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Wang D, Wang SJ, Lababidi S. The impact of misclassification errors on the performance of biomarkers based on next-generation sequencing, a simulation study. J Biopharm Stat 2024; 34:700-718. [PMID: 37819021 DOI: 10.1080/10543406.2023.2269251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023]
Abstract
The development of next-generation sequencing (NGS) opens opportunities for new applications such as liquid biopsy, in which tumor mutation genotypes can be determined by sequencing circulating tumor DNA after blood draws. However, with highly diluted samples like those obtained with liquid biopsy, NGS invariably introduces a certain level of misclassification, even with improved technology. Recently, there has been a high demand to use mutation genotypes as biomarkers for predicting prognosis and treatment selection. Many methods have also been proposed to build classifiers based on multiple loci with machine learning algorithms as biomarkers. How the higher misclassification rate introduced by liquid biopsy will affect the performance of these biomarkers has not been thoroughly investigated. In this paper, we report the results from a simulation study focused on the clinical utility of biomarkers when misclassification is present due to the current technological limit of NGS in the liquid biopsy setting. The simulation covers a range of performance profiles for current NGS platforms with different machine learning algorithms and uses actual patient genotypes. Our results show that, at the high end of the performance spectrum, the misclassification introduced by NGS had very little effect on the clinical utility of the biomarker. However, in more challenging applications with lower accuracy, misclassification could have a notable effect on clinical utility. The pattern of this effect can be complex, especially for machine learning-based classifiers. Our results show that simulation can be an effective tool for assessing different scenarios of misclassification.
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Affiliation(s)
- Dong Wang
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, USA
| | - Sue-Jane Wang
- Office of Biostatistics, Center for Drug Evaluation Research, FDA, Maryland, USA
| | - Samir Lababidi
- Office of Data, Analytics and Research, Office of Digital Transformation, Office of Commissioner, FDA, Maryland, USA
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2
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Zhu Y, Fan L, Zhu H, Gong Y, Chi C, Wang Y, Pan J, Dong B, Xue W. Transcriptomic signature defines two subtypes of locally advanced PCa with distinct neoadjuvant therapy benefits. Front Oncol 2023; 13:963411. [PMID: 37265786 PMCID: PMC10229793 DOI: 10.3389/fonc.2023.963411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/28/2023] [Indexed: 06/03/2023] Open
Abstract
Background Patients with locally advanced prostate cancer (LAPCa) received docetaxel-based neoadjuvant chemo-hormonal therapy (NCHT) had better clinical outcomes after surgery compared to neoadjuvant hormonal therapy (NHT) groups, but not all patients experienced favorable clinical outcomes with NCHT, raising the necessity for potential biomarker assessment. The transcriptomic profiling offers a unique opportunity to interrogate the accurate response to NCHT and NHT treatment and to identify the predictive biomarkers for neoadjuvant therapy. Methods The whole transcriptomic profiling was performed on baseline biopsies and surgical tissue specimens from 64 patients with LAPCa at Renji Hospital between 2014 and 2018. Biochemical progression-free survival (bPFS)-based gene-by-treatment interaction effects were used to identify predictive biomarkers for guiding treatment selection. Results Comparing the transcriptome profiling of pre- and post-treatment LAPCa specimens, NHT and NCHT shared 1917 up- and 670 down-regulated DEGs at least 2-fold. Pathway enrichment analysis showed up-regulated pathways in response to NHT and NCHT were both enriched in cytokine receptor interaction pathways, and down-regulated pathways in response to NCHT were enriched in cell cycle pathways. By comprehensive transcriptome profiling of 64 baseline specimens, ten predictive markers were identified. We integrated them into the signature to evaluate the relative benefits of neoadjuvant therapy, which categorizes patients into two subgroups with relative bPFS benefits from either NHCT or NHT. In the high-score (≥ -95.798) group (n = 37), NCHT treatment led to significantly longer bPFS (P< 0.0001), with a clear and early separation of the Kaplan-Meier curves. In the low-score (< -95.798) group (n = 27), NHT also led to significantly longer bPFS (P=0.0025). Conclusions In this study, we proposed the first predictive transcriptomic signature might potentially guide the effective selection of neoadjuvant therapy in LAPCa and might provide precise guidance toward future personalized adjuvant therapy. Trial registration The study was approved by the Ethics Committee of Renji Hospital affiliated to Shanghai Jiao Tong University (Ky2019-087).
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Affiliation(s)
| | | | | | | | | | | | | | | | - Wei Xue
- *Correspondence: Baijun Dong, ; Wei Xue,
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Kawaguchi ES, Li G, Lewinger JP, Gauderman WJ. Two-step hypothesis testing to detect gene-environment interactions in a genome-wide scan with a survival endpoint. Stat Med 2022; 41:1644-1657. [PMID: 35075649 PMCID: PMC9007892 DOI: 10.1002/sim.9319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/10/2021] [Accepted: 12/26/2021] [Indexed: 01/13/2023]
Abstract
Defined by their genetic profile, individuals may exhibit differential clinical outcomes due to an environmental exposure. Identifying subgroups based on specific exposure-modifying genes can lead to targeted interventions and focused studies. Genome-wide interaction scans (GWIS) can be performed to identify such genes, but these scans typically suffer from low power due to the large multiple testing burden. We provide a novel framework for powerful two-step hypothesis tests for GWIS with a time-to-event endpoint under the Cox proportional hazards model. In the Cox regression setting, we develop an approach that prioritizes genes for Step-2 G × E testing based on a carefully constructed Step-1 screening procedure. Simulation results demonstrate this two-step approach can lead to substantially higher power for identifying gene-environment ( G × E ) interactions compared to the standard GWIS while preserving the family wise error rate over a range of scenarios. In a taxane-anthracycline chemotherapy study for breast cancer patients, the two-step approach identifies several gene expression by treatment interactions that would not be detected using the standard GWIS.
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Affiliation(s)
- Eric S Kawaguchi
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Gang Li
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, California, USA.,Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Juan Pablo Lewinger
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - W James Gauderman
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
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Liu SY, Bao H, Wang Q, Mao WM, Chen Y, Tong X, Xu ST, Wu L, Wei YC, Liu YY, Chen C, Cheng Y, Yin R, Yang F, Ren SX, Li XF, Li J, Huang C, Liu ZD, Xu S, Chen KN, Xu SD, Liu LX, Yu P, Wang BH, Ma HT, Yan HH, Dong S, Zhang XC, Su J, Yang JJ, Yang XN, Zhou Q, Wu X, Shao Y, Zhong WZ, Wu YL. Genomic signatures define three subtypes of EGFR-mutant stage II-III non-small-cell lung cancer with distinct adjuvant therapy outcomes. Nat Commun 2021; 12:6450. [PMID: 34750392 PMCID: PMC8575965 DOI: 10.1038/s41467-021-26806-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 10/25/2021] [Indexed: 02/08/2023] Open
Abstract
The ADJUVANT study reported the comparative superiority of adjuvant gefitinib over chemotherapy in disease-free survival of resected EGFR-mutant stage II–IIIA non-small cell lung cancer (NSCLC). However, not all patients experienced favorable clinical outcomes with tyrosine kinase inhibitors (TKI), raising the necessity for further biomarker assessment. In this work, by comprehensive genomic profiling of 171 tumor tissues from the ADJUVANT trial, five predictive biomarkers are identified (TP53 exon4/5 mutations, RB1 alterations, and copy number gains of NKX2-1, CDK4, and MYC). Then we integrate them into the Multiple-gene INdex to Evaluate the Relative benefit of Various Adjuvant therapies (MINERVA) score, which categorizes patients into three subgroups with relative disease-free survival and overall survival benefits from either adjuvant gefitinib or chemotherapy (Highly TKI-Preferable, TKI-Preferable, and Chemotherapy-Preferable groups). This study demonstrates that predictive genomic signatures could potentially stratify resected EGFR-mutant NSCLC patients and provide precise guidance towards future personalized adjuvant therapy. Adjuvant gefitinib improves outcomes in non-small cell lung cancer (NSCLC) patients compared to chemotherapy, but not in all cases. Here, the authors find genomic biomarkers of response to gefitinib in NSCLC patients from the ADJUVANT trial, and propose a score to stratify them by potential benefit from the treatment.
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Affiliation(s)
- Si-Yang Liu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Hua Bao
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Qun Wang
- Fudan University Affiliated Zhongshan Hospital, Shanghai, China
| | | | - Yedan Chen
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | | | - Song-Tao Xu
- Fudan University Affiliated Zhongshan Hospital, Shanghai, China
| | - Lin Wu
- Hunan Cancer Hospital, Changsha, China
| | - Yu-Cheng Wei
- The Affiliated Hospital of Medical College Qingdao University, Qingdao, China
| | | | - Chun Chen
- Fujian Medical University Union Hospital, Fuzhou, China
| | - Ying Cheng
- Jilin Provincial Tumor Hospital, Changchun, China
| | - Rong Yin
- Jiangsu Cancer Hospital, Nanjing, China
| | - Fan Yang
- The People's Hospital of Peking University, Beijing, China
| | | | | | - Jian Li
- Peking University First Hospital, Beijing, China
| | | | | | - Shun Xu
- The First Hospital of China Medical University, Shenyang, China
| | | | - Shi-Dong Xu
- Harbin Medical University Cancer Hospital, Harbin, China
| | - Lun-Xu Liu
- West China Hospital of Sichuan University, Chengdu, China
| | - Ping Yu
- Sichuan Cancer Hospital, Chengdu, China
| | - Bu-Hai Wang
- The Northern Jiangsu People's Hospital, Yangzhou, China
| | - Hai-Tao Ma
- The First Affiliated Hospital of Suzhou University, Suzhou, China
| | - Hong-Hong Yan
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Song Dong
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jian Su
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jin-Ji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xue-Ning Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wen-Zhao Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China.
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, and Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou, China.
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Chou PH, Liao WC, Tsai KW, Chen KC, Yu JS, Chen TW. TACCO, a Database Connecting Transcriptome Alterations, Pathway Alterations and Clinical Outcomes in Cancers. Sci Rep 2019; 9:3877. [PMID: 30846808 PMCID: PMC6405743 DOI: 10.1038/s41598-019-40629-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
Because of innumerable cancer sequencing projects, abundant transcriptome expression profiles together with survival data are available from the same patients. Although some expression signatures for prognosis or pathologic staging have been identified from these data, systematically discovering such kind of expression signatures remains a challenge. To address this, we developed TACCO (Transcriptome Alterations in CanCer Omnibus), a database for identifying differentially expressed genes and altered pathways in cancer. TACCO also reveals miRNA cooperative regulations and supports construction of models for prognosis. The resulting signatures have great potential for patient stratification and treatment decision-making in future clinical applications. TACCO is freely available at http://tacco.life.nctu.edu.tw/.
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Affiliation(s)
- Po-Hao Chou
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Chao Liao
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan.,Center for General Education Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Ku-Chung Chen
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jau-Song Yu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Cell and Molecular Biology, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Ting-Wen Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.
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Ternès N, Rotolo F, Michiels S. biospear: an R package for biomarker selection in penalized Cox regression. Bioinformatics 2017; 34:112-113. [DOI: 10.1093/bioinformatics/btx560] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/05/2017] [Indexed: 01/07/2023] Open
Affiliation(s)
- Nils Ternès
- Gustave Roussy, Université Paris-Saclay, Service de biostatistique et d’épidémiologie, Villejuif, France
- Université Paris-Saclay, Univ. Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France
| | - Federico Rotolo
- Gustave Roussy, Université Paris-Saclay, Service de biostatistique et d’épidémiologie, Villejuif, France
- Université Paris-Saclay, Univ. Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France
| | - Stefan Michiels
- Gustave Roussy, Université Paris-Saclay, Service de biostatistique et d’épidémiologie, Villejuif, France
- Université Paris-Saclay, Univ. Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France
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