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Zhang Y, Dong X, Zhang J, Zhao M, Wang J, Chu J, Yang Z, Ma S, Lin K, Sun H, Luo Z. FLT4 gene polymorphisms influence isolated ventricular septal defect predisposition in a Southwest China population. BMC Med Genomics 2024; 17:197. [PMID: 39107825 PMCID: PMC11302092 DOI: 10.1186/s12920-024-01971-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Ventricular septal defect (VSD) is the most common congenital heart disease. Although a small number of genes associated with VSD have been found, the genetic factors of VSD remain unclear. In this study, we evaluated the association of 10 candidate single nucleotide polymorphisms (SNPs) with isolated VSD in a population from Southwest China. METHODS Based on the results of 34 congenital heart disease whole-exome sequencing and 1000 Genomes databases, 10 candidate SNPs were selected. A total of 618 samples were collected from the population of Southwest China, including 285 VSD samples and 333 normal samples. Ten SNPs in the case group and the control group were identified by SNaPshot genotyping. The chi-square (χ2) test was used to evaluate the relationship between VSD and each candidate SNP. The SNPs that had significant P value in the initial stage were further analysed using linkage disequilibrium, and haplotypes were assessed in 34 congenital heart disease whole-exome sequencing samples using Haploview software. The bins of SNPs that were in very strong linkage disequilibrium were further used to predict haplotypes by Arlequin software. ViennaRNA v2.5.1 predicted the haplotype mRNA secondary structure. We evaluated the correlation between mRNA secondary structure changes and ventricular septal defects. RESULTS The χ2 results showed that the allele frequency of FLT4 rs383985 (P = 0.040) was different between the control group and the case group (P < 0.05). FLT4 rs3736061 (r2 = 1), rs3736062 (r2 = 0.84), rs3736063 (r2 = 0.84) and FLT4 rs383985 were in high linkage disequilibrium (r2 > 0.8). Among them, rs3736061 and rs3736062 SNPs in the FLT4 gene led to synonymous variations of amino acids, but predicting the secondary structure of mRNA might change the secondary structure of mRNA and reduce the free energy. CONCLUSIONS These findings suggest a possible molecular pathogenesis associated with isolated VSD, which warrants investigation in future studies.
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Affiliation(s)
- Yunhan Zhang
- The Department of Ultrasound Imaging, Affiliated Cardiovascular Hospital of Kunming Medical University, Kunming, Yunnan, China
- The Department of Ultrasound Imaging, Fuwai Yunnan Cardiovascular Hospital, Chinese Academy of Medical Sciences, 528 Shahe Road, Kunming, Yunnan, 650032, China
| | - Xiaoli Dong
- The Department of Ultrasound Imaging, Fuwai Yunnan Cardiovascular Hospital, Chinese Academy of Medical Sciences, 528 Shahe Road, Kunming, Yunnan, 650032, China
| | - Jun Zhang
- The Department of Ultrasound Imaging, Fuwai Yunnan Cardiovascular Hospital, Chinese Academy of Medical Sciences, 528 Shahe Road, Kunming, Yunnan, 650032, China
| | - Miao Zhao
- The Department of Ultrasound Imaging, Fuwai Yunnan Cardiovascular Hospital, Chinese Academy of Medical Sciences, 528 Shahe Road, Kunming, Yunnan, 650032, China
| | - Jiang Wang
- The Department of Ultrasound Imaging, Fuwai Yunnan Cardiovascular Hospital, Chinese Academy of Medical Sciences, 528 Shahe Road, Kunming, Yunnan, 650032, China
| | - Jiayou Chu
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Zhaoqing Yang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Shaohui Ma
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Keqin Lin
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, Yunnan, 650118, China
| | - Hao Sun
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, Yunnan, 650118, China.
| | - Zhiling Luo
- The Department of Ultrasound Imaging, Affiliated Cardiovascular Hospital of Kunming Medical University, Kunming, Yunnan, China.
- The Department of Ultrasound Imaging, Fuwai Yunnan Cardiovascular Hospital, Chinese Academy of Medical Sciences, 528 Shahe Road, Kunming, Yunnan, 650032, 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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Pedroza Matute S, Turvey K, Iyavoo S. Advancing human genotyping: The Infinium HTS iSelect Custom microarray panel (Rita) development study. Forensic Sci Int Genet 2024; 71:103049. [PMID: 38653142 DOI: 10.1016/j.fsigen.2024.103049] [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: 12/15/2023] [Revised: 04/04/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Single Nucleotide Polymorphisms (SNPs), as the most prevalent type of variation in the human genome, play a pivotal role in influencing human traits. They are extensively utilized in diverse fields such as population genetics, forensic science, and genetic medicine. This study focuses on the 'Rita' BeadChip, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel facilitates the analysis of over 4000 markers efficiently and cost-effectively. After careful clustering performed on a set of 1000 samples, an evaluation of the Rita panel was undertaken, assessing its sensitivity, repeatability, reproducibility, precision, accuracy, and resistance to contamination. The panel's performance was evaluated in various scenarios, including sex estimation and parental relationship assessment, using GenomeStudio data analysis software. Findings show that over 95 % of the custom BeadChip assay markers were successful, with better performance of transitions over other mutations, and a considerably lower success rate for Y chromosome loci. An exceptional call rate exceeding 99 % was demonstrated for control samples, even with DNA input as low as 0.781 ng. Call rates above 80 % were still obtained with DNA quantities under 0.1 ng, indicating high sensitivity and suitability for forensic applications where DNA quantity is often limited. Repeatability, reproducibility, and precision studies revealed consistency of the panel's performance across different batches and operators, with no significant deviations in call rates or genotyping results. Accuracy assessments, involving comparison with multiple available genetic databases, including the 1000 Genome Project and HapMap, denoted over 99 % concordance, establishing the Rita panel's reliability in genotyping. The contamination study revealed insights into background noise and allowed the definition of thresholds for sample quality evaluation. Multiple metrics for differentiating between negative controls and true samples were highlighted, increasing the reliability of the obtained results. The sex estimation tool in GenomeStudio proved highly effective, correctly assigning sex in all samples with autosomal loci call rates above 97 %. The parental relationship assessment of family trios highlighted the utility of GenomeStudio in identifying genotyping errors or potential Mendelian inconsistencies, promoting the application of arrays such as Rita in kinship testing. Overall, this evaluation confirms the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications. With its custom content and adaptable design, it not only meets current genotyping demands but also opens avenues for further research and application expansion in the field of genetic analysis.
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Affiliation(s)
| | - Kiera Turvey
- IDna Genetics Limited, Scottow Enterprise Park, Norwich, Norfolk NR10 5FB, United Kingdom
| | - Sasitaran Iyavoo
- IDna Genetics Limited, Scottow Enterprise Park, Norwich, Norfolk NR10 5FB, United Kingdom; School of Chemistry, College of Health and Science, University of Lincoln, Lincoln, Lincolnshire LN6 7TS, United Kingdom.
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Jin Y, Zhao M, Guo Q, Zhao W, Lei M, Zhang Y, Zhang Y, Shen Y, Lin K, Yang Z, Chu J, Sun H, Luo Z. Association study of FLT4 and HYDIN single nucleotide polymorphisms with atrial septal defect susceptibility in the Han Chinese population of Southwest China. Ital J Pediatr 2024; 50:62. [PMID: 38581027 PMCID: PMC10998412 DOI: 10.1186/s13052-024-01630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Atrial septal defect (ASD) is a common form of congenital heart disease. Although several genes related to ASD have been found, the genetic factors of ASD remain unclear. This study aimed to evaluate the correlation between 10 candidate single nucleotide polymorphisms (SNPs) and sporadic atrial septal defects. METHODS Based on the results of 34 individual whole exome sequences, 10 candidate SNPs were selected. In total, 489 ASD samples and 420 normal samples were collected. The 10 SNPs in the case group and the control group were identified through Snapshot genotyping technology. The χ2-test and unconditional regression model were used to evaluate the relationship between ASD and each candidate SNP. Haploview software was used to perform linkage disequilibrium and haplotype analysis. RESULTS The χ2 results showed that the FLT4 rs383985 (P = 0.003, OR = 1.115-1.773), HYDIN rs7198975 (P = 0.04621, OR = 1.003-1.461), and HYDIN rs1774266 (P = 0.04621, OR = 1.003-1.461) alleles were significantly different between the control group and the case group (P < 0.05). Only the association with the FLT4 polymorphism was statistically significant after adjustment for multiple comparisons. CONCLUSION These findings suggest that a possible molecular pathogenesis associated with sporadic ASD is worth exploring in future studies.
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Affiliation(s)
- Ye Jin
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Miao Zhao
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Qiuzhe Guo
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Wanyu Zhao
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Min Lei
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Yifei Zhang
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Yunhan Zhang
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Yan Shen
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China
| | - Keqin Lin
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiao ling Road, 650118, Kunming, Yunnan, China
| | - Zhaoqing Yang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiao ling Road, 650118, Kunming, Yunnan, China
| | - Jiayou Chu
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiao ling Road, 650118, Kunming, Yunnan, China
| | - Hao Sun
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiao ling Road, 650118, Kunming, Yunnan, China.
| | - Zhiling Luo
- Yunnan Fuwai Cardiovascular Hospital, 528 Shahe Road, 650032, Kunming, Yunnan, China.
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Čanović V, Slović Ž, Todorović D, Todorović M, Andrić I, Radojević D, Ilić M, Vitošević K. The use of vitreous humour as a potential source of DNA for postmortem identification in forensic science. Forensic Sci Med Pathol 2024:10.1007/s12024-023-00760-w. [PMID: 38170325 DOI: 10.1007/s12024-023-00760-w] [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] [Accepted: 12/06/2023] [Indexed: 01/05/2024]
Abstract
Vitreous humour (VH) is routinely collected for toxicological analyses. However, only a few studies have examined its possible use in genotyping. Because of its isolation from the rest of the body, later onset of postmortem changes, and availability, VH could be a potential source of DNA for postmortem identification and other molecular analyses in forensic genetics. During forensic autopsies, samples of different VH volumes (5 ml, 4 ml, 3 ml, 2 ml, 1 ml, and 0.5 ml) were taken from 66 cadavers 24-48 h after death. DNA was also isolated from the samples immediately after collection and after a specific time of storage (1, 2, and 6 months). DNA was isolated using phenol‒chloroform‒isoamyl alcohol (PCI), and the yield and purity of the obtained DNA were determined spectrophotometrically using a FastGene NanoView Photometer. The integrity of the isolated DNA molecule was determined by PCR amplification of the hTERT (113 bp) gene. The results showed that VH could be a reliable source of genetic material for forensic analysis, and the method used for DNA extraction was effective. The yield of the isolated DNA ranged from 6.20 to 609.5 ng/µl, and the purity of the samples was 1.24-2.34. The isolated DNA concentration and integrity depend on the sample volume, but the DNA purity does not. It is also shown that DNA can be extracted from VH samples that have been stored for up to 6 months at - 20 °C. Therefore, using VH can be a valuable material for DNA identification.
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Affiliation(s)
- Vanja Čanović
- Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Živana Slović
- Department of Forensic Medicine, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia.
| | - Danijela Todorović
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Miloš Todorović
- Department of Forensic Medicine, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
| | - Ivana Andrić
- Department of Forensic Medicine, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Dušan Radojević
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Milena Ilić
- Department of Pathology, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Katarina Vitošević
- Department of Forensic Medicine, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
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Tao R, Li M, Chai S, Xia R, Qu Y, Yuan C, Yang G, Dong X, Bian Y, Zhang S, Li C. Developmental validation of a 381 Y-chromosome SNP panel for haplogroup analysis in the Chinese populations. Forensic Sci Int Genet 2023; 62:102803. [PMID: 36368220 DOI: 10.1016/j.fsigen.2022.102803] [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: 01/19/2022] [Revised: 09/19/2022] [Accepted: 10/26/2022] [Indexed: 01/15/2023]
Abstract
Y-chromosome single nucleotide polymorphism (Y-SNP) shows great variation in geographical distribution and population heterogeneity and can be used to map population genetics around the world. Massive parallel sequencing (MPS) methodology enables high-resolution Y-SNP haplogrouping for a certain male and is widely used in forensic genetics and evolutionary studies. In this present study, we used MPS to develop a customized 381 Y-SNP panel (SifaMPS 381 Y-SNP panel) to investigate the basic structure and subbranches of the haplogroup tree of the Chinese populations. The SifaMPS 381 Y-SNP panel covers all the Y-SNPs from our previously designed 183 Y-SNP panel and additional SNPs under the predominant haplogroups in the Chinese populations based on certain criteria. We also evaluated the sequencing matrix, concordance, sensitivity, repeatability of this panel and the ability to analyze mixed and case-type samples based on the Illumina MiSeq System. The results demonstrated that the novel MPS Y-SNP panel possessed good sequencing performance and generated accurate Y-SNP genotyping results. Although the recommended DNA input was greater than 1.25 ng, we observed that a lower DNA amount could still be used to analyze haplogroups correctly. In addition, this panel could handle mixed samples and common case-type samples and had higher resolution among Chinese Han males than previously reported. In conclusion, the SifaMPS 381 Y-SNP panel showed an overall good performance and offers a better choice for Y-SNP haplogrouping of the Chinese population, thereby facilitating paternal lineage classification, familial searching and other forensic applications.
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Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
| | - Min Li
- School of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Siyu Chai
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China
| | - Chunyan Yuan
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China
| | - Guangyuan Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China
| | - Xinyu Dong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China.
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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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Dash HR, Arora M. CRISPR-CasB technology in forensic DNA analysis: challenges and solutions. Appl Microbiol Biotechnol 2022; 106:4367-4374. [PMID: 35704073 DOI: 10.1007/s00253-022-12016-8] [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: 04/10/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 01/23/2023]
Abstract
CRISPR-Cas technology has revolutionized the field of biotechnology with its precise therapeutic use from genetic as well as infectious diseases point of view. This technology is rapidly evolving to single tool enabling site-directed cut in the genome and highly specific activation or inhibition of gene expression or the exchange of single bases. Besides clinical applications, CRISPR-Cas technology has also shown promising use in the field of forensic DNA analysis. Enrichment of targeted genetic marker for identification followed by sequencing and non-PCR-dependent technique ensures the use of CRISPR-Cas technology in challenging forensic biological samples. The use of this advanced technology is also deemed helpful in mixed profile attribution, mostly in LCN contributors and the generation of a useful DNA profile in degraded samples. Besides its useful applications in forensic DNA analysis, CRISPR-Cas technology poses a huge threat from the generation of ghost DNA profiles by modification/alteration of target genetic markers. Forensic DNA analysts should carry out analysis of additional markers such as non-CODIS markers, Y-, X-chromosome markers, and mitochondrial DNA sequencing in a suspected ghost DNA profile case. KEY POINTS: • CRISPR-Cas9 technique is useful in analyzing LCN, mixed and degraded samples • Alteration of DNA using this technique can lead to generation of ghost DNA profiles • Alternative genetic markers and methylation pattern may detect a ghost DNA profile.
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Affiliation(s)
- Hirak Ranjan Dash
- School of Forensic Sciences, National Forensic Sciences University, Delhi Campus, Sector-3, Rohini, New Delhi, 110085, India.
| | - Mansi Arora
- School of Forensic Sciences, National Forensic Sciences University, Delhi Campus, Sector-3, Rohini, New Delhi, 110085, India
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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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Lee HJ, Shin KH, Jeong SJ, Kim IS. Comparison of single nucleotide polymorphisms and short tandem repeats as markers for differentiating between donors and recipients in solid organ transplantation. KOREAN JOURNAL OF TRANSPLANTATION 2021; 35:1-7. [PMID: 35769615 PMCID: PMC9235337 DOI: 10.4285/kjt.20.0035] [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: 08/14/2020] [Revised: 11/12/2020] [Accepted: 12/10/2020] [Indexed: 11/04/2022] Open
Abstract
Background Methods Results Conclusions
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Affiliation(s)
- Hyun-Ji Lee
- Department of Laboratory Medicine, and Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Kyoung-Hwa Shin
- Department of Laboratory Medicine, Pusan National University Hospital, Busan, Korea
| | - Su Jeong Jeong
- Department of Laboratory Medicine, and Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - In Suk Kim
- Department of Laboratory Medicine, and Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
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11
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Zhang J, Zhang J, Tao R, Jiang L, Chen L, Li X, Li C, Zhang S. A newly devised multiplex assay of novel polymorphic non-CODIS STRs as a valuable tool for forensic application. Forensic Sci Int Genet 2020; 48:102341. [PMID: 32599549 DOI: 10.1016/j.fsigen.2020.102341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/05/2020] [Accepted: 06/15/2020] [Indexed: 11/18/2022]
Abstract
DNA profiling that relies on sets of highly polymorphic autosomal STR markers is widely used in the forensic field for human identification and paternity testing. However, the number of markers that are included in the STR kits that are currently available is insufficient to conclusively prove or disprove a relationship between individuals, especially when complex family scenarios are suspected or indirect analyses are required. In these cases, it becomes necessary to increase the number of loci under analysis to reach an adequate likelihood ratio (LR). In this study, we discovered 18 new autosomal non-CODIS STR loci (D1S1616, D1S1608, D2S437, D3S2457, D4S2406, D4S3249, D5S2843, D5S2501, D6S1010, D8S1039, D12S1301, D14S586, D15S815, SHGC-145653, CHLC.GATA14D12, D1S1603, HUMUT7148, and CHLC.GATA84D07) by web scanning and experimental screening. On the basis of this discovery, we developed a novel multiplex typing system named the "SiFaSTR 21plex_NCII Typing System" comprising 1) the 18 non-CODIS autosomal STRs mentioned above, 2) a CODIS locus of D2S1338, and 3) Amelogenin and DYS391. A forensic developmental validation, including sensitivity, species specificity, concordance, reproducibility, sample suitability, testing stability, and mixture testing, was performed following SWGDAM. The results of the validation studies indicated that this system is accurate, reliable and suitable for human DNA profiling. The sensitivity study of the system demonstrated that a full profile was obtainable with DNA as low as 125 pg. Species specificity was proven by the lack of cross-reactivity with a series of common animal species. The stability study demonstrated that 1 ng of control DNA could be fully genotyped with concentrations of haematin ≤ 150 μM, indigotin ≤ 5000 ng/μl, urea ≤ 16000 ng/μl, nigrosine ≤ 100 ng/μl and humic acid ≤ 20 ng/μl. In the mixture test, all of the minor alleles could be called at mixed ratios of 1:1, 1:3 and 3:1. We also investigated the allelic frequencies and forensic parameters of the included markers in 259 Chinese Han individuals. The forensic efficiency parameters, including the total power of discrimination (TDP) and the combined exclusion power in duos (CPEduos) and in trios (CPEtrios) of the system were calculated to be greater than 0.9999999, 0.9997347 and 0.9999997, respectively. This result proved that the system is suitable for human identification and paternity testing. The 18 newly discovered non-CODIS STRs and the developed system will be a valuable supplementary tool for the forensic community and will help solve complex paternity cases, evolutionary studies and population investigations.
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Affiliation(s)
- Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China; Key Laboratory of Evidence Identification in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan, 250014, PR China
| | - Jingyi Zhang
- 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
| | - Ruiyang Tao
- 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
| | - Lei Jiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, 200063, PR China
| | - Liqin Chen
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010030, PR China
| | - Xuebo Li
- Key Laboratory of Evidence Identification in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan, 250014, 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.
| | - Suhua Zhang
- 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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12
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Delest A, Godfrin D, Chantrel Y, Ulus A, Vannier J, Faivre M, Hollard C, Laurent FX. Sequenced-based French population data from 169 unrelated individuals with Verogen's ForenSeq DNA signature prep kit. Forensic Sci Int Genet 2020; 47:102304. [PMID: 32417726 DOI: 10.1016/j.fsigen.2020.102304] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022]
Abstract
Massively Parallel Sequencing (MPS) applied to forensic genetics allows the simultaneous analysis of hundreds of genetic markers and the access to full amplicon sequences which help to increase available allele diversity. Meanwhile, sequence variation within the repeat regions represents the majority of the allele diversity, flanking regions adjacent to the repeat core provide an additional degree of variation. The forensic genetics community needs access to population data, from relevant parts of the world that contain this new sequence diversity in order to perform statistical calculations. In this study, we report sequence-based Short Tandem Repeat (STR) and identity Single Nucleotide Polymorphism (iSNPs) allele data for 169 French individuals across 58 STRs and 92 SNPs included in the Verogen ForenSeq DNA Signature Prep kit. 42 STRs out of 58 showed an increased number of alleles due to sequence variation in the repeat motif and/or the flanking regions. D9S1122 showed the largest overall gain with an increase of observed heterozygosities of almost 25 %. The combined match probability combining 27 autosomal STRs and 91 identity SNPs was 1.11E-69. Sequence-based allele frequencies included in this publication will help forensic laboratories to increase the power of discrimination for identification, kinship analysis and mixture interpretation.
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Affiliation(s)
- Anna Delest
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France.
| | - Dominique Godfrin
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Yann Chantrel
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Ayhan Ulus
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Julien Vannier
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Magalie Faivre
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - Clémence Hollard
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France
| | - François-Xavier Laurent
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, 31 Avenue, Franklin Roosevelt, 69134, Ecully Cedex, France.
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13
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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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14
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Cho S, Kim MY, Lee JH, Lee HY, Lee SD. Large-scale identification of human bone remains via SNP microarray analysis with reference SNP database. Forensic Sci Int Genet 2020; 47:102293. [PMID: 32276230 DOI: 10.1016/j.fsigen.2020.102293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are valuable markers complementary to conventional forensic short tandem repeat (STR) markers in genetic typing, with potential advantages in challenging forensic casework. With the advent of high-throughput technologies, such as microarrays and massively parallel sequencing, the use of SNP typing has now expanded to large-scale forensic applications. Herein, a forensic case is presented to demonstrate the usefulness of SNP typing in identifying large-scale human bone remains with reference database construction. A total of 402 bone remains were recovered from an island in the Jeju Province of Korea where a massive disaster occurred in 1948. The first phase of the identification process was accomplished via conventional DNA typing methods including autosomal and Y-chromosomal STR typing, and mitochondrial DNA sequencing, which resulted in the identification of 74 of 402 remains. The second phase of the identification involved the remaining 327 unidentified remains using SNP typing as a supplementary tool based on Affymetrix resequencing array. The SNP markers of 782 family members were also analyzed and a reference database was constructed for comparison. An additional 51 bone remains were identified in the second phase. SNP data obtained from the supplementary genotyping yielded additional genetic information as well as contributed to kinship testing to determine the second degrees of relationship. In addition SNPs are useful in discriminating ambiguous relationship when only STR data are available. A software program developed for SNP typing system enabled efficient kinship analysis for large-scale forensic identification. The results and the casework are described and discussed.
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Affiliation(s)
- Sohee Cho
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Moon-Young Kim
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Hwan Young Lee
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea; Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Soong Deok Lee
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea; Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea.
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15
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Hwa HL, Wu MY, Lee JCI, Yin HI, Hsu PM, Li SF, Hwu WL, Su CW. Analysis of nondegraded and degraded DNA mixtures of close relatives using massively parallel sequencing. Leg Med (Tokyo) 2020; 42:101631. [DOI: 10.1016/j.legalmed.2019.101631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/30/2019] [Accepted: 09/21/2019] [Indexed: 10/25/2022]
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16
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Qu N, Lin S, Gao Y, Liang H, Zhao H, Ou X. A microhap panel for kinship analysis through massively parallel sequencing technology. Electrophoresis 2019; 41:246-253. [PMID: 31816113 DOI: 10.1002/elps.201900337] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/07/2019] [Accepted: 12/03/2019] [Indexed: 12/31/2022]
Abstract
It is widely recognized that microhaps are powerful markers for different forensic purposes, mainly due to their advantages of both short tandem repeats and single nucleotide polymorphisms, including multiple alleles, low mutation rate, and absence of stutter peaks. In the present study, a panel of 60 microhap loci was developed and utilized in forensic kinship analysis as a preliminary study. Genotyping of microhap was performed by massively parallel sequencing and haplotypes were directly achieved from sequence reads of 73 samples from Chinese Han population. We observed that 49 out of 60 loci have effective number of alleles greater than 3.0 and 10 out of 60 have values above 4.0, with an average value of 3.5598. The heterozygosity values were in a range from 0.5840 to 0.8546 with an average of 0.7268 and the cumulative power of exclusion value of the 60 loci is equal to 1-4.78 × 10-18 . Moreover, we demonstrated the applicability of this method by different relationship inference problems, including identification of single parent-offspring, full-sibling, and second-degree relative. The results indicated that the assembled microhap panel provided more power for relationship inference, than commonly used short tandem repeats or single nucleotide polymorphism system.
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Affiliation(s)
- Ning Qu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, P. R. China
| | - Shaobin Lin
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, P. R. China
| | - Yu Gao
- Department of Obstetrics, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, P. R. China
| | - Hao Liang
- 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.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, P. R. China
| | - Xueling Ou
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, P. R. China
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17
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Vitoševic K, Todorovic D, Slovic Z, Zivkovic-Zaric R, Todorovic M. Forensic Genetics and Genotyping. SERBIAN JOURNAL OF EXPERIMENTAL AND CLINICAL RESEARCH 2019. [DOI: 10.1515/sjecr-2016-0074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractForensic genetics represents a combination of molecular and population genetics. Personal identification and kinship analysis (e.g. paternity testing) are the two main subjects of forensic DNA analysis. Biological specimens from which DNA is isolated are blood, semen, saliva, tissues, bones, teeth, hairs. Genotyping has become a basis in the characterization of forensic biological evidence. It is performed using a variety of genetic markers, which are divided into two large groups: bi-allelic (single-nucleotide polymorphisms, SNP) and multi-allelic polymorphisms (variable number of tandem repeats, VNTR and short tandem repeats, STR). This review describes the purpose of genetic markers in forensic investigation and their limitations. The STR loci are currently the most informative genetic markers for identity testing, but in cases without a suspect SNP can predict offender’s ancestry and phenotype traits such as skin, eyes and hair color. Nowadays, many countries worldwide have established forensic DNA databases based on autosomal short tandem repeats and other markers. In order for DNA profile database to be useful at a national or international level, it is essential to standardize genetic markers used in laboratories.
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Affiliation(s)
- Katarina Vitoševic
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Danijela Todorovic
- Department of Human Genetics, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Zivana Slovic
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Radica Zivkovic-Zaric
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Milos Todorovic
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
- Department of Forensic Medicine and Toxicology , Clinical Centre Kragujevac , Kragujevac , Serbia
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18
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Zhu J, Chen P, Qu S, Wang Y, Jian H, Cao S, Liu Y, Zhang R, Lv M, Liang W, Zhang L. Evaluation of the microhaplotype markers in kinship analysis. Electrophoresis 2019; 40:1091-1095. [DOI: 10.1002/elps.201800351] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 11/02/2018] [Accepted: 12/12/2018] [Indexed: 01/28/2023]
Affiliation(s)
- Jing Zhu
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Peng Chen
- Department of Forensic MedicineNanjing Medical University Nanjing P. R. China
| | - Shengqiu Qu
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Yinji Wang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Hui Jian
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Shuqiang Cao
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Yuqing Liu
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Ranran Zhang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Meili Lv
- Department of ImmunologyWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Weibo Liang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
| | - Lin Zhang
- Department of Forensic GeneticsWest China School of Basic Medical Sciences and Forensic MedicineSichuan University Chengdu P. R. China
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Set up of cutoff thresholds for kinship determination using SNP loci. Forensic Sci Int Genet 2017; 29:1-8. [DOI: 10.1016/j.fsigen.2017.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 03/04/2017] [Accepted: 03/06/2017] [Indexed: 12/20/2022]
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Paterno M, Schiavina M, Aglieri G, Ben Souissi J, Boscari E, Casagrandi R, Chassanite A, Chiantore M, Congiu L, Guarnieri G, Kruschel C, Macic V, Marino IAM, Papetti C, Patarnello T, Zane L, Melià P. Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas. Ecol Evol 2017; 7:2463-2479. [PMID: 28428839 PMCID: PMC5395429 DOI: 10.1002/ece3.2844] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/20/2017] [Accepted: 01/28/2017] [Indexed: 01/15/2023] Open
Abstract
Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long-distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic-Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b-RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic-Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic-Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic-Ionian locations indicates species-specific differences in genetic connectivity patterns and warns against generalizing single-species results to the entire community of rocky shore habitats.
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Affiliation(s)
- Marta Paterno
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Marcello Schiavina
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di MilanoMilanoItaly
| | - Giorgio Aglieri
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Department of Biological and Environmental Sciences and TechnologiesUniversity of SalentoLecceItaly
| | | | - Elisa Boscari
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Renato Casagrandi
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di MilanoMilanoItaly
| | - Aurore Chassanite
- USR 3278 CNRS‐EPHECRIOBEUniversité de Perpignan Via DominitiaPerpignan CedexFrance
| | - Mariachiara Chiantore
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Department for Earth, Environment and Life Sciences (DiSTAV)University of GenoaGenoaItaly
| | - Leonardo Congiu
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Giuseppe Guarnieri
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Department of Biological and Environmental Sciences and TechnologiesUniversity of SalentoLecceItaly
| | | | - Vesna Macic
- Institute of Marine Biology Kotor (IBMK)KotorMontenegro
| | - Ilaria A. M. Marino
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Chiara Papetti
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Tomaso Patarnello
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroPadovaItaly
| | - Lorenzo Zane
- Department of BiologyUniversity of PadovaPadovaItaly
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
| | - Paco Melià
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomaItaly
- Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di MilanoMilanoItaly
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Goodwin W, Alimat S. Analysis of four PCR/SNaPshot multiplex assays analyzing 52 SNP forID markers. Electrophoresis 2017; 38:1007-1015. [DOI: 10.1002/elps.201600383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/05/2016] [Accepted: 12/10/2016] [Indexed: 11/10/2022]
Affiliation(s)
- William Goodwin
- School of Forensic and Applied Sciences; University of Central Lancashire; Preston United Kingdom of Great Britain and Northern Ireland
| | - Sharizah Alimat
- School of Forensic and Applied Sciences; University of Central Lancashire; Preston United Kingdom of Great Britain and Northern Ireland
- Biotechnology Section; Department of Chemistry Malaysia (MOSTI); Jalan Sultan, Petaling Jaya Selangor Malaysia
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22
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Cho S, Seo HJ, Lee J, Yu HJ, Lee SD. Kinship Testing Based on SNPs Using Microarray System. Transfus Med Hemother 2016; 43:429-432. [PMID: 27994531 DOI: 10.1159/000446322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/15/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Kinship testing using biallelic SNP markers has been demonstrated to be a promising approach as a supplement to standard STR typing, and several systems, such as pyrosequencing and microarray, have been introduced and utilized in real forensic cases. The Affymetrix microarray containing 169 autosomal SNPs developed for forensic application was applied to our practical case for kinship analysis that had remained inconclusive due to partial STR profiles of degraded DNA and possibility of inbreeding within the population. CASE REPORT 169 autosomal SNPs were typed on array with severely degraded DNA of two bone samples, and the kinship compared to genotypes in a reference database of their putative family members. RESULTS Two bone samples remained unidentified through traditional STR typing with partial profiles of 10 or 14 of 16 alleles. Because these samples originated from a geographically isolated population, a cautious approach was required when analyzing and declaring true paternity only based on PI values. In a supplementary SNP typing, 106 and 78 SNPs were obtained, and the match candidates were found in each case with improved PI values than using only STRs and with no discrepant SNPs in comparison. CONCLUSION Our case showed that the utility of multiple SNPs on array is expected in practical forensic caseworks with an establishment of reference database.
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Affiliation(s)
- Sohee Cho
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea
| | - Hee Jin Seo
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea
| | - Jihyun Lee
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea
| | - Hyung Jin Yu
- DNA Link, Seoul, South Korea, Seoul, South Korea
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University, College of Medicine, Seoul, South Korea; Institute of Forensic Science, Seoul National University, College of Medicine, Seoul, South Korea
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Morimoto C, Manabe S, Kawaguchi T, Kawai C, Fujimoto S, Hamano Y, Yamada R, Matsuda F, Tamaki K. Pairwise Kinship Analysis by the Index of Chromosome Sharing Using High-Density Single Nucleotide Polymorphisms. PLoS One 2016; 11:e0160287. [PMID: 27472558 PMCID: PMC4966930 DOI: 10.1371/journal.pone.0160287] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/15/2016] [Indexed: 11/18/2022] Open
Abstract
We developed a new approach for pairwise kinship analysis in forensic genetics based on chromosomal sharing between two individuals. Here, we defined "index of chromosome sharing" (ICS) calculated using 174,254 single nucleotide polymorphism (SNP) loci typed by SNP microarray and genetic length of the shared segments from the genotypes of two individuals. To investigate the expected ICS distributions from first- to fifth-degree relatives and unrelated pairs, we used computationally generated genotypes to consider the effect of linkage disequilibrium and recombination. The distributions were used for probabilistic evaluation of the pairwise kinship analysis, such as likelihood ratio (LR) or posterior probability, without allele frequencies and haplotype frequencies. Using our method, all actual sample pairs from volunteers showed significantly high LR values (i.e., ≥ 108); therefore, we can distinguish distant relationships (up to the fifth-degree) from unrelated pairs based on LR. Moreover, we can determine accurate degrees of kinship in up to third-degree relationships with a probability of > 80% using the criterion of posterior probability ≥ 0.90, even if the kinship of the pair is totally unpredictable. This approach greatly improves pairwise kinship analysis of distant relationships, specifically in cases involving identification of disaster victims or missing persons.
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Affiliation(s)
- Chie Morimoto
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Sho Manabe
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takahisa Kawaguchi
- Unit of Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Chihiro Kawai
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shuntaro Fujimoto
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuya Hamano
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Forensic Science Laboratory, Kyoto Prefectural Police Headquarters, Kyoto, Japan
| | - Ryo Yamada
- Unit of Statistical Genetics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Matsuda
- Unit of Human Disease Genomics, Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Keiji Tamaki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- * E-mail:
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