دورية أكاديمية
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Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction.

التفاصيل البيبلوغرافية
العنوان: Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction.
المؤلفون: Li X; Department of Gastrointestinal Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, P. R. China., Liu T; Department of Thoracic Surgery, Peking University First Hospital, Beijing, 100034, China., Bacchiocchi A; Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA., Li M; Department of Thoracic Surgery, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China., Cheng W; Department of Thoracic Surgery, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China., Wittkop T; Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA., Mendez FL; Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA., Wang Y; Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA., Tang P; Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA., Yao Q; Department of Medical Science, Shanghai YunSheng Medical Laboratory Co., Ltd, Shanghai, 200437, China., Bosenberg MW; Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA.; Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.; Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, USA., Sznol M; Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.; Department of Internal Medicine, Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA., Yan Q; Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.; Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, USA.; Department of Pathology, Yale University, New Haven, CT, USA., Faham M; Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA., Weng L; Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA. lweng@accuragen.com., Halaban R; Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA. ruth.halaban@yale.edu.; Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA. ruth.halaban@yale.edu., Jin H; Department of Thoracic Surgery, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China. jinhai@smmu.edu.cn., Hu Z; Department of Gastrointestinal Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, P. R. China. 2105203@tongji.edu.cn.; Department of General Surgery, Changzheng Hospital Naval Medical University, Shanghai, 200003, P. R. China. 2105203@tongji.edu.cn.
المصدر: EMBO molecular medicine [EMBO Mol Med] 2024 Sep; Vol. 16 (9), pp. 2188-2209. Date of Electronic Publication: 2024 Aug 20.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Wiley-Blackwell Country of Publication: Germany NLM ID: 101487380 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1757-4684 (Electronic) Linking ISSN: 17574676 NLM ISO Abbreviation: EMBO Mol Med Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Chichester, West Sussex : Wiley-Blackwell
مواضيع طبية MeSH: Neoplasm, Residual*/diagnosis , Neoplasm, Residual*/genetics , Whole Genome Sequencing*/methods , Circulating Tumor DNA*/genetics , Circulating Tumor DNA*/blood, Humans ; Sensitivity and Specificity ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/diagnosis ; Melanoma/genetics ; Melanoma/diagnosis ; Esophageal Neoplasms/genetics ; Esophageal Neoplasms/diagnosis
مستخلص: While whole genome sequencing (WGS) of cell-free DNA (cfDNA) holds enormous promise for detection of molecular residual disease (MRD), its performance is limited by WGS error rate. Here we introduce AccuScan, an efficient cfDNA WGS technology that enables genome-wide error correction at single read-level, achieving an error rate of 4.2 × 10 -7 , which is about two orders of magnitude lower than a read-centric de-noising method. The application of AccuScan to MRD demonstrated analytical sensitivity down to 10 -6 circulating variant allele frequency at 99% sample-level specificity. AccuScan showed 90% landmark sensitivity (within 6 weeks after surgery) and 100% specificity for predicting relapse in colorectal cancer. It also showed 67% sensitivity and 100% specificity in esophageal cancer using samples collected within one week after surgery. When AccuScan was applied to monitor immunotherapy in melanoma patients, the circulating tumor DNA (ctDNA) levels and dynamic profiles were consistent with clinical outcomes. Overall, AccuScan provides a highly accurate WGS solution for MRD detection, empowering ctDNA detection at parts per million range without requiring high sample input or personalized reagents.
(© 2024. The Author(s).)
التعليقات: Update of: medRxiv. 2024 Jan 22:2024.01.13.24301070. doi: 10.1101/2024.01.13.24301070. (PMID: 38260271)
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معلومات مُعتمدة: ITJ(ZD)2104 Tongji Hospital (TJH); 2021 Tongji Hospital (TJH); P50 CA121974 United States CA NCI NIH HHS; 21ZR1458200 Shanghai Natural Science Foundation; NCI P50CA121974 HHS | National Institutes of Health (NIH)
فهرسة مساهمة: Keywords: Circulating Tumor DNA; Molecular Residual Disease; Single-read Error Correction; White Blood Cell-free; Whole Genome Sequencing
المشرفين على المادة: 0 (Circulating Tumor DNA)
تواريخ الأحداث: Date Created: 20240820 Date Completed: 20240912 Latest Revision: 20240925
رمز التحديث: 20240926
مُعرف محوري في PubMed: PMC11393307
DOI: 10.1038/s44321-024-00115-0
PMID: 39164471
قاعدة البيانات: MEDLINE
الوصف
تدمد:1757-4684
DOI:10.1038/s44321-024-00115-0