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Background <p>The detection of <i>BRAF</i> fusions by using next-generation sequencing (NGS) is essential for comprehensive analysis.</p> Methods <p>Data <i>BRAF</i> positive rearrangements from Chinese cancer patients were analyzed. DNA NGS was performed on FFPE samples, and RNA NGS was used to confirm fusion transcripts.</p> Results <p><i>BRAF</i> fusions were identified in various cancers, predominantly glioma (87.8%). DNA NGS detected 371 <i>BRAF</i> fusion-positive samples, with 338 retaining the serine/threonine receptor tyrosine kinase domain (RTKD), divided into four groups: common (<i>n</i> = 254), rare (<i>n</i> = 66), intergenic (<i>n</i> = 7), and exonic (<i>n</i> = 11) fusions. Common fusions, mainly <i>KIAA1549-BRAF</i>, comprised the majority, with variations at introns 8, 9, and 10. Rare fusions and intergenic/exonic breakpoints displayed diverse structural patterns. RNA NGS verified transcriptional consistency in most samples from common fusions. However, various outcomes at the RNA level were found in other groups, involving mechanisms like alternative splicing, antisense rearrangement, and frameshift rearrangement. Additionally, 33 fusions lacked the RTKD, demonstrating significant structural diversity. Furthermore, 22 novel fusions were identified, which were distributed in tongue cancer, liver cancer, lung cancer, melanoma, brain cancer, and colon cancer.</p> Conclusions <p>Comprehensive molecular profiling and RNA sequencing are essential for accurate fusion detection, improving the design of NGS panels and aiding in the targeted therapy of <i>BRAF</i> fusion-positive cancers.</p>

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Unveiling the BRAF fusion structure variations through DNA and RNA sequencing

  • 期刊论文

  • 发表日期：

    2025年4月19日

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  • Qiong Yang,
  • Baoming Wang,
  • Xuli Meng,
  • Tonghui Ma,
  • Zhenyuan Qian,
  • Xufan Cai,
  • Xiaochen Sun,
  • Yan Xu,
  • Qifeng Luo,
  • Tianyao Yang,
  • Houquan Tao,
  • Yangyang Qian,
  • Jianzhong Shao,
  • Zaiyuan Ye

摘要

Background

The detection of BRAF fusions by using next-generation sequencing (NGS) is essential for comprehensive analysis.

Methods

Data BRAF positive rearrangements from Chinese cancer patients were analyzed. DNA NGS was performed on FFPE samples, and RNA NGS was used to confirm fusion transcripts.

Results

BRAF fusions were identified in various cancers, predominantly glioma (87.8%). DNA NGS detected 371 BRAF fusion-positive samples, with 338 retaining the serine/threonine receptor tyrosine kinase domain (RTKD), divided into four groups: common (n = 254), rare (n = 66), intergenic (n = 7), and exonic (n = 11) fusions. Common fusions, mainly KIAA1549-BRAF, comprised the majority, with variations at introns 8, 9, and 10. Rare fusions and intergenic/exonic breakpoints displayed diverse structural patterns. RNA NGS verified transcriptional consistency in most samples from common fusions. However, various outcomes at the RNA level were found in other groups, involving mechanisms like alternative splicing, antisense rearrangement, and frameshift rearrangement. Additionally, 33 fusions lacked the RTKD, demonstrating significant structural diversity. Furthermore, 22 novel fusions were identified, which were distributed in tongue cancer, liver cancer, lung cancer, melanoma, brain cancer, and colon cancer.

Conclusions

Comprehensive molecular profiling and RNA sequencing are essential for accurate fusion detection, improving the design of NGS panels and aiding in the targeted therapy of BRAF fusion-positive cancers.