A multiomics dataset of paired CT image and plasma cell-free DNA end motif for patients with pulmonary nodules
Abstract Diagnosing lung cancer at a curable stage offers the opportunity for a favorable prognosis. The emerging epigenomics analysis on plasma cell-free DNA (cfDNA), including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications, has acted as a promising approach facilitating th...
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Nature Portfolio
2025-04-01
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| Online Access: | https://doi.org/10.1038/s41597-025-04912-1 |
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| author | Mengmeng Zhao Gang Xue Bingxi He Jiajun Deng Tingting Wang Yifan Zhong Shenghui Li Yang Wang Yiming He Tao Chen Jun Zhang Ziyue Yan Xinlei Hu Liuning Guo Wendong Qu Yongxiang Song Minglei Yang Guofang Zhao Bentong Yu Minjie Ma Lunxu Liu Xiwen Sun Deping Zhao Dan Xie Chang Chen Yunlang She |
| author_facet | Mengmeng Zhao Gang Xue Bingxi He Jiajun Deng Tingting Wang Yifan Zhong Shenghui Li Yang Wang Yiming He Tao Chen Jun Zhang Ziyue Yan Xinlei Hu Liuning Guo Wendong Qu Yongxiang Song Minglei Yang Guofang Zhao Bentong Yu Minjie Ma Lunxu Liu Xiwen Sun Deping Zhao Dan Xie Chang Chen Yunlang She |
| author_sort | Mengmeng Zhao |
| collection | DOAJ |
| description | Abstract Diagnosing lung cancer at a curable stage offers the opportunity for a favorable prognosis. The emerging epigenomics analysis on plasma cell-free DNA (cfDNA), including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications, has acted as a promising approach facilitating the identification of lung cancer. And, integrating 5mC biomarker with chest computed tomography (CT) image features could optimize the diagnosis of lung cancer, exceeding the performance of models built on single feature. However, the clinical applicability of integrated markers might be limited by the potential risk of overfitting due to small sample size. Hence, we prospectively collected peripheral blood sample and the paired chest CT images of 2032 patients with indeterminate pulmonary nodules across 5 centers, and constructed a large-scale, multi-institutional, multiomics database that encompass CT imaging data and plasma cfDNA fragmentomic in 5mC-, 5hmC-enriched regions. To our best knowledge, this dataset is the first radio-epigenomic dataset with the largest sample size, and provides multi-dimensional insights for early diagnosis of lung cancer, facilitating the individuated management for lung cancer. |
| format | Article |
| id | doaj-art-752e4a16f78443ffa070b985ff280a51 |
| institution | DOAJ |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-752e4a16f78443ffa070b985ff280a512025-08-20T03:04:58ZengNature PortfolioScientific Data2052-44632025-04-011211810.1038/s41597-025-04912-1A multiomics dataset of paired CT image and plasma cell-free DNA end motif for patients with pulmonary nodulesMengmeng Zhao0Gang Xue1Bingxi He2Jiajun Deng3Tingting Wang4Yifan Zhong5Shenghui Li6Yang Wang7Yiming He8Tao Chen9Jun Zhang10Ziyue Yan11Xinlei Hu12Liuning Guo13Wendong Qu14Yongxiang Song15Minglei Yang16Guofang Zhao17Bentong Yu18Minjie Ma19Lunxu Liu20Xiwen Sun21Deping Zhao22Dan Xie23Chang Chen24Yunlang She25Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of MedicineLaboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityBeijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang UniversityDepartment of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of MedicineDepartment of Radiology, Zhongshan Hospital, Fudan UniversityDepartment of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of MedicineDepartment of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of MedicineDepartment of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of MedicineDepartment of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of MedicineDepartment of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of MedicineTailai Inc.Tailai Inc.Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityDepartment of Thoracic Surgery, Affiliated Hospital of Zunyi Medical College, Zunyi Medical CollegeDepartment of Thoracic Surgery, Affiliated Hospital of Zunyi Medical College, Zunyi Medical CollegeDepartment of Thoracic Surgery, Affiliated Hospital of Zunyi Medical College, Zunyi Medical CollegeDepartment of Thoracic Surgery, Ningbo No.2 HospitalDepartment of Thoracic Surgery, Ningbo No.2 HospitalDepartment of Thoracic Surgery, The First Affiliated Hospital of Nanchang UniversityDepartment of Thoracic Surgery, The First Hospital of Lanzhou UniversityInstitute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan UniversityDepartment of Radiology, Shanghai Pulmonary Hospital, Tongji University School of MedicineDepartment of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of MedicineLaboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan UniversityDepartment of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of MedicineDepartment of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of MedicineAbstract Diagnosing lung cancer at a curable stage offers the opportunity for a favorable prognosis. The emerging epigenomics analysis on plasma cell-free DNA (cfDNA), including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications, has acted as a promising approach facilitating the identification of lung cancer. And, integrating 5mC biomarker with chest computed tomography (CT) image features could optimize the diagnosis of lung cancer, exceeding the performance of models built on single feature. However, the clinical applicability of integrated markers might be limited by the potential risk of overfitting due to small sample size. Hence, we prospectively collected peripheral blood sample and the paired chest CT images of 2032 patients with indeterminate pulmonary nodules across 5 centers, and constructed a large-scale, multi-institutional, multiomics database that encompass CT imaging data and plasma cfDNA fragmentomic in 5mC-, 5hmC-enriched regions. To our best knowledge, this dataset is the first radio-epigenomic dataset with the largest sample size, and provides multi-dimensional insights for early diagnosis of lung cancer, facilitating the individuated management for lung cancer.https://doi.org/10.1038/s41597-025-04912-1 |
| spellingShingle | Mengmeng Zhao Gang Xue Bingxi He Jiajun Deng Tingting Wang Yifan Zhong Shenghui Li Yang Wang Yiming He Tao Chen Jun Zhang Ziyue Yan Xinlei Hu Liuning Guo Wendong Qu Yongxiang Song Minglei Yang Guofang Zhao Bentong Yu Minjie Ma Lunxu Liu Xiwen Sun Deping Zhao Dan Xie Chang Chen Yunlang She A multiomics dataset of paired CT image and plasma cell-free DNA end motif for patients with pulmonary nodules Scientific Data |
| title | A multiomics dataset of paired CT image and plasma cell-free DNA end motif for patients with pulmonary nodules |
| title_full | A multiomics dataset of paired CT image and plasma cell-free DNA end motif for patients with pulmonary nodules |
| title_fullStr | A multiomics dataset of paired CT image and plasma cell-free DNA end motif for patients with pulmonary nodules |
| title_full_unstemmed | A multiomics dataset of paired CT image and plasma cell-free DNA end motif for patients with pulmonary nodules |
| title_short | A multiomics dataset of paired CT image and plasma cell-free DNA end motif for patients with pulmonary nodules |
| title_sort | multiomics dataset of paired ct image and plasma cell free dna end motif for patients with pulmonary nodules |
| url | https://doi.org/10.1038/s41597-025-04912-1 |
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