Genomic landscape and comparative analysis of tissue and liquid-based NGS in Taiwanese anaplastic thyroid carcinoma
Abstract Anaplastic thyroid carcinoma (ATC) is an aggressive cancer that requirements rapid diagnosis and multimodal treatment. Next-generation sequencing (NGS) aids in personalized therapies and improved trial enrollment. The role of liquid-based NGS in ATC remains unclear. This study analyzed ATC...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | npj Precision Oncology |
| Online Access: | https://doi.org/10.1038/s41698-025-00802-2 |
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| author | Chun-Nan Yeh Shu-Fu Lin Chia-Ling Wu Miaw-Jene Liou I-Wen Chen Chiao-Ping Chen Ching-Fu Chang Qi‑An Wang Chiao-En Wu |
| author_facet | Chun-Nan Yeh Shu-Fu Lin Chia-Ling Wu Miaw-Jene Liou I-Wen Chen Chiao-Ping Chen Ching-Fu Chang Qi‑An Wang Chiao-En Wu |
| author_sort | Chun-Nan Yeh |
| collection | DOAJ |
| description | Abstract Anaplastic thyroid carcinoma (ATC) is an aggressive cancer that requirements rapid diagnosis and multimodal treatment. Next-generation sequencing (NGS) aids in personalized therapies and improved trial enrollment. The role of liquid-based NGS in ATC remains unclear. This study analyzed ATC samples using tissue-based NGS, liquid-based NGS, or both platforms. Genetic alterations showed highly heterogeneity, including mutations in RAS/RAF/MEK/ERK, PI3K/AKT/mTOR, cell cycle regulation, other receptor tyrosine kinases, DNA damage response, mismatch repair, and chromatin remodeling. TP53 (65.4%) and BRAF (30.8%) were the most frequently mutated genes in tissue NGS. In paired samples, the concordance rates were 69.2% for TP53 and 84.6% for BRAF. One of two patients treated with dabrafenib and trametinib showed a copy number gain in post-treatment tissue NGS, potentially indicating resistance. Liquid biopsy provides valuable supplementary information when tissue samples are insufficient. Further studies are necessary to understand resistance mechanisms and develop strategies to overcome them in BRAF-targeted therapy. |
| format | Article |
| id | doaj-art-4509dbf9e6554e44b223a9c485cce5ba |
| institution | Kabale University |
| issn | 2397-768X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Precision Oncology |
| spelling | doaj-art-4509dbf9e6554e44b223a9c485cce5ba2025-01-19T12:08:14ZengNature Portfolionpj Precision Oncology2397-768X2025-01-01911910.1038/s41698-025-00802-2Genomic landscape and comparative analysis of tissue and liquid-based NGS in Taiwanese anaplastic thyroid carcinomaChun-Nan Yeh0Shu-Fu Lin1Chia-Ling Wu2Miaw-Jene Liou3I-Wen Chen4Chiao-Ping Chen5Ching-Fu Chang6Qi‑An Wang7Chiao-En Wu8Department of Surgery, Chang Gung Memorial Hospital at LinkouCollege of Medicine, Chang Gung UniversityACT Genomics Co. Ltd.College of Medicine, Chang Gung UniversityCollege of Medicine, Chang Gung UniversityCollege of Medicine, Chang Gung UniversityCollege of Medicine, Chang Gung UniversityCollege of Medicine, Chang Gung UniversityCollege of Medicine, Chang Gung UniversityAbstract Anaplastic thyroid carcinoma (ATC) is an aggressive cancer that requirements rapid diagnosis and multimodal treatment. Next-generation sequencing (NGS) aids in personalized therapies and improved trial enrollment. The role of liquid-based NGS in ATC remains unclear. This study analyzed ATC samples using tissue-based NGS, liquid-based NGS, or both platforms. Genetic alterations showed highly heterogeneity, including mutations in RAS/RAF/MEK/ERK, PI3K/AKT/mTOR, cell cycle regulation, other receptor tyrosine kinases, DNA damage response, mismatch repair, and chromatin remodeling. TP53 (65.4%) and BRAF (30.8%) were the most frequently mutated genes in tissue NGS. In paired samples, the concordance rates were 69.2% for TP53 and 84.6% for BRAF. One of two patients treated with dabrafenib and trametinib showed a copy number gain in post-treatment tissue NGS, potentially indicating resistance. Liquid biopsy provides valuable supplementary information when tissue samples are insufficient. Further studies are necessary to understand resistance mechanisms and develop strategies to overcome them in BRAF-targeted therapy.https://doi.org/10.1038/s41698-025-00802-2 |
| spellingShingle | Chun-Nan Yeh Shu-Fu Lin Chia-Ling Wu Miaw-Jene Liou I-Wen Chen Chiao-Ping Chen Ching-Fu Chang Qi‑An Wang Chiao-En Wu Genomic landscape and comparative analysis of tissue and liquid-based NGS in Taiwanese anaplastic thyroid carcinoma npj Precision Oncology |
| title | Genomic landscape and comparative analysis of tissue and liquid-based NGS in Taiwanese anaplastic thyroid carcinoma |
| title_full | Genomic landscape and comparative analysis of tissue and liquid-based NGS in Taiwanese anaplastic thyroid carcinoma |
| title_fullStr | Genomic landscape and comparative analysis of tissue and liquid-based NGS in Taiwanese anaplastic thyroid carcinoma |
| title_full_unstemmed | Genomic landscape and comparative analysis of tissue and liquid-based NGS in Taiwanese anaplastic thyroid carcinoma |
| title_short | Genomic landscape and comparative analysis of tissue and liquid-based NGS in Taiwanese anaplastic thyroid carcinoma |
| title_sort | genomic landscape and comparative analysis of tissue and liquid based ngs in taiwanese anaplastic thyroid carcinoma |
| url | https://doi.org/10.1038/s41698-025-00802-2 |
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