Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing

Hu, Taobo; Li, Jingjing; Long, Mengping; Wu, Jia‐Zhu; Zhang, Zhen; Xie, Fei; Zhao, Jin; Yang, Houpu; Song, Qianqian; Lian, Sheng; Shi, Jiandong; Guo, Xueyu; Ding, Yuan Chun; Lang, Dandan; Yu, Guoliang; Liang, Baosheng; Zhou, Xiao‐Hua; Ishibashi, Toyotaka; Fan, Xiaodan; Yu, Weichuan; Wang, Depeng; Wang, Yan; Peng, I-Feng; Wang, Shu

doi:10.3389/fcell.2022.854640

Cited by 12 publications

(7 citation statements)

References 38 publications

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“…In addiKon to two-segment fusions that are frequently observed, three-segment fusion were discovered in the previous research 63 , while majority of the predicted three-segment fusions may result from arKficial chimera events or mis-alignment. To test the ability of three-segment fusion discovery, Table 1 lists 12 fusion transcripts detected from MCF7 and H838 by JAFFAL 27 .…”

Section: Two-segment and Three-segment Fusion Detec9on In Real Data A...mentioning

confidence: 84%

IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data

Wang,

Li,

et al. 2024

Preprint

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Advancements in long-read transcriptome sequencing (long-RNA-seq) technology have revolutionized the study of isoform diversity. These full-length transcripts enhance the detection of various transcriptome structural variations, including novel isoforms, alternative splicing events, and fusion transcripts. By shifting the open reading frame or altering gene expressions, studies have proved that these transcript alterations can serve as crucial biomarkers for disease diagnosis and therapeutic targets. In this project, we proposed IFDlong, a bioinformatics and biostatistics tool to detect isoform and fusion transcripts using bulk or single-cell long-RNA-seq data. Specifically, the software performed gene and isoform annotation for each long-read, defined novel isoforms, quantified isoform expression by a novel expectation-maximization algorithm, and profiled the fusion transcripts. For evaluation, IFDlong pipeline achieved overall the best performance when compared with several existing tools in large-scale simulation studies. In both isoform and fusion transcript quantification, IFDlong is able to reach more than 0.8 Spearman correlation with the truth, and more than 0.9 cosine similarity when distinguishing multiple alternative splicing events. In novel isoform simulation, IFDlong can successfully balance the sensitivity (higher than 90%) and specificity (higher than 90%). Furthermore, IFDlong has proved its accuracy and robustness in diverse in-house and public datasets on healthy tissues, cell lines and multiple types of diseases. Besides bulk long-RNA-seq, IFDlong pipeline has proved its compatibility to single-cell long-RNA-seq data. This new software may hold promise for significant impact on long-read transcriptome analysis. The IFDlong software is available at https://github.com/wenjiaking/IFDlong.

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Section: Two-segment and Three-segment Fusion Detec9on In Real Data A...mentioning

confidence: 84%

IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data

Wang,

Li,

et al. 2024

Preprint

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“…PacBio sequencing detected five to ten times more fusion transcripts than Illumina, the majority of which were novel [78]. More recently, structural variants and fusion genes were detected in breast cancer samples through long-read genomic and transcriptomic sequencing via the ONT and PacBio platforms [79]. The utilisation of Pacbio full-length transcriptome sequencing in breast cancer cell lines revealed the presence of various new gene fusions within nested genomic variants [57].…”

Section: Full-length Transcriptome Of Cancer Cellsmentioning

confidence: 99%

The Application of Long-Read Sequencing to Cancer

Ermini,

Driguez

2024

Cancers

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Cancer is a multifaceted disease arising from numerous genomic aberrations that have been identified as a result of advancements in sequencing technologies. While next-generation sequencing (NGS), which uses short reads, has transformed cancer research and diagnostics, it is limited by read length. Third-generation sequencing (TGS), led by the Pacific Biosciences and Oxford Nanopore Technologies platforms, employs long-read sequences, which have marked a paradigm shift in cancer research. Cancer genomes often harbour complex events, and TGS, with its ability to span large genomic regions, has facilitated their characterisation, providing a better understanding of how complex rearrangements affect cancer initiation and progression. TGS has also characterised the entire transcriptome of various cancers, revealing cancer-associated isoforms that could serve as biomarkers or therapeutic targets. Furthermore, TGS has advanced cancer research by improving genome assemblies, detecting complex variants, and providing a more complete picture of transcriptomes and epigenomes. This review focuses on TGS and its growing role in cancer research. We investigate its advantages and limitations, providing a rigorous scientific analysis of its use in detecting previously hidden aberrations missed by NGS. This promising technology holds immense potential for both research and clinical applications, with far-reaching implications for cancer diagnosis and treatment.

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“…Firstly, it efficiently conducts comprehensive sequencing of the livestock genome, providing a holistic genomic dataset that facilitates the discovery of genetic variations and the elucidation of gene functions [7]. Secondly, through long-read sequencing, TGS can more accurately detect structural variations within the genome, including insertions, deletions, and inversions, thereby offering more precise genomic information for the study of relevant traits [8]. Moreover, this technology proves advantageous in the superior assembly of complex genomes, particularly those in livestock characterized by highly repetitive sequences and chromosomal structures with intricate features [9].…”

Section: Advances Of Tgs In the Genomic Research Of Livestockmentioning

confidence: 99%

When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications

Liu,

Zheng,

Ding

et al. 2024

Genes

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Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing

Cited by 12 publications

References 38 publications

IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data

IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data

The Application of Long-Read Sequencing to Cancer

When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications

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