principal component analyses, phylogenetic trees and STRUCTURE analyses were performed to investigate the genetic affinities between Ankang Han and reference groups. Population genetic investigations indicated that Ankang Han population had a close genetic relationship with Southern Han population compared with other reference groups.
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Affiliation(s)
- Wei Cui
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoye Jin
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Yating Fang
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qiong Lan
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Jiangwei Lan
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Man Chen
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Shuyan Mei
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Tong Xie
- Multi-Omics Innovative Research Center of Forensic Identification; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China,CONTACT Tong Xie ;
| | - Bofeng Zhu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China,Bofeng Zhu
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Liu Y, Zhang H, He G, Ren Z, Zhang H, Wang Q, Ji J, Yang M, Guo J, Yang X, Sun J, Ba J, Peng D, Hu R, Wei LH, Wang CC, Huang J. Forensic Features and Population Genetic Structure of Dong, Yi, Han, and Chuanqing Human Populations in Southwest China Inferred From Insertion/Deletion Markers. Front Genet 2020; 11:360. [PMID: 32425974 PMCID: PMC7205039 DOI: 10.3389/fgene.2020.00360] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Guizhou province in southwest China has abundant genetic and cultural diversities, but the forensic features and genetic structure of Guizhou populations remain poorly understood due to the sparse sampling of present-day populations. Here, we present 30 insertion/deletion polymorphisms (InDels) data of 591 human individuals collected from four populations, Dong, Yi, Han, and Chuanqing residing in Guizhou. We calculated the forensic parameters of 30 InDel loci and found that this panel meets the efficiency of forensic personal identification based on the high combined power of discrimination, but it could only be used as a complementary tool in the parentage testing because of the lower combined probability of exclusion values. The studied populations are genetically closer related to geographically adjacent or linguistically related populations in southern China, such as the Tai-Kadai and Hmong-Mien speaking groups. The unrecognized ethnic Chuanqing people show an additional genetic affinity with Han Chinese, highlighting the role of possible military immigrations in their origin.
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Affiliation(s)
- Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Han Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Guanglin He
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China.,Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Jinxing Ba
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Rong Hu
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, China
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Population data of 21 autosomal STR loci in Malaysian populations for human identification. Int J Legal Med 2020; 134:1675-1678. [PMID: 32222814 DOI: 10.1007/s00414-020-02279-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
Abstract
The use of 21 autosomal STR loci for human identification has been gaining popularity throughout the world. It has been indicated that the forensic statistical parameters for supporting the use of 21 STR loci varied among different populations. Hitherto, such data for the diverse Malaysian populations remain unreported, rendering doubts in the court of law about its real ability for human identification in Malaysian population. Using the GlobalFiler™ Express PCR Amplification Kit, complete DNA profiles of 21 STR loci from buccal swabs of convicted Malaysian criminal (n = 570; 190 each for Malays, Chinese, and Indians) (by the year 2016-2017) were analyzed for their allele frequencies, exact test of Hardy-Weinberg equilibrium, observed and expected heterozygosity, power of discrimination, power of exclusion, match probability, and polymorphism information content. Most of the loci were found to be in the Hardy-Weinberg equilibrium after the Bonferroni correction. Being the most informative locus, SE33 demonstrated the highest power of discrimination and power of exclusion, indicating its usefulness to discriminate individuals. In contrast, TPOX had the lowest power of discrimination and power of exclusion, as well as being the less informative genetic locus for all Malaysian population studied here. The probabilities that two individuals would share the same DNA profiles among the Malaysian Malays, Chinese, and Indians, as well as in general Malaysian population, were 1.3713 × 10-25, 2.8822 × 10-25, 7.5668 × 10-26, and 1.0385 × 10-26, respectively. The results obtained here were found comparable with similar studies reported in other populations. Hence, its robustness for forensic human identification among the Malaysian populations is, therefore, statistically supported.
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Alsafiah HM, Aljanabi AA, Hadi S, Alturayeif SS, Goodwin W. An evaluation of the SureID 23comp Human Identification Kit for kinship testing. Sci Rep 2019; 9:16859. [PMID: 31727926 PMCID: PMC6856129 DOI: 10.1038/s41598-019-52838-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 10/21/2019] [Indexed: 01/16/2023] Open
Abstract
Short tandem repeat (STR) profiling has been routinely used in kinship testing since the introduction of commercial kits in the mid-1990s. While 15 to 23 STR loci normally give definitive results in simple kinship testing, additional loci are sometimes required to resolve complex cases. The SureID 23comp Human Identification Kit, recently released by Health Gene Technologies (China), multiplexes amelogenin and 22 autosomal STRs, 17 of which are non-CODIS STRs. This enables the profiling of 38–40 loci when used in conjunction with widely used commercial kits. In this study, the kit was evaluated for kinship applications as a supplementary STR kit following the minimum criteria for validation recommended by the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM) using 500 samples. Performance was comparable with other commercial kits demonstrating: repeatability and reproducibility; precision (maximum s.d. 0.1048 nt); accuracy, all alleles were within ±0.41 nt compared to the actual sizes; heterozygous peak balances at all loci >68%; stutter ratios ranged from 3.8% to 16.15%; full profiles were generated with 125 pg DNA (95.12% of alleles at 62 pg),; and we found 100% concordance over 5 common STRs with the GlobalFiler kit.
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Affiliation(s)
- Hussain M Alsafiah
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom. .,Forensic Genetics Laboratory, General Administration of Criminal Evidences, Public Security, Ministry of Interior, Riyadh, Saudi Arabia.
| | - Ali A Aljanabi
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom
| | - Sibte Hadi
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom
| | - Saleh S Alturayeif
- Forensic Genetics Laboratory, General Administration of Criminal Evidences, Public Security, Ministry of Interior, Riyadh, Saudi Arabia
| | - William Goodwin
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston, United Kingdom.
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