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Li H, Ren H, Yang F, Chen M, Sun W, Jiang L, Gao Z, Liu Y, Liu X. Developmental Validation of the Microreader 23HS Plex ID System: A Novel Supplementary Non-CODIS STR Multiplex Assay for Forensic Application. Electrophoresis 2024. [PMID: 39347556 DOI: 10.1002/elps.202400106] [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: 05/23/2024] [Revised: 08/29/2024] [Accepted: 09/09/2024] [Indexed: 10/01/2024]
Abstract
A novel supplementary non-CODIS STR multiplex assay designated as the "Microreader 23HS Plex ID System" was developed. The Microreader 23HS Plex ID System enables simultaneous profiling of 23 STR loci and the amelogenin locus. The majority of these loci are non-CODIS STRs (D4S2408, D9S2157, D20S161, D3S2459, D18S1364, D13S305, D1S2142, D19S400, D6S1017, D7S1517, D2S1776, D2S1360, D3S1744, D16S3391, D3S1545, D11S4463, D20S85, D1S549, D10S2325, D21S2055), with the exception of three CODIS STRs (D2S441, D12S391, and D22S1045). Followed the recommendations of Scientific Working Group on DNA Analysis Methods (SWGDAM) and the Chinese validation standards, a comprehensive set of validation studies were conducted, encompassing PCR conditions, stutter ratio and peak height balance, sensitivity, precision and accuracy, reproducibility, species specificity, inhibition, as well as mixture testing. The results demonstrated that the Microreader 23HS Plex ID System is a reliable and robust assay, with well-balanced peak heights, high precision and accuracy, species specificity, and resistance to common inhibitors. The sensitivity of the assay was determined to be 0.125 ng of template DNA. In mixture study, all minor alleles were detected in two-sample mixtures across various ratios (1:19, 1:9, 1:4, 3:7, 2:3, 1:1, 3:2, 4:1, 9:1, and 19:1). In population study, a total of 500 unrelated individuals of Han ethnicity from East China were genotyped. The allele frequencies and forensic population genetic parameters were calculated, with a cumulative random match probability of 7.757 × 10-27, and a total power of discrimination exceeding 0.999,999,999,999,999,999,999,999,99. In conclusion, the Microreader 23HS Plex ID System shows promise as a valuable supplementary tool for forensic applications, particularly in addressing complex kinship testing and challenges posed by STR mutation.
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Affiliation(s)
- Hui Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, China
| | - He Ren
- Beijing Police College, Beijing, China
| | - Fan Yang
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai, China
| | - Man Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, China
| | - Weifen Sun
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, China
| | - Lei Jiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, China
| | | | - Yacheng Liu
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, China
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Li H, Li B, Liu Y, Yang F, Cao Y, Xie J, Liu X, Zhao Z, Li C. Characterization of sequence variations in the extended flanking regions using massively parallel sequencing in 21 A-STRs and 21 Y-STRs. BMC Genomics 2024; 25:841. [PMID: 39244600 PMCID: PMC11380771 DOI: 10.1186/s12864-024-10762-9] [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: 01/09/2024] [Accepted: 09/02/2024] [Indexed: 09/09/2024] Open
Abstract
In forensic genetics, utilizing massively parallel sequencing (MPS) to analyze short tandem repeats (STRs) has demonstrated several advantages compared to conventional capillary electrophoresis (CE). Due to the current technical limitations, although flanking region polymorphisms had been mentioned in several previous studies, most studies focused on the core repeat regions of STRs or the variations in the adjacent flanking regions. In this study, we developed an MPS system consisting of two sets of multiplex PCR systems to detect not only the STR core repeat regions but also to observe variants located at relatively distant positions in the flanking regions. The system contained 42 commonly used forensic STRs, including 21 autosomal STRs (A-STRs) and 21 Y-chromosomal STRs (Y-STRs), and a total of 350 male individuals from a Chinese Han population were genotyped. The length and sequence variants per locus were tallied and categorized based on length (length-based, LB), sequence without flanking region (core repeat regions sequence-based, RSB), and sequence with flanking region (core repeat and flanking regions sequence-based, FSB), respectively. Allele frequencies, Y-haplotype frequencies, and forensic parameters were calculated based on LB, RSB, and FSB, respectively, to evaluate the improvement in discrimination power, heterozygosity, and effectiveness of forensic systems. The results suggested the sequence variations have more influence on A-STRs and could improve the identification ability of MPS-STR genotyping. Concordance between MPS and CE methods was confirmed by using commercial CE-based STR kits. The impact of flanking region variations on STR genotype analysis and potential factors contributing to discordances were discussed. A total of 58 variations in the flanking regions (53 SNPs/SNVs and 5 InDels) were observed and most variations (48/58) were distributed in A-STRs. In summary, this study delved deeper into the genetic information of forensic commonly used STR and advanced the application of massively parallel sequencing in forensic genetics.
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Affiliation(s)
- Hui Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, China
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Beixu Li
- School of Policing Studies, Shanghai University of Political Science and Law, Shanghai, 201701, China
| | - Yanan Liu
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai, 200083, China
- Ministry of Education's Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Fan Yang
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai, 200083, China
| | - Yu Cao
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai, 200083, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, China
| | - Zhenmin Zhao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, China.
| | - Chengtao Li
- Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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Nishikubo M, Matsuo H, Manabe S, Ota K, Ishii J, Hiramoto N, Hara S, Kondo T, Ishikawa T. Donor-derived CD8-predominant T cells in human graft-versus-host disease of the brain after allogeneic transplantation. Br J Haematol 2024; 204:2516-2519. [PMID: 38693664 DOI: 10.1111/bjh.19504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/20/2024] [Indexed: 05/03/2024]
Affiliation(s)
- Masashi Nishikubo
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Hidemasa Matsuo
- Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sho Manabe
- Department of Legal Medicine, Kansai Medical University, Hirakata, Osaka, Japan
| | - Kazuma Ota
- Department of Neurology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Junko Ishii
- Department of Neurology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Nobuhiro Hiramoto
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Shigeo Hara
- Department of Pathology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Tadakazu Kondo
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Takayuki Ishikawa
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
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Davidson CL, de Klerk J, Matejovsky Z, Fabris-Rotelli I, Uys A. Metric evaluation of the anterior nasal spine to estimate sex and population group in South African individuals. Int J Legal Med 2024; 138:1117-1137. [PMID: 38010514 PMCID: PMC11003921 DOI: 10.1007/s00414-023-03130-x] [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: 05/26/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023]
Abstract
INTRODUCTION The anterior nasal spine is a pointed, midline projection of the maxilla. This bony structure dictates the overlying soft tissues providing the phenotypic features of the nose and upper lip and determines the differences in the mid-face morphology. Little data is available on the metric features of the Anterior nasal spine (ANS). This study aimed to perform metric evaluations of the ANS of white and black South African males and females to ascertain if morphological variations exist and if the differences are viable for the use in sex and population identification. MATERIALS AND METHODS The sample included 100 CBCT images for each population and sex group. Linear and angular measurements of the ANS were recorded in both the sagittal and axial planes. RESULTS Classification decision trees (pruned) were fitted to ascertain the relationship between population group, sex and the ANS measurements including and excluding age. For population group, all the ANS measurements were statistically significant for females but in males, all the ANS measurements were significant when performed individually. However, when fitted to the classification tree, Sagittal 2 did not show any statistical significance. When considering sex, only 2 of the ANS measurements (Sagittal 2 and Axial 1) were found to be significant. The results did not differ significantly when comparing the decision trees including and excluding age. CONCLUSIONS White South African individuals presented with a longer ANS that produced a more acute angle whereas black South African individuals presented with a shorter ANS and a more obtuse angle. Additionally, males presented with a longer ANS compared to females. ANS measurements were found to be more relevant for population discernment than for sex.
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Affiliation(s)
- Christy Lana Davidson
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Faculty of Health Sciences, University of Pretoria, PO Box 1266, Pretoria, 0001, South Africa.
| | - Johan de Klerk
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Faculty of Health Sciences, University of Pretoria, PO Box 1266, Pretoria, 0001, South Africa
| | - Zina Matejovsky
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Faculty of Health Sciences, University of Pretoria, PO Box 1266, Pretoria, 0001, South Africa
| | - Inger Fabris-Rotelli
- Department of Statistics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Andre Uys
- Department of Anatomy, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Non-invasive prenatal paternity testing by analysis of Y-chromosome mini-STR haplotype using next-generation sequencing. PLoS One 2022; 17:e0266332. [PMID: 35363835 PMCID: PMC8974964 DOI: 10.1371/journal.pone.0266332] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/19/2022] [Indexed: 11/23/2022] Open
Abstract
Objectives To assess the efficacy of Y-chromosome mini-STR-based next-generation sequencing (NGS) for non-invasive prenatal paternity testing (NIPPT). Methods DNA was extracted from the plasma of 24 pregnant women, and cell-free fetal DNA (cffDNA) haplotyping was performed at 12 Y-chromosome mini-STR loci using the Illumina NextSeq 500 system. The cffDNA haplotype was validated by the paternal haplotype. Subsequentlly, the paternity testing parameters were attributed to each case quantitatively. Results The biological relationship between the alleged fathers and infants in all 24 family cases were confirmed by capillary electrophoresis (CE). The Y-chromosome mini-STR haplotypes of all 14 male cffDNA were obtained by NGS without any missing loci. The alleles of cffDNA and paternal genomic DNA were matched in 13 cases, and a mismatched allele was detected at the DYS393 locus in one case and considered as mutation. No allele was detected in the 10 female cffDNA. The combined paternity index (CPI) and probability of paternity calculation was based on 6 loci Y-haplotype distributions of a local population. The probability of paternity was 98.2699–99.8828% for the cases without mutation, and 14.8719% for the case harboring mutation. Conclusions Our proof-of-concept study demonstrated that Y-chromosome mini-STR can be used for NGS-based NIPPT with high accuracy in real cases, and is a promising tool for familial searching, paternity exclusion and sex selection in forensic and medical applications.
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Poetsch M, Markwerth P, Konrad H, Bajanowski T, Helmus J. About the influence of environmental factors on the persistence of DNA - a long-term study. Int J Legal Med 2022; 136:687-693. [PMID: 35195781 PMCID: PMC9005405 DOI: 10.1007/s00414-022-02800-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/09/2022] [Indexed: 11/05/2022]
Abstract
DNA persistence and DNA transfer are important features in the assessment of a crime scene. The question how long DNA may persist at a certain location is similarly important as the one how the DNA has been transferred to this location. Depending on the source of the DNA as well as the conditions at the crime scene, the answer to this question is quite difficult. In this study, persistence of DNA from epithelial abrasions, blood cells, and saliva cells in indoor and outdoor scenarios has been investigated with regard to exposure time and exposure conditions including sunlight, temperature, and humidity in summer and winter scenarios. Overall, we generated 338 epithelial samples, 572 blood samples, and 572 saliva samples. A complete profile of the cell/DNA donor after exposure could be obtained in 47%, 65%, and 58% of epithelial abrasions, blood samples, and saliva samples, respectively. Regarding blood samples, there were no differences between supporting materials cloth and plastic; however, the percentage of complete profiles was higher for saliva samples on plastic and for epithelial samples on cloth. In indoor scenarios, complete profiles could be recovered from nearly all blood and saliva samples up to 9 months, whereas the amount of epithelial complete profiles already started to decline after 3 months. In outdoor scenarios, we observed a tipping point at an exposure time of 3 months. Blood and saliva samples collected after this period displayed complete profiles in less than 25% of samples. After 12 months, no outdoor sample showed a complete profile. The results of this study facilitate decisions on the relevance of recovered DNA from crime scenes.
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Affiliation(s)
- Micaela Poetsch
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany.
| | - Philipp Markwerth
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Helen Konrad
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Thomas Bajanowski
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Janine Helmus
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
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Li H, Zhang C, Song G, Ma K, Cao Y, Zhao X, Yang Q, Xie J. Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population. Mol Genet Genomic Med 2021; 9:e1626. [PMID: 33630413 PMCID: PMC8123751 DOI: 10.1002/mgg3.1626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/17/2021] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Massively parallel sequencing (MPS) is a promising supplementary method for forensic casework in short tandem repeats (STRs) genotyping, owing to several advantageous features in comparison to traditional capillary electrophoresis (CE). However, the application of MPS in casework requires accessible datasets from the worldwide population to enrich the allele frequencies of sequence-based STR genotypes. METHODS In this study, we report the characterization of sequence-based allele frequencies of 58 STRs from a Tibetan population comprising 120 unrelated individuals using the ForenSeq™ DNA Signature Prep Kit. A concordance study evaluating MPS and CE allele data was performed to ensure that MPS is compatible with current CE-based forensic databases. The diversity of observed alleles, allele frequencies, and forensic parameters per locus by length (LB), sequence without flanking region (RSB), and sequence with flanking region (FSB) were analyzed and compared. RESULTS The concordance study demonstrated a concordance rate exceeding 99%. The combined random match probability (RMP) for the 26 A-STRs was 2.04 × 10-29 , 1.93 × 10-31 , and 9.56 × 10-33 for LB, RSB, and FSB, respectively. Similar trends were observed in other forensic parameters resulting from the increase in the number of unique alleles available. A total of 111 and 113 unique haplotypes in the Y-STR loci were observed when using length-based and sequence-based alleles, respectively. In addition, we identified 35 novel alleles at 25 loci and 25 polymorphisms in the flanking regions at 17 STRs. CONCLUSIONS Our data suggest that MPS- and CE-derived alleles are compatible. MPS-based analysis of the STR data substantially increased the allele diversity and improved the forensic parameters, which clearly demonstrated the advantages of MPS in comparison to CE. With more pooled data and larger-scale validation, MPS could play a valuable role in forensic genetics and might be an additional tool for routine casework.
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Affiliation(s)
- Hui Li
- Department of Forensic MedicineSchool of Basic Medical SciencesFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Crime Scene EvidenceShanghai Research Institute of Criminal Science and TechnologyShanghai Municipal Public Security BureauShanghaiChina
| | - Cheng Zhang
- Center for Material EvidenceTibet Autonomous Region Public SecurityLhasa, TibetChina
| | - Guoqing Song
- Laboratory of Forensic Evidence and Science TechnologyXianyang Municipal Public Security BureauXianyangShaanxiChina
| | - Ke Ma
- Shanghai Key Laboratory of Crime Scene EvidenceShanghai Research Institute of Criminal Science and TechnologyShanghai Municipal Public Security BureauShanghaiChina
| | - Yu Cao
- Shanghai Key Laboratory of Crime Scene EvidenceShanghai Research Institute of Criminal Science and TechnologyShanghai Municipal Public Security BureauShanghaiChina
| | - Xueying Zhao
- National Demonstration Center for Experimental Biology EducationSchool of Life SciencesFudan UniversityShanghaiChina
| | - Qinrui Yang
- Department of Forensic MedicineSchool of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Jianhui Xie
- Department of Forensic MedicineSchool of Basic Medical SciencesFudan UniversityShanghaiChina
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DNA typing from skeletal remains: a comparison between capillary electrophoresis and massively parallel sequencing platforms. Int J Legal Med 2020; 134:2029-2035. [DOI: 10.1007/s00414-020-02327-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/28/2020] [Indexed: 10/24/2022]
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9
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Xu W, Wang Y, Zhang D, Wang D, Zhou L, Ye X, Zhu C, Shi Y. Mutation analysis of 21 autosomal short tandem repeats in Han population from Hunan, China. Ann Hum Biol 2020; 46:254-260. [PMID: 31264462 DOI: 10.1080/03014460.2019.1638966] [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] [Indexed: 10/26/2022]
Abstract
Background: Short tandem repeats (STRs) are powerful genetic markers widely used in human genetics. Population data and locus-specific mutation rates of STRs are crucial for the evaluation and interpretation of genetic evidence in forensic and population genetics.Aim: To investigate the mutation rates of 21 autosomal STRs in a population from central south China.Subjects and methods: This study analysed 3420 paternity cases with a Combined Paternity Index >10,000 from Han population in Hunan. A total of 68,743 meiotic transfers were analysed and 62 mutations were identified.Results: The overall mutation rate of STR loci was 0.9 × 10-3 (95% CI, 0.0007-0.0011) and the locus-specific mutation rates were estimated ranging from 0.0000-0.0023. Locus D1S1656 exhibited the highest mutation rate of 2.3 × 10-3 (95% CI, 0.0005-0.0006), followed by D12S391 with a mutation rate of 2.0 × 10-3 (95% CI, 0.0007-0.0044). No mutation was observed at TPOX, D2S1338 or Penta D. One-step mutation cases accounted for 96.77% of total mutations and the ratio of paternal vs maternal mutations was ∼4.85:1. Inter-population comparisons of locus-specific mutation rates of several STRs revealed significant differences between Han in Hunan and Han in other regions of China. Conclusion: The data justified the use of geographical data in further genetic applications.
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Affiliation(s)
- Wei Xu
- Institute of Translational Medicine, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, PR China
| | - Yuequn Wang
- Institute of Life Science, Hunan Normal University, Changsha, PR China
| | - Dandan Zhang
- School of Public Health, University of South China, Hengyang, PR China
| | - Daixin Wang
- Center of Forensic Science, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan School of Physical Sciences, Changsha, PR China
| | - Liang Zhou
- School of Public Health, Changsha Normal University, Changsha, PR China
| | - Xiangli Ye
- School of Medicine, Hunan Normal University, Changsha, PR China
| | - Chaogeng Zhu
- Translational Medicine Laboratory of Pancreatic Diseases, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, PR China
| | - Yongzhong Shi
- Institute of Translational Medicine, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, PR China
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Garrigós L, Caputo M, Corach D. Single step strategy for estimating unknown STR allele frequencies in a population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Voutsinos V, Munk SHN, Oestergaard VH. Common Chromosomal Fragile Sites-Conserved Failure Stories. Genes (Basel) 2018; 9:E580. [PMID: 30486458 PMCID: PMC6315858 DOI: 10.3390/genes9120580] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/17/2022] Open
Abstract
In order to pass on an intact copy of the genome during cell division, complete and faithful DNA replication is crucial. Yet, certain areas of the genome are intrinsically challenging to replicate, which manifests as high local mutation propensity. Such regions include trinucleotide repeat sequences, common chromosomal fragile sites (CFSs), and early replicating fragile sites (ERFSs). Despite their genomic instability CFSs are conserved, suggesting that they have a biological function. To shed light on the potential function of CFSs, this review summarizes the similarities and differences of the regions that challenge DNA replication with main focus on CFSs. Moreover, we review the mechanisms that operate when CFSs fail to complete replication before entry into mitosis. Finally, evolutionary perspectives and potential physiological roles of CFSs are discussed with emphasis on their potential role in neurogenesis.
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Affiliation(s)
- Vasileios Voutsinos
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.
| | - Sebastian H N Munk
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.
| | - Vibe H Oestergaard
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark.
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Zhang QX, Yang M, Pan YJ, Zhao J, Qu BW, Cheng F, Yang YR, Jiao ZP, Liu L, Yan JW. Development of a massively parallel sequencing assay for investigating sequence polymorphisms of 15 short tandem repeats in a Chinese Northern Han population. Electrophoresis 2018; 39:2725-2731. [DOI: 10.1002/elps.201800071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/11/2018] [Accepted: 05/07/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Qing-Xia Zhang
- Forensic Science Service; Beijing Public Security Bureau; Beijing P. R. China
| | - Meng Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
| | | | - Jing Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | | | - Feng Cheng
- College of forensic medicine; Shanxi Medical University; Taiyuan P. R. China
| | - Ya-Ran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
| | - Zhang-Ping Jiao
- Forensic Science Service; Beijing Public Security Bureau; Beijing P. R. China
| | - Li Liu
- Forensic Science Service; Beijing Public Security Bureau; Beijing P. R. China
- College of forensic medicine; Shanxi Medical University; Taiyuan P. R. China
| | - Jiang-Wei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
- College of forensic medicine; Shanxi Medical University; Taiyuan P. R. China
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Li H, Zhao X, Ma K, Cao Y, Zhou H, Ping Y, Shao C, Xie J, Liu W. Applying massively parallel sequencing to paternity testing on the Ion Torrent Personal Genome Machine. Forensic Sci Int Genet 2017; 31:155-159. [PMID: 28946114 DOI: 10.1016/j.fsigen.2017.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 11/30/2022]
Abstract
Massively parallel sequencing (MPS) is a promising supplementary method for forensic genetics and has gradually been applied to forensic casework. In this study, we applied MPS to forensic casework on an Ion Torrent Personal Genome Machine to evaluate its performance in paternity testing with mismatched STR loci. A total of 15 samples from seven cases containing one mismatched locus by capillary electrophoresis typing were analyzed. Combined paternity index (CPI) and relative chance of paternity were calculated according to the International Society for Forensic Genetics guidelines and the Chinese national standards recommended for paternity testing. With simultaneous analysis of enough STR loci, the results support the certainty of paternity, and the mismatched alleles were considered to be mutations (CPI>10,000). With the detection of allele sequence structures, the origins of the mutations were inferred in some cases. Meanwhile, nine STRs (CSF1PO, D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D12S391, D21S11 and D4S2408) were found in an increased number of unique alleles and three new alleles in three STRs (D2S441, D21S11, and FGA) that have not been reported before were detected. Therefore, MPS can provide valuable information for forensic genetics research and play a promising role in paternity testing.
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Affiliation(s)
- Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.
| | - Xueying Zhao
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - Ke Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China
| | - Yu Cao
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China
| | - Huaigu Zhou
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China
| | - Yuan Ping
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai 200083, China
| | - Chengchen Shao
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jianhui Xie
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai 200083, China.
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Whole Genome Amplification of Day 3 or Day 5 Human Embryos Biopsies Provides a Suitable DNA Template for PCR-Based Techniques for Genotyping, a Complement of Preimplantation Genetic Testing. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1209158. [PMID: 28717645 PMCID: PMC5498896 DOI: 10.1155/2017/1209158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/31/2017] [Accepted: 04/24/2017] [Indexed: 12/20/2022]
Abstract
Our objective was to determine if whole genome amplification (WGA) provides suitable DNA for qPCR-based genotyping for human embryos. Single blastomeres (Day 3) or trophoblastic cells (Day 5) were isolated from 342 embryos for WGA. Comparative Genomic Hybridization determined embryo sex as well as Trisomy 18 or Trisomy 21. To determine the embryo's sex, qPCR melting curve analysis for SRY and DYS14 was used. Logistic regression indicated a 4.4%, 57.1%, or 98.8% probability of a male embryo when neither gene, SRY only, or both genes were detected, respectively (accuracy = 94.1%, kappa = 0.882, and p < 0.001). Fluorescent Capillary Electrophoresis for the amelogenin genes (AMEL) was also used to determine sex. AMELY peak's height was higher and this peak's presence was highly predictive of male embryos (AUC = 0.93, accuracy = 81.7%, kappa = 0.974, and p < 0.001). Trisomy 18 and Trisomy 21 were determined using the threshold cycle difference for RPL17 and TTC3, respectively, which were significantly lower in the corresponding embryos. The Ct difference for TTC3 specifically determined Trisomy 21 (AUC = 0.89) and RPL17 for Trisomy 18 (AUC = 0.94). Here, WGA provides adequate DNA for PCR-based techniques for preimplantation genotyping.
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15
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Ham SK, Kim SY, Seo BY, Woo KM, Lee SH, Choi CY. Differential pre-amplification of STR loci for fragmented forensic DNA profiling. Electrophoresis 2016; 37:3002-3009. [PMID: 27510307 DOI: 10.1002/elps.201500478] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 02/01/2023]
Abstract
DNA profiling of short tandem repeats (STR) has been successfully used for the identification of individuals in forensic samples, accidents and natural disasters. However, STR profiling of DNA isolated from old crime scenes and damaged biological samples is difficult due to DNA degradation and fragmentation. Here, we show that pre-amplification of STR loci using biotinylated primers for the STR loci is an efficient strategy to obtain STR profiling results from fragmented forensic samples. Analysis of STR loci with longer amplicon sizes is generally hampered, since these relatively long loci are vulnerable to DNA fragmentation. This problem was overcome by using reduced or increased primer concentrations for loci with shorter or longer amplicon sizes, respectively, in our pre-amplification strategy. In addition, pre-amplification of STR loci into two groups of short or long amplicon size increases the efficiency of STR profiling from highly fragmented forensic DNA samples. Therefore, differential pre-amplification of STR loci is an effective way to obtain DNA profiling results from fragmented forensic samples.
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Affiliation(s)
- Seon-Kyu Ham
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Se-Yong Kim
- DNA Analysis Laboratory, Division of Forensic DNA, Supreme Prosecutors' Office, Seoul, Republic of Korea
| | - Bo Young Seo
- DNA Analysis Laboratory, Division of Forensic DNA, Supreme Prosecutors' Office, Seoul, Republic of Korea
| | - Kwang-Man Woo
- DNA Analysis Laboratory, Division of Forensic DNA, Supreme Prosecutors' Office, Seoul, Republic of Korea
| | - Seung-Hwan Lee
- DNA Analysis Laboratory, Division of Forensic DNA, Supreme Prosecutors' Office, Seoul, Republic of Korea
| | - Cheol Yong Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
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16
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Shao C, Lin M, Zhou Z, Zhou Y, Shen Y, Xue A, Zhou H, Tang Q, Xie J. Mutation analysis of 19 autosomal short tandem repeats in Chinese Han population from Shanghai. Int J Legal Med 2016; 130:1439-1444. [DOI: 10.1007/s00414-016-1427-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
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17
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Burguete-Argueta N, Martínez De la Cruz B, Camacho-Mejorado R, Santana C, Noris G, López-Bayghen E, Arellano-Galindo J, Majluf-Cruz A, Antonio Meraz-Ríos M, Gómez R. Forensic-paternity effectiveness and genetics population analysis of six non-CODIS mini-STR loci (D1S1656, D2S441, D6S1043, D10S1248, D12S391, D22S1045) and SE33 in Mestizo and Amerindian populations from Mexico. Ann Hum Biol 2016; 43:563-571. [DOI: 10.3109/03014460.2015.1127424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Braulio Martínez De la Cruz
- Departamento de Ingeniería, Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Laguna, Torreón, Coahuila, México
| | | | - Carla Santana
- Laboratorio BIMODI (Biología Molecular Diagnóstica), Querétaro, Qro., México
| | - Gino Noris
- Laboratorio BIMODI (Biología Molecular Diagnóstica), Querétaro, Qro., México
| | | | - José Arellano-Galindo
- Laboratorio de Virología, Hospital Infantil de México Federico Gómez, México D.F., México
| | - Abraham Majluf-Cruz
- Unidad de Investigación Médica en Trombosis, Hemostasia y Aterogénesis, Instituto Mexicano del Seguro Social, México D.F., México
| | | | - Rocío Gómez
- Departamento de Toxicología, Cinvestav-IPN, México D.F., México
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18
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Kim EH, Lee HY, Yang IS, Jung SE, Yang WI, Shin KJ. Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons. Forensic Sci Int Genet 2016; 22:1-7. [DOI: 10.1016/j.fsigen.2016.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 12/09/2015] [Accepted: 01/05/2016] [Indexed: 11/26/2022]
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19
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Giusti I, Cervelli C, D'Ascenzo S, Di Francesco M, Ligas C, D'Alessandro E, Papola F, Dolo V. The human ovarian cancer cell line CABA I: A peculiar genetic evolution. Int J Mol Med 2016; 37:879-88. [PMID: 26934856 PMCID: PMC4790663 DOI: 10.3892/ijmm.2016.2501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 12/22/2015] [Indexed: 12/21/2022] Open
Abstract
The objective of this study was to study the human ovarian cancer cell line CABA I by means of short tandem repeats (STR) profiling and cytogenetic analysis in order to prevent future misidentification or cross-contamination and verify its stability during in vitro cultivation. To this end, cells at passages 18 and 38 were analyzed using cytogenetic techniques in order to verify possible chromosomal aberrations and the karyotypic evolution of this cell line; GTG-banding and FISH were also performed. For STR analysis, DNA was extracted using the automated extractor MagNA pure and analyzed by means of PowerPlex 16 HS. STR profiles were analyzed by GeneMapper 3.2.1 software. Whereas comparative cytogenetic analysis of CABA I cells at passage 18 and 38 has demonstrated considerable genetic instability, we found that STR profiles were essentially unaltered in both analyzed passages, suggesting that the STR profile is reliable and could be used for the regular authentication of CABA I over time. It should be emphasized, however, that of the 16 loci generally used in human STR profiles, only 3 were properly detectable in CABA I. The data highlight that the CABA I cell line demonstrates an anomalous STR profile that does not fully adjust the criteria currently used for the identification of human cells; in spite of this, it remains stable during the in vitro maintainance. Moreover, the genetic instability of the CABA I cell line overlaps with those observed in vivo in tumor cells, making it a suitable candidate to analyze, in vitro, the peculiar genetic evolution of ovarian cancer cells.
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Affiliation(s)
- Ilaria Giusti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Carla Cervelli
- Regional Center of Immunohematology and Tissue Typing, L'Aquila, Italy
| | - Sandra D'Ascenzo
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Marianna Di Francesco
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Claudio Ligas
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Elvira D'Alessandro
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Franco Papola
- Regional Center of Immunohematology and Tissue Typing, L'Aquila, Italy
| | - Vincenza Dolo
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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20
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Kloor M, von Knebel Doeberitz M. The Immune Biology of Microsatellite-Unstable Cancer. Trends Cancer 2016; 2:121-133. [PMID: 28741532 DOI: 10.1016/j.trecan.2016.02.004] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/03/2016] [Accepted: 02/09/2016] [Indexed: 12/16/2022]
Abstract
Deficient DNA mismatch repair (MMR) boosts the accumulation of frameshift mutations in genes encompassing coding microsatellites (cMS). This results in the translation of proteins with mutation-induced frameshift peptides (neoantigens) rendering microsatellite-unstable (MSI) cancers highly immunogenic. MSI cancers express a defined set of neoantigens resulting from functionally relevant driver mutations, which are shared by most MSI cancers. Patients with MSI cancers and healthy individuals affected by Lynch syndrome, an inherited predisposition for MSI cancers, develop specific immune responses against these neoantigens. In this review, we summarize our current understanding of the immune biology of MSI cancers and outline new concepts and research directions to develop not only therapeutic treatments, but also preventive vaccines based on the MSI cancer genome landscapes.
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Affiliation(s)
- Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Clinical Cooperation Unit (CCU 105) of the German Cancer Research Center and Molecular Medicine Partner Unit (MMPU) of the European Molecular Biology Laboratory, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany.
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Clinical Cooperation Unit (CCU 105) of the German Cancer Research Center and Molecular Medicine Partner Unit (MMPU) of the European Molecular Biology Laboratory, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany.
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21
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Asprer JST, Lakshmipathy U. Current methods and challenges in the comprehensive characterization of human pluripotent stem cells. Stem Cell Rev Rep 2016; 11:357-72. [PMID: 25504379 DOI: 10.1007/s12015-014-9580-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pluripotent stem cells (PSCs) are powerful tools for basic scientific research and promising agents for drug discovery and regenerative medicine. Technological advances have made it increasingly easy to generate PSCs but the various lines generated may differ in their characteristics based on their origin, derivation, number of passages, and culture conditions. In order to confirm the pluripotency, quality, identity, and safety of pluripotent cell lines as they are derived and maintained, it is critical to perform a panel of characterization assays. Functional pluripotency is determined using tests that rely on the expression of specific markers in the undifferentiated and differentiated states; tests for quality, identity and safety are less specialized. This article provides a comprehensive review of current practices in PSC characterization and explores challenges in the field, from the selection of markers to the development of simple and scalable methods. It also delves into emerging trends like the adoption of alternative assays that could be used to supplement or replace traditional methods, specifically the use of in silico assays for determining pluripotency.
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Affiliation(s)
- Joanna S T Asprer
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, CA, 92008, USA
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22
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Abstract
Rapidly mutating (RM) Y-STRs were recently identified and can help to differentiate between paternally related males in paternity and forensic casework. Normal Y-STRs are often used in casework due to their paternal inheritance, which can help to resolve kinship cases, and identify male components in male/female mixtures; however, more discriminating profiles are obtained if rapidly mutating Y-STRs are used. Previously two or three multiplex PCRs have been used to amplify 13 RM Y-STRs; here, an assay amplifying these 13 markers in a single multiplex PCR is described. Commercially available male control DNA samples have been genotyped during the validation of this assay, thus providing a tool for calibrating genotyping results. It is expected that the assay will provide a niche tool for genotyping casework samples.
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Affiliation(s)
- Sibte Hadi
- School of Forensic and Investigative Sciences, University of Central Lancashire, Preston, UK.
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23
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Ham SK, Kim SY, Ahn JW, Seo BY, Woo KM, Choi CY, Lee SH. Optimization of STR locus enrichment for STR profiling of fragmented DNA. Electrophoresis 2014; 35:3158-64. [PMID: 25142119 DOI: 10.1002/elps.201400102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 07/03/2014] [Accepted: 08/12/2014] [Indexed: 11/09/2022]
Abstract
DNA degradation is a major obstacle in gaining an accurate profile with standard DNA typing technology. Although alternative genotyping strategies such as mini-STRs and SNPs have proven to be more successful in profiling degraded DNA, these approaches also have limitations. Here, we show that locus enrichment by hybridization of degraded genomic DNA with an STR locus-specific biotinylated oligonucleotide is a powerful approach to overcome problems in STR typing of highly degraded DNA. An experimental investigation of factors affecting the efficiency of this method indicates that the choice of primer and molar ratio of primers to genomic DNA are critical factors in improving enrichment of the STR locus before genotyping with multiplex kits. In addition, we find that indirect capture rather than direct capture with magnetic beads yields better enrichment efficiency for STR locus enrichments. Using these strategies, we demonstrate an improvement in STR typing of DNA from cultured cells damaged by exposure to sunlight or UV. We suggest that this approach could be applied to highly degraded forensic samples alone or in combination with mini-STRs.
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Affiliation(s)
- Seon-Kyu Ham
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
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24
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DNA evidence: Current perspective and future challenges in India. Forensic Sci Int 2014; 241:183-9. [DOI: 10.1016/j.forsciint.2014.05.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/22/2014] [Accepted: 05/20/2014] [Indexed: 11/22/2022]
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25
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Timbers J, Wilkinson D, Hause CC, Smith ML, Zaidi MA, Laframboise D, Wright KE. Elimination of bioweapons agents from forensic samples during extraction of human DNA. J Forensic Sci 2014; 59:1530-40. [PMID: 25069670 DOI: 10.1111/1556-4029.12561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 10/07/2013] [Accepted: 10/26/2013] [Indexed: 11/27/2022]
Abstract
Collection of DNA for genetic profiling is a powerful means for the identification of individuals responsible for crimes and terrorist acts. Biologic hazards, such as bacteria, endospores, toxins, and viruses, could contaminate sites of terrorist activities and thus could be present in samples collected for profiling. The fate of these hazards during DNA isolation has not been thoroughly examined. Our goals were to determine whether the DNA extraction process used by the Royal Canadian Mounted Police eliminates or neutralizes these agents and if not, to establish methods that render samples safe without compromising the human DNA. Our results show that bacteria, viruses, and toxins were reduced to undetectable levels during DNA extraction, but endospores remained viable. Filtration of samples after DNA isolation eliminated viable spores from the samples but left DNA intact. We also demonstrated that contamination of samples with some bacteria, endospores, and toxins for longer than 1 h compromised the ability to complete genetic profiling.
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Affiliation(s)
- Jason Timbers
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1B 8M5, Canada; Forensic Sciences Identification Services, Royal Canadian Mounted Police, 1200 Vanier Parkway, Ottawa, ON, K1A 0R2, Canada
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26
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Miller JK, Buchner N, Timms L, Tam S, Luo X, Brown AMK, Pasternack D, Bristow RG, Fraser M, Boutros PC, McPherson JD. Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples. PLoS One 2014; 9:e88163. [PMID: 24551080 PMCID: PMC3923782 DOI: 10.1371/journal.pone.0088163] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 01/03/2014] [Indexed: 11/23/2022] Open
Abstract
Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS). The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework.
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Affiliation(s)
- Jessica K. Miller
- Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada
| | - Nicholas Buchner
- Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada
| | - Lee Timms
- Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada
| | - Shirley Tam
- Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada
| | - Xuemei Luo
- Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada
| | - Andrew M. K. Brown
- Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada
| | - Danielle Pasternack
- Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada
| | - Robert G. Bristow
- Ontario Cancer Institute/Princess Margaret Hospital, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Michael Fraser
- Ontario Cancer Institute/Princess Margaret Hospital, Toronto, Canada
| | - Paul C. Boutros
- Informatics & Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada
| | - John D. McPherson
- Department of Genome Technologies, Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
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27
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Kim EH, Jung SE, Shin KJ, Yang WI, Yang IS. Sequence Generation and Genotyping of 15 Autosomal STR Markers Using Next Generation Sequencing. ACTA ACUST UNITED AC 2014. [DOI: 10.7580/kjlm.2014.38.2.48] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eun Hye Kim
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
| | - Sang-Eun Jung
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
| | - Woo Ick Yang
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - In Seok Yang
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
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28
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Madi HA, Swaid S, Al-Amad S. Assessment of the uniqueness of human dentition. THE JOURNAL OF FORENSIC ODONTO-STOMATOLOGY 2013; 31:30-9. [PMID: 24776439 PMCID: PMC5734832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Comparing ante-mortem and post-mortem dental characteristics has been a reliable, accurate and quick human identification method. This is based on the assumption that each individual's set of teeth is unique; however, there is little evidence to support this assumption. This research aimed to determine the uniqueness of basic dental features in a cohort of multinational dental patients. Dental charts were retrieved from the archives of the College of Dentistry at the University of Sharjah. Dental patterns were coded into letters representing basic dental characteristics, and entered into a computer program that was written specifically for analysing the results of this research. Two thousand dental charts were included in this research; the average age of the sample was 31.9 years (11-87 years). The male:female ratio was 1.4:1 from 55 nationalities. One thousand one hundred and fifty-nine dental charts (57.95%) had absolutely unique dental patterns. The remaining charts (n=841 [42.05%]) were found to have identical patterns with others, the most common of which was 'all virgin' teeth (n=482 [24.1%]). Introducing a single dental modification dropped this percentage to 1.05%. This percentage was further narrowed down to 0.7% when the gender variable was introduced to the comparison. The results of this research support the assumption that dental characteristics show a diversity that is useful for human identification, even when those characteristics are recorded in their simplest forms.
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Affiliation(s)
| | - Salam Swaid
- College of Dentistry, University of Sharjah, P.O. Box 27272 , Sharjah, United Arab Emirates
| | - Suhail Al-Amad
- College of Dentistry, University of Sharjah, P.O. Box 27272 , Sharjah, United Arab Emirates
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29
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Caputo M, Irisarri M, Alechine E, Corach D. A DNA extraction method of small quantities of bone for high-quality genotyping. Forensic Sci Int Genet 2013; 7:488-93. [DOI: 10.1016/j.fsigen.2013.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 04/27/2013] [Accepted: 05/09/2013] [Indexed: 10/26/2022]
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30
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Anagnostou P, Capocasa M, Milia N, Bisol GD. Research data sharing: Lessons from forensic genetics. Forensic Sci Int Genet 2013; 7:e117-e119. [PMID: 23972948 DOI: 10.1016/j.fsigen.2013.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 07/22/2013] [Accepted: 07/24/2013] [Indexed: 11/26/2022]
Affiliation(s)
- P Anagnostou
- Università di Roma "La Sapienza", Dipartimento di Biologia Ambientale, Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy
| | - M Capocasa
- Università di Roma "La Sapienza", Dipartimento Biologia e Biotecnologie "Charles Darwin", Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy
| | - N Milia
- Università di Cagliari, Dipartimento di Biologia Sperimentale, Cagliari, Italy
| | - G Destro Bisol
- Università di Roma "La Sapienza", Dipartimento di Biologia Ambientale, Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy.
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31
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