Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumors
Abstract Background A number of genetic aberrations are associated with the BCL6-correpresor gene (BCOR), including internal tandem duplications (ITDs) and gene fusions (BCOR::CCNB3 and BCOR::MAML3), as well as YWHAE::NUTM2, which are found in clear cell sarcoma of the kidney (CCSK), sarcoma with BC...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | Diagnostic Pathology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13000-025-01604-7 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832572098714796032 |
|---|---|
| author | Meng Zhang Xingfeng Yao Nan Zhang Yongbo Yu Chao Jia Xiaoxing Guan Wenjian Xu Xin Ni Yongli Guo Lejian He |
| author_facet | Meng Zhang Xingfeng Yao Nan Zhang Yongbo Yu Chao Jia Xiaoxing Guan Wenjian Xu Xin Ni Yongli Guo Lejian He |
| author_sort | Meng Zhang |
| collection | DOAJ |
| description | Abstract Background A number of genetic aberrations are associated with the BCL6-correpresor gene (BCOR), including internal tandem duplications (ITDs) and gene fusions (BCOR::CCNB3 and BCOR::MAML3), as well as YWHAE::NUTM2, which are found in clear cell sarcoma of the kidney (CCSK), sarcoma with BCOR genetic alterations, primitive myxoid mesenchymal tumor of infancy, and high-grade neuroepithelial tumors in children. Detecting these gene aberrations is crucial for tumor diagnosis. ITDs can be identified by Sanger sequencing or agarose gel electrophoresis. However, gene fusions are usually detected through reverse transcription-polymerase chain reaction (RT-PCR) or fluorescence in situ hybridization. Methods that analyze these variants simultaneously in a sensitive and convenient manner are lacking in clinical practice. Methods This study validated a Universal Fluorescence Multiplex PCR-based assay that assessed BCOR ITDs, BCOR::CCNB3, BCOR::MAML3 and YWHAE::NUTM2 fusions simultaneously. Results The assay achieved a detection threshold of 10 copies for fusion genes and 0.32 ng genomic DNA for BCOR ITDs. The performance of this assay was also tested in a cohort of 43 pediatric tumors (17 undifferentiated small round cell sarcomas, and 26 tumors with a histological diagnosis of CCSK). In total, 20 BCOR ITDs, 4 BCOR::CCNB3 and one YWHAE::NUTM2 were detected. When compared with the final diagnosis, the assay achieved 93% sensitivity and 100% specificity. Conclusions Accordingly, this assay provided an effective and convenient method for detecting BCOR- and YWHAE-related abnormalities in tumors. |
| format | Article |
| id | doaj-art-d078dbe717464defb7933b87c8010018 |
| institution | Kabale University |
| issn | 1746-1596 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Diagnostic Pathology |
| spelling | doaj-art-d078dbe717464defb7933b87c80100182025-02-02T12:06:18ZengBMCDiagnostic Pathology1746-15962025-01-0120111210.1186/s13000-025-01604-7Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumorsMeng Zhang0Xingfeng Yao1Nan Zhang2Yongbo Yu3Chao Jia4Xiaoxing Guan5Wenjian Xu6Xin Ni7Yongli Guo8Lejian He9Department of Pathology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthDepartment of Pathology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthDepartment of Pathology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthBeijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthDepartment of Pathology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthDepartment of Pathology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthBeijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthBig Data and Engineering Research Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthBeijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthDepartment of Pathology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s HealthAbstract Background A number of genetic aberrations are associated with the BCL6-correpresor gene (BCOR), including internal tandem duplications (ITDs) and gene fusions (BCOR::CCNB3 and BCOR::MAML3), as well as YWHAE::NUTM2, which are found in clear cell sarcoma of the kidney (CCSK), sarcoma with BCOR genetic alterations, primitive myxoid mesenchymal tumor of infancy, and high-grade neuroepithelial tumors in children. Detecting these gene aberrations is crucial for tumor diagnosis. ITDs can be identified by Sanger sequencing or agarose gel electrophoresis. However, gene fusions are usually detected through reverse transcription-polymerase chain reaction (RT-PCR) or fluorescence in situ hybridization. Methods that analyze these variants simultaneously in a sensitive and convenient manner are lacking in clinical practice. Methods This study validated a Universal Fluorescence Multiplex PCR-based assay that assessed BCOR ITDs, BCOR::CCNB3, BCOR::MAML3 and YWHAE::NUTM2 fusions simultaneously. Results The assay achieved a detection threshold of 10 copies for fusion genes and 0.32 ng genomic DNA for BCOR ITDs. The performance of this assay was also tested in a cohort of 43 pediatric tumors (17 undifferentiated small round cell sarcomas, and 26 tumors with a histological diagnosis of CCSK). In total, 20 BCOR ITDs, 4 BCOR::CCNB3 and one YWHAE::NUTM2 were detected. When compared with the final diagnosis, the assay achieved 93% sensitivity and 100% specificity. Conclusions Accordingly, this assay provided an effective and convenient method for detecting BCOR- and YWHAE-related abnormalities in tumors.https://doi.org/10.1186/s13000-025-01604-7BCORITDCCNB3MAML3YWHAEAssay |
| spellingShingle | Meng Zhang Xingfeng Yao Nan Zhang Yongbo Yu Chao Jia Xiaoxing Guan Wenjian Xu Xin Ni Yongli Guo Lejian He Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumors Diagnostic Pathology BCOR ITD CCNB3 MAML3 YWHAE Assay |
| title | Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumors |
| title_full | Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumors |
| title_fullStr | Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumors |
| title_full_unstemmed | Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumors |
| title_short | Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumors |
| title_sort | development optimization and application of a universal fluorescence multiplex pcr based assay to detect bcor genetic alterations in pediatric tumors |
| topic | BCOR ITD CCNB3 MAML3 YWHAE Assay |
| url | https://doi.org/10.1186/s13000-025-01604-7 |
| work_keys_str_mv | AT mengzhang developmentoptimizationandapplicationofauniversalfluorescencemultiplexpcrbasedassaytodetectbcorgeneticalterationsinpediatrictumors AT xingfengyao developmentoptimizationandapplicationofauniversalfluorescencemultiplexpcrbasedassaytodetectbcorgeneticalterationsinpediatrictumors AT nanzhang developmentoptimizationandapplicationofauniversalfluorescencemultiplexpcrbasedassaytodetectbcorgeneticalterationsinpediatrictumors AT yongboyu developmentoptimizationandapplicationofauniversalfluorescencemultiplexpcrbasedassaytodetectbcorgeneticalterationsinpediatrictumors AT chaojia developmentoptimizationandapplicationofauniversalfluorescencemultiplexpcrbasedassaytodetectbcorgeneticalterationsinpediatrictumors AT xiaoxingguan developmentoptimizationandapplicationofauniversalfluorescencemultiplexpcrbasedassaytodetectbcorgeneticalterationsinpediatrictumors AT wenjianxu developmentoptimizationandapplicationofauniversalfluorescencemultiplexpcrbasedassaytodetectbcorgeneticalterationsinpediatrictumors AT xinni developmentoptimizationandapplicationofauniversalfluorescencemultiplexpcrbasedassaytodetectbcorgeneticalterationsinpediatrictumors AT yongliguo developmentoptimizationandapplicationofauniversalfluorescencemultiplexpcrbasedassaytodetectbcorgeneticalterationsinpediatrictumors AT lejianhe developmentoptimizationandapplicationofauniversalfluorescencemultiplexpcrbasedassaytodetectbcorgeneticalterationsinpediatrictumors |