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Nguyen, Van Thien Chi; Nguyen, Trong Hieu; Doan, Nhu Nhat Tan; Pham, Thi Mong Quynh; Nguyen, Giang Thi Huong; Nguyen, Thanh Dat; Tran, Thuy Thi Thu; Vo, Duy Long; Phan, Thanh Hai; Jasmine, Thanh Xuan; Nguyen, Van Chu; Nguyen, Huu Thinh; Nguyen, Trieu Vu; Nguyen, Thi Hue Hanh; Huynh, Le Anh Khoa; Tran, Trung Hieu; Dang, Quang Thong; Doan, Thuy Nguyen; Tran, Anh Minh; Nguyen, Viet Hai; Nguyen, Vu Tuan Anh; Ho, Le Minh Quoc; Tran, Quang Dat; Pham, Thi Thu Thuy; [...]

Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization

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  • Media type: E-Article
  • Title: Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization
  • Contributor: Nguyen, Van Thien Chi; Nguyen, Trong Hieu; Doan, Nhu Nhat Tan; Pham, Thi Mong Quynh; Nguyen, Giang Thi Huong; Nguyen, Thanh Dat; Tran, Thuy Thi Thu; Vo, Duy Long; Phan, Thanh Hai; Jasmine, Thanh Xuan; Nguyen, Van Chu; Nguyen, Huu Thinh; Nguyen, Trieu Vu; Nguyen, Thi Hue Hanh; Huynh, Le Anh Khoa; Tran, Trung Hieu; Dang, Quang Thong; Doan, Thuy Nguyen; Tran, Anh Minh; Nguyen, Viet Hai; Nguyen, Vu Tuan Anh; Ho, Le Minh Quoc; Tran, Quang Dat; Pham, Thi Thu Thuy; [...]
  • imprint: eLife Sciences Publications, Ltd, 2023
  • Published in: eLife
  • Language: English
  • DOI: 10.7554/elife.89083.3
  • ISSN: 2050-084X
  • Origination:
  • Footnote:
  • Description: <jats:p>Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (screening for the presence of tumor by methylation and size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (~0.55×) of cell-free DNA. We applied SPOT-MAS to 738 non-metastatic patients with breast, colorectal, gastric, lung, and liver cancer, and 1550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 73.9% and 62.3% for stages I and II, respectively, increasing to 88.3% for non-metastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening.</jats:p>
  • Access State: Open Access