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Hu T, Li J, Long M, Wu J, Zhang Z, Xie F, Zhao J, Yang H, Song Q, Lian S, Shi J, Guo X, Yuan D, Lang D, Yu G, Liang B, Zhou X, Ishibashi T, Fan X, Yu W, Wang D, Wang Y, Peng IF, Wang S. Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing. Front Cell Dev Biol 2022; 10:854640. [PMID: 35493102 PMCID: PMC9043247 DOI: 10.3389/fcell.2022.854640] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/23/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Structural variations (SVs) are common genetic alterations in the human genome that could cause different phenotypes and diseases, including cancer. However, the detection of structural variations using the second-generation sequencing was limited by its short read length, which restrained our understanding of structural variations. Methods: In this study, we developed a 28-gene panel for long-read sequencing and employed it to Oxford Nanopore Technologies and Pacific Biosciences platforms. We analyzed structural variations in the 28 breast cancer-related genes through long-read genomic and transcriptomic sequencing of tumor, para-tumor, and blood samples in 19 breast cancer patients. Results: Our results showed that some somatic SVs were recurring among the selected genes, though the majority of them occurred in the non-exonic region. We found evidence supporting the existence of hotspot regions for SVs, which extended our previous understanding that they exist only for single nucleotide variations. Conclusion: In conclusion, we employed long-read genomic and transcriptomic sequencing to identify SVs from breast cancer patients and proved that this approach holds great potential in clinical application.
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Affiliation(s)
- Taobo Hu
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- GrandOmics Inc., Beijing, China
| | - Mengping Long
- Department of Pathology, Peking University Cancer Hospital, Beijing, China
| | - Jinbo Wu
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
| | - Zhen Zhang
- Department of Statistics, The Chinese University of Hong Kong, Sha Tin, China
| | - Fei Xie
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
| | - Jin Zhao
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
| | - Houpu Yang
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
| | - Qianqian Song
- Department of Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Sheng Lian
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Jiandong Shi
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | | | | | | | | | - Baosheng Liang
- Department of Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xiaohua Zhou
- Department of Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Xiaodan Fan
- Department of Statistics, The Chinese University of Hong Kong, Sha Tin, China
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | | | - Yang Wang
- GrandOmics Inc., Beijing, China
- *Correspondence: Yang Wang, ; I-Feng Peng, ; Shu Wang,
| | - I-Feng Peng
- GrandOmics Inc., Beijing, China
- *Correspondence: Yang Wang, ; I-Feng Peng, ; Shu Wang,
| | - Shu Wang
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
- *Correspondence: Yang Wang, ; I-Feng Peng, ; Shu Wang,
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