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Li X, Liu T, Bacchiocchi A, Li M, Cheng W, Wittkop T, Mendez FL, Wang Y, Tang P, Yao Q, Bosenberg MW, Sznol M, Yan Q, Faham M, Weng L, Halaban R, Jin H, Hu Z. Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction. EMBO Mol Med 2024; 16:2188-2209. [PMID: 39164471 PMCID: PMC11393307 DOI: 10.1038/s44321-024-00115-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 08/22/2024] Open
Abstract
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.
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Affiliation(s)
- Xinxing Li
- Department of Gastrointestinal Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, P. R. China
| | - Tao Liu
- Department of Thoracic Surgery, Peking University First Hospital, Beijing, 100034, China
| | | | - Mengxing Li
- Department of Thoracic Surgery, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Wen Cheng
- Department of Thoracic Surgery, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Tobias Wittkop
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA
| | - Fernando L Mendez
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA
| | - Yingyu Wang
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA
| | - Paul Tang
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA
| | - Qianqian Yao
- Department of Medical Science, Shanghai YunSheng Medical Laboratory Co., Ltd, Shanghai, 200437, China
| | - Marcus W Bosenberg
- 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
| | - Mario Sznol
- 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
| | - Qin Yan
- 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
| | - Malek Faham
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA
| | - Li Weng
- Department of Research and Development, AccuraGen Inc, San Jose, CA, 95134, USA.
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
| | - Hai Jin
- Department of Thoracic Surgery, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, 200433, China.
| | - Zhiqian Hu
- Department of Gastrointestinal Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, P. R. China.
- Department of General Surgery, Changzheng Hospital Naval Medical University, Shanghai, 200003, P. R. China.
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2
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Li S, Li W, Liu B, Krysan K, Dubinett SM. Noninvasive Lung Cancer Subtype Classification Using Tumor-Derived Signatures and cfDNA Methylome. CANCER RESEARCH COMMUNICATIONS 2024; 4:1738-1747. [PMID: 38856716 PMCID: PMC11249519 DOI: 10.1158/2767-9764.crc-23-0564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/05/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
Accurate diagnosis of lung cancer is important for treatment decision-making. Tumor biopsy and histologic examination are the standard for determining histologic lung cancer subtypes. Liquid biopsy, particularly cell-free DNA (cfDNA), has recently shown promising results in cancer detection and classification. In this study, we investigate the potential of cfDNA methylome for the noninvasive classification of lung cancer histologic subtypes. We focused on the two most prevalent lung cancer subtypes, lung adenocarcinoma and lung squamous cell carcinoma. Using a fragment-based marker discovery approach, we identified robust subtype-specific methylation markers from tumor samples. These markers were successfully validated in independent cohorts and associated with subtype-specific transcriptional activity. Leveraging these markers, we constructed a subtype classification model using cfDNA methylation profiles, achieving an AUC of 0.808 in cross-validation and an AUC of 0.747 in the independent validation. Tumor copy-number alterations inferred from cfDNA methylome analysis revealed potential for treatment selection. In summary, our study demonstrates the potential of cfDNA methylome analysis for noninvasive lung cancer subtyping, offering insights for cancer monitoring and early detection. SIGNIFICANCE This study explores the use of cfDNA methylomes for the classification of lung cancer subtypes, vital for effective treatment. By identifying specific methylation markers in tumor tissues, we developed a robust classification model achieving high accuracy for noninvasive subtype detection. This cfDNA methylome approach offers promising avenues for early detection and monitoring.
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Affiliation(s)
- Shuo Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.
| | - Wenyuan Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.
| | - Bin Liu
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, California.
| | - Kostyantyn Krysan
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, California.
- VA Greater Los Angeles Health Care System, Los Angeles, California.
| | - Steven M. Dubinett
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.
- Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, California.
- VA Greater Los Angeles Health Care System, Los Angeles, California.
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.
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3
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Li X, Liu T, Bacchiocchi A, Li M, Cheng W, Wittkop T, Mendez F, Wang Y, Tang P, Yao Q, Bosenberg MW, Sznol M, Yan Q, Faham M, Weng L, Halaban R, Jin H, Hu Z. Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.13.24301070. [PMID: 38260271 PMCID: PMC10802755 DOI: 10.1101/2024.01.13.24301070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
While whole genome sequencing (WGS) of cell-free DNA (cfDNA) holds enormous promise for molecular residual disease (MRD) detection, 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. When applied to MRD detection, AccuScan demonstrated analytical sensitivity down to 10 -6 circulating tumor allele fraction at 99% sample level specificity. In colorectal cancer, AccuScan showed 90% landmark sensitivity for predicting relapse. It also showed robust MRD performance with esophageal cancer using samples collected as early as 1 week after surgery, and predictive value for immunotherapy monitoring with melanoma patients. Overall, AccuScan provides a highly accurate WGS solution for MRD, empowering circulating tumor DNA detection at parts per million range without high sample input nor personalized reagents. One Sentence Summary AccuScan showed remarkable ultra-low limit of detection with a short turnaround time, low sample requirement and a simple workflow for MRD detection.
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Li S, Zeng W, Ni X, Liu Q, Li W, Stackpole ML, Zhou Y, Gower A, Krysan K, Ahuja P, Lu DS, Raman SS, Hsu W, Aberle DR, Magyar CE, French SW, Han SHB, Garon EB, Agopian VG, Wong WH, Dubinett SM, Zhou XJ. Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring. Proc Natl Acad Sci U S A 2023; 120:e2305236120. [PMID: 37399400 PMCID: PMC10334733 DOI: 10.1073/pnas.2305236120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/16/2023] [Indexed: 07/05/2023] Open
Abstract
Plasma cell-free DNA (cfDNA) is a noninvasive biomarker for cell death of all organs. Deciphering the tissue origin of cfDNA can reveal abnormal cell death because of diseases, which has great clinical potential in disease detection and monitoring. Despite the great promise, the sensitive and accurate quantification of tissue-derived cfDNA remains challenging to existing methods due to the limited characterization of tissue methylation and the reliance on unsupervised methods. To fully exploit the clinical potential of tissue-derived cfDNA, here we present one of the largest comprehensive and high-resolution methylation atlas based on 521 noncancer tissue samples spanning 29 major types of human tissues. We systematically identified fragment-level tissue-specific methylation patterns and extensively validated them in orthogonal datasets. Based on the rich tissue methylation atlas, we develop the first supervised tissue deconvolution approach, a deep-learning-powered model, cfSort, for sensitive and accurate tissue deconvolution in cfDNA. On the benchmarking data, cfSort showed superior sensitivity and accuracy compared to the existing methods. We further demonstrated the clinical utilities of cfSort with two potential applications: aiding disease diagnosis and monitoring treatment side effects. The tissue-derived cfDNA fraction estimated from cfSort reflected the clinical outcomes of the patients. In summary, the tissue methylation atlas and cfSort enhanced the performance of tissue deconvolution in cfDNA, thus facilitating cfDNA-based disease detection and longitudinal treatment monitoring.
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Affiliation(s)
- Shuo Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
| | - Weihua Zeng
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
| | - Xiaohui Ni
- EarlyDiagnostics Inc., Los Angeles, CA90095
| | - Qiao Liu
- Department of Statistics, Stanford University, Stanford, CA94305
| | - Wenyuan Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
- Institute for Quantitative & Computational Biosciences, University of California at Los Angeles, Los Angeles, CA90095
| | - Mary L. Stackpole
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
- EarlyDiagnostics Inc., Los Angeles, CA90095
| | - Yonggang Zhou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
| | - Arjan Gower
- Department of Medicine, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA90095
| | - Kostyantyn Krysan
- Department of Medicine, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA90095
- Veterans Administration (VA) Greater Los Angeles Health Care System, Los Angeles, CA90073
| | - Preeti Ahuja
- Department of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
| | - David S. Lu
- Department of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA90095
| | - Steven S. Raman
- Department of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA90095
- Department of Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA90095
| | - William Hsu
- Department of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA90095
| | - Denise R. Aberle
- Department of Radiological Sciences, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
- Department of Bioengineering, University of California, Los Angeles, CA90095
| | - Clara E. Magyar
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA90095
| | - Samuel W. French
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA90095
| | - Steven-Huy B. Han
- Department of Medicine, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA90095
| | - Edward B. Garon
- Department of Medicine, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA90095
| | - Vatche G. Agopian
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA90095
- Department of Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA90095
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA94305
- Department of Biomedical Data Science, Stanford University, Stanford, CA94305
| | - Steven M. Dubinett
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
- Department of Medicine, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA90095
- Veterans Administration (VA) Greater Los Angeles Health Care System, Los Angeles, CA90073
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA90095
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA90095
| | - Xianghong Jasmine Zhou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA90095
- Institute for Quantitative & Computational Biosciences, University of California at Los Angeles, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA90095
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Li S, Hu R, Small C, Kang TY, Liu CC, Zhou XJ, Li W. cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA. Nat Protoc 2023; 18:1563-1583. [PMID: 36849599 PMCID: PMC10411976 DOI: 10.1038/s41596-023-00807-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/24/2022] [Indexed: 03/01/2023]
Abstract
Cell-free DNA (cfDNA) in blood, viewed as a surrogate for tumor biopsy, has many clinical applications, including diagnosing cancer, guiding cancer treatment and monitoring treatment response. All these applications depend on an indispensable, yet underdeveloped task: detecting somatic mutations from cfDNA. The task is challenging because of the low tumor fraction in cfDNA. Recently, we developed the computational method cfSNV, the first method that comprehensively considers the properties of cfDNA for the sensitive detection of mutations from cfDNA. cfSNV vastly outperformed the conventional methods that were developed primarily for calling mutations from solid tumor tissues. cfSNV can accurately detect mutations in cfDNA even with medium-coverage (e.g., ≥200×) sequencing, which makes whole-exome sequencing (WES) of cfDNA a viable option for various clinical utilities. Here, we present a user-friendly cfSNV package that exhibits fast computation and convenient user options. We also built a Docker image of it, which is designed to enable researchers and clinicians with a limited computational background to easily carry out analyses on both high-performance computing platforms and local computers. Mutation calling from a standard preprocessed WES dataset (~250× and ~70 million base pair target size) can be carried out in 3 h on a server with eight virtual CPUs and 32 GB of random access memory.
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Affiliation(s)
- Shuo Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ran Hu
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Graduate Program, University of California at Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative & Computational Biosciences, University of California at Los Angeles, Los Angeles, CA, USA
| | - Colin Small
- Institute for Quantitative & Computational Biosciences, University of California at Los Angeles, Los Angeles, CA, USA
| | | | - Chun-Chi Liu
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
- EarlyDiagnostics Inc., Los Angeles, CA, USA
| | - Xianghong Jasmine Zhou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.
- Institute for Quantitative & Computational Biosciences, University of California at Los Angeles, Los Angeles, CA, USA.
- EarlyDiagnostics Inc., Los Angeles, CA, USA.
| | - Wenyuan Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.
- EarlyDiagnostics Inc., Los Angeles, CA, USA.
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6
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Akhoundova D, Rubin MA. Clinical application of advanced multi-omics tumor profiling: Shaping precision oncology of the future. Cancer Cell 2022; 40:920-938. [PMID: 36055231 DOI: 10.1016/j.ccell.2022.08.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/22/2022] [Accepted: 08/11/2022] [Indexed: 12/17/2022]
Abstract
Next-generation DNA sequencing technology has dramatically advanced clinical oncology through the identification of therapeutic targets and molecular biomarkers, leading to the personalization of cancer treatment with significantly improved outcomes for many common and rare tumor entities. More recent developments in advanced tumor profiling now enable dissection of tumor molecular architecture and the functional phenotype at cellular and subcellular resolution. Clinical translation of high-resolution tumor profiling and integration of multi-omics data into precision treatment, however, pose significant challenges at the level of prospective validation and clinical implementation. In this review, we summarize the latest advances in multi-omics tumor profiling, focusing on spatial genomics and chromatin organization, spatial transcriptomics and proteomics, liquid biopsy, and ex vivo modeling of drug response. We analyze the current stages of translational validation of these technologies and discuss future perspectives for their integration into precision treatment.
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Affiliation(s)
- Dilara Akhoundova
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Department of Medical Oncology, Inselspital, University Hospital of Bern, 3010 Bern, Switzerland
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, 3008 Bern, Switzerland.
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