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Bu C, Zheng X, Mai J, Nie Z, Zeng J, Qian Q, Xu T, Sun Y, Bao Y, Xiao J. CCLHunter: An efficient toolkit for cancer cell line authentication. Comput Struct Biotechnol J 2023; 21:4675-4682. [PMID: 37841327 PMCID: PMC10568302 DOI: 10.1016/j.csbj.2023.09.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Cancer cell lines are essential in cancer research, yet accurate authentication of these cell lines can be challenging, particularly for consanguineous cell lines with close genetic similarities. We introduce a new Cancer Cell Line Hunter (CCLHunter) method to tackle this challenge. This approach utilizes the information of single nucleotide polymorphisms, expression profiles, and kindred topology to authenticate 1389 human cancer cell lines accurately. CCLHunter can precisely and efficiently authenticate cell lines from consanguineous lineages and those derived from other tissues of the same individual. Our evaluation results indicate that CCLHunter has a complete accuracy rate of 93.27%, with an accuracy of 89.28% even for consanguineous cell lines, outperforming existing methods. Additionally, we provide convenient access to CCLHunter through standalone software and a web server at https://ngdc.cncb.ac.cn/cclhunter.
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Affiliation(s)
- Congfan Bu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Xinchang Zheng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Jialin Mai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Nie
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingyao Zeng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Qiheng Qian
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianyi Xu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanling Sun
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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De Wolf J, Robin E, Vallee A, Cohen J, Hamid A, Roux A, Leguen M, Beaurepere R, Bieche I, Masliah-Planchon J, Glorion M, Allory Y, Sage E. Donor/recipient origin of lung cancer after lung transplantation by DNA short tandem repeat analysis. Front Oncol 2023; 13:1225538. [PMID: 37841427 PMCID: PMC10568626 DOI: 10.3389/fonc.2023.1225538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Background Lung cancer is more common in posttransplant recipients than in the general population. The objective of this study was to examine the chimerism donor/recipient cell origin of graft cancer in recipients of lung transplant. Methods A retrospective chart review was conducted at Foch Hospital for all lung transplantations from 1989 to 2020. Short tandem repeat PCR (STR-PCR) analysis, the gold standard technique for chimerism quantification, was used to determine the donor/recipient cell origin of lung cancers in transplant patients. Results Fourteen (1.4%) of the 1,026 patients were found to have graft lung cancer after lung transplantation, and one developed two different lung tumors in the same lobe. Among the 15 lung tumors, 10 (67%) presented with adenocarcinoma, four (27%) with squamous cell carcinoma and one with small cell lung cancer. STR analysis showed that the origin of the cancer was the donor in 10 patients (71%), the recipient in three patients (21%), and was undetermined in one patient. Median time to diagnosis was 62 months. Conclusion The prevalence of lung cancer in lung transplant recipients is very low. However, the results of our study showed heterogeneity of genetic alterations, with 21% being of recipient origin. Our results highlight the importance of donor selection and medical supervision after lung transplantation.
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Affiliation(s)
- Julien De Wolf
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, Suresnes, France
| | - Edouard Robin
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, Suresnes, France
| | - Alexandre Vallee
- Department of Clinical Research and Innovation Foch Hospital, Suresnes, France
| | - Justine Cohen
- Department of Anatomopathology, Foch Hospital, Suresnes, France
| | - Abdul Hamid
- Department of Pneumology, Foch Hospital, Suresnes, France
| | - Antoine Roux
- Department of Pneumology, Foch Hospital, Suresnes, France
| | - Morgan Leguen
- Department of Anesthesiology, Foch Hospital, Suresnes, France
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | | | - Ivan Bieche
- Genetics Department, Curie Institut, Paris, France
| | | | - Matthieu Glorion
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, Suresnes, France
| | - Yves Allory
- Department of Anatomopathology, Foch Hospital, Suresnes, France
- Department of Anatomopathology, Curie Institut, Paris, France
| | - Edouard Sage
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, Suresnes, France
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
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Muacevic A, Adler JR. The Impact of Leukemia on the Detection of Short Tandem Repeat (STR) Markers. Cureus 2022; 14:e30954. [PMID: 36465210 PMCID: PMC9711926 DOI: 10.7759/cureus.30954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION Short tandem repeats (STRs) have been used for various identity typing methods worldwide. They have high discrimination power in human identification in forensics, paternity testing, missed personal identification, genetic diseases, and gene regulatory functions. They have also been used to detect and monitor the stability of diseases, including various types of cancer. This study aimed to investigate the impact of leukemia on the detection and stability of STR markers. METHODS DNA was isolated from 30 participants (15 with chronic myeloid leukemia( CML) and 15 healthy controls) and used to amplify STR markers using specific primers. RESULTS We found that the blood of those with leukemia had more 9.3 and 9 alleles at the tyrosine hydroxylase 1 (TH01) marker than the blood of the healthy control samples. The results of this study will help researchers understand leukemia's effect on the detection and stability of STR markers in leukemic patients compared to healthy individuals. CONCLUSION Our results demonstrate that STR markers could become useful in genetic studies of leukemia cases.
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Chen A, Xiong L, Qu Y, Xi S, Tao R, Li C, Zhang S. Opportunity of Next-Generation Sequencing-Based Short Tandem Repeat System for Tumor Source Identification. Front Oncol 2022; 12:800028. [PMID: 35223480 PMCID: PMC8873583 DOI: 10.3389/fonc.2022.800028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/21/2022] [Indexed: 11/29/2022] Open
Abstract
Personal identification using the tumor DNA not only plays an important role in postoperative tissue management but also might be the only accessible source of biological material in forensic identification. Short tandem repeat (STR) is the worldwide accepted forensic marker; however, widespread loss of heterozygosity (L) in tumor tissues challenges the personal identification using the conventional capillary electrophoresis (CE)-based STR typing system (CE-STR). Because the tumors are mixtures of tumor cells and basal cells, we inferred that every germline-originated allele should be detected if the detection method was sensitive enough. Next-generation sequencing (NGS) is known as a highly sensitive application, which might be a promising tool for tumor source identification. In the study, we genotyped and compared the STR results between the platforms, and we found that the concordance was only 91.43%. Higher sensitivity did help identify more germline-originated alleles as expected, and 93.89% of them could be captured by using an NGS-based STR system (NGS-STR). The identity-by-state (IBS) scoring system was applied to generate a new tumor source identification method based on NGS-STR, and the number of loci with 2 identical alleles (A2) proved to be an ideal criterion for the larger area under the receiver operating characteristic (ROC) curve (AUC). Both the sensitivity and specificity were above 98% in the cutoff of A2 to distinguish the paired carcinoma (PC) sample group from the unrelated individual (UI) group, the simulated full sibling (FS) group, and the simulated parent–offspring (PO) group.
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Affiliation(s)
- Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Xiong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Shihan Xi
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
- Department of Forensic Medicine, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Chengtao Li, ; Suhua Zhang,
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
- *Correspondence: Chengtao Li, ; Suhua Zhang,
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Jin R, Cui W, Fang Y, Jin X, Wang H, Lan Q, Guo Y, Chen C, Zhang X, Zhu B. A Novel Panel of 43 Insertion/Deletion Loci for Human Identifications of Forensic Degraded DNA Samples: Development and Validation. Front Genet 2021; 12:610540. [PMID: 33777093 PMCID: PMC7990895 DOI: 10.3389/fgene.2021.610540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 02/02/2021] [Indexed: 11/18/2022] Open
Abstract
Insertion/deletion polymorphism is a promising genetic marker in the forensic genetic fields, especially in the forensic application of degraded sample at crime scene. In this research, a novel five-dye multiplex amplification panel containing 43 highly polymorphic Insertion/deletion (InDel) loci and one Amelogenin gene locus is designed and constructed in-house for the individual identification in East Asian populations. The amplicon sizes of 43 InDel loci are less than 200 bp, which help to ensure that full allele profiles can be obtained from degraded DNA sample. A series of optimizations and developmental validations including optimization of PCR conditions, detection efficiency of the degraded and casework samples, sensitivity, reproducibility, precision, tolerance for inhibitors, species specificity and DNA mixtures are performed according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) guideline. The results of the internal validation demonstrated that this novel InDel panel was a reliable, sensitive and accurate system with good tolerances to different inhibitors, and performed the considerable detection efficiency for the degraded or mixed samples, which could be used in the forensic applications.
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Affiliation(s)
- Rui Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Department of Radiology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yating Fang
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Hongdan Wang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiong Lan
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Investigation of an Alternative Marker for Hypermutability Evaluation in Different Tumors. Genes (Basel) 2021; 12:genes12020197. [PMID: 33572856 PMCID: PMC7910966 DOI: 10.3390/genes12020197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 02/01/2023] Open
Abstract
A growing number of studies have shown immunotherapy to be a promising treatment strategy for several types of cancer. Short tandem repeats (STRs) have been proven to be alternative markers for the evaluation of hypermutability in gastrointestinal (GI) cancers. However, the status of STRs and microsatellite instability (MSI) in other tumors have not yet been investigated. To further compare STR and MSI alterations in different tumors, a total of 407 paired DNAs were analyzed from the following eight tumor types: breast cancer (BC), hepatocellular cancer (HCC), pancreatic cancer (PC), colorectal cancer (CRC), gastric cancer (GC), lung cancer (LC), esophageal cancer (EC), and renal cell cancer (RCC). The STR alteration frequencies varied in different tumors as expected. Interestingly, none of the patients possessed MSI-low (MSI-L) or MSI-high (MSI-H), except for the GI patients. The highest STR alteration was detected in EC (77.78%), followed by CRC (69.77%), HCC (63.33%), GC (54.55%), LC (48.00%), RCC (40.91%), BC (36.11%), and PC (25.71%). The potential cutoff for hypermutability was predicted using the published objective response rate (ORR), and the cutoff of LC and HCC was the same as that of GI cancers (26.32%). The cutoffs of 31.58% and 10.53% should be selected for BC and RCC, respectively. In summary, we compared MSI and STR status in eight tumor types, and predicted the potential threshold for hypermutability of BC, HCC, CRC, GC, LC, EC, and RCC.
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Cui W, Jin X, Guo Y, Chen C, Zhang W, Wang Y, Lan J, Zhu B. Development and Validation of a Novel Five-Dye Short Tandem Repeat Panel for Forensic Identification of 11 Species. Front Genet 2020; 11:1005. [PMID: 33193588 PMCID: PMC7541953 DOI: 10.3389/fgene.2020.01005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/06/2020] [Indexed: 01/16/2023] Open
Abstract
Species identification of unknown biological samples is of fundamental importance for forensic applications, especially in crime detection, poaching, and illegal trade of endangered animals as well as meat fraud. In this study, a novel panel was developed to simultaneously identify 10 different animal species (Gallus domesticus, Anas platyrhynchos domesticus, Ovis aries, Sus scrofa domesticus, Bos taurus, Equus caballus, Columba livia domestica, Rattus norvegicus, Mus musculus, and Canis lupus familiaris) and human beings by amplifying 22 short tandem repeat (STR) loci in a multiplex PCR using a set of five fluorescently labeled dyes. This novel 22-STR panel was validated by optimization of PCR conditions as well as species specificity, sensitivity, reproducibility, precision, DNA mixture, and tissue/organ consistency. The results of developmental validation showed that the 22-STR loci achieved high species specificity among 10 animal species and human beings, and the sensitivity of this panel was 0.09 ng. This 22-STR panel identified different meats in mixed samples, and the minimum detected mixture ratio in the current test was 10% (0.1 ng/1 ng). This sensitive, accurate, and specific 22-STR panel can be used for forensic species identification and the detection of meat fraud and adulteration.
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Affiliation(s)
- Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Yijie Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Jiangwei Lan
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Dang Z, Li L, Kong X, Zhang G, Liu Q, Li H, Li L, Zhang R, Cui W, Wang Y. Evaluation of allelic alterations in short tandem repeats in papillary thyroid cancer. Mol Genet Genomic Med 2020; 8:e1164. [PMID: 32043756 PMCID: PMC7196467 DOI: 10.1002/mgg3.1164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/07/2019] [Accepted: 01/27/2020] [Indexed: 01/08/2023] Open
Abstract
Background Malignant tissue samples may be the only source of biological material for forensic investigations, including individual identification or paternity testing; however, such samples may lead to uncertainties due to frequent genomic aberrations associated with tumors, including alterations of the short tandem repeat (STR) loci used for forensic casework. Methods Short tandem repeat loci routinely used in forensic analysis (n = 23) were analyzed in 68 surgically removed papillary thyroid cancer specimens. Tumor cells and normal stromal cells were separated by laser capture microdissection. Results Four kinds of changes were detected between normal and tumor tissues: partial loss of heterozygosity (pLOH), complete loss of heterozygosity, an additional allele, and a new allele not found in normal tissue. These changes were distributed across 20 of the tested STRs, with no mutations in VWA, D16S539, or Penta D. The most frequently affected locus was D2S1338, and the most frequent type of alteration was pLOH. Samples from patients aged 40–59 years exhibited the highest frequencies of STR variation. Conclusion Our results suggest that great care should be taken in the evaluation of DNA typing results obtained from malignant tissues, particularly when no normal tissue reference samples are available.
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Affiliation(s)
- Zhen Dang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Lu Li
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining, Shandong, PR China
| | - Xia Kong
- Department of Pharmacy, The First People' s Hospital Affiliated to Jining Medical University, Jining, Shandong, PR China
| | - Guoan Zhang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Qi Liu
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Haibin Li
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Liang Li
- Department of Pathology, The First People' s Hospital Affiliated to Jining Medical University, Jining, Shandong, PR China
| | - Renya Zhang
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining, Shandong, PR China
| | - Wen Cui
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
| | - Yequan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, Shandong, PR China
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