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Ryu WK, Yong SH, Lee SH, Gwon HR, Kim HR, Hong MH, Oh GE, Jung S, Kim CY, Chang YS, Kim EY. Usefulness of bronchial washing fluid for detection of EGFR mutations in non-small cell lung cancer. Lung Cancer 2023; 186:107390. [PMID: 37820540 DOI: 10.1016/j.lungcan.2023.107390] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/04/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
INTRODUCTION The implementation of bronchial washing fluid (BWF) as a diagnostic specimen may complement the low diagnostic yields of plasma in detecting EGFR mutation (mEGFR) in non-small cell lung cancer. However, the diagnostic value of BWF in detecting mEGFR has yet to be clarified. MATERIALS AND METHODS From March 2021 to August 2022, patients with histologically confirmed NSCLC with matched tumor tissue, BWF, and/or plasma samples were enrolled. Patients were classified into either initial diagnosis or rebiopsy groups. Diagnostic yields of mEGFR in BWF and plasma were evaluated using droplet digital polymerase chain reaction and compared to mEGFR in tumor tissue as standard. RESULTS The study included 123 patients (74.1 %) in the initial diagnosis and 43 patients (25.9 %) in the rebiopsy group. BWF showed higher sensitivity, specificity, and concordance rates than plasma in both the initial diagnosis (57.4 %, 96.4 %, and 74.0 % vs. 16.4 %, 96.2 %, and 53.1 %) and the rebiopsy group (87.9 %, 60.0 %, and 81.4 % vs. 25.0 %, 75.0 %, and 41.7 %). In the initial diagnosis group, mEGFR was detected in the BWF of 13 out of 16 patients, even in the absence of tumor cells in the tissue biopsy. In these cases, EGFR test results obtained from BWF showed concordance with EGFR test results from the tumor tissue obtained through repeated biopsy or surgery later. In the rebiopsy group, T790M was detected in 16 patients (37.2 %) by tissue biopsy. The combined use of tissue biopsy and BWF increased detection, confirming T790M in 22 patients (51.2 %). DISCUSSION The detection of mEGFR using BWF shows higher diagnostic yields than plasma for both initial diagnosis and rebiopsy. T790M was detected earlier in BWF than in tissue rebiopsy in some cases, providing patients with an early opportunity to access third-generation EGFR-TKIs. The complementary use of BWF with tumor tissue may improve precision in EGFR-mutated NSCLC treatment strategies.
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Affiliation(s)
- Woo Kyung Ryu
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Division of Pulmonology, Department of Internal Medicine, Inha University Hospital, Inha University College of Medicine, 27, Inhang‑ro, Jung‑gu, Incheon 22332, Republic of Korea
| | - Seung Hyun Yong
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sang Hoon Lee
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hye Ran Gwon
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hye Ryun Kim
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Min Hee Hong
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Go Eun Oh
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sehee Jung
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Chi Young Kim
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yoon Soo Chang
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Eun Young Kim
- Department of Internal Medicine, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
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Xi Y, Bai Z, Gao S, Guo J, Zhang Z, Zhang H, Qu L, Xu B, Wang W, Shan G, Cui W, Bai W, Ji X. Genomic profiling of NGS-based ctDNA from Chinese non-small cell lung cancer patients. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04794-z. [PMID: 37186065 DOI: 10.1007/s00432-023-04794-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 05/17/2023]
Abstract
PURPOSE Cell-free circulating tumor DNA (ctDNA) in plasma enables rapid and repeat testing of actionable mutations. Next-generation sequencing (NGS) is an attractive platform for multiplex sequencing capabilities compared to traditional methods such as PCR. The purpose of this study is to evaluate the value of the NGS-based ctDNA assay and to identify the genomic alteration profile of ctDNA in real-world Chinese non-small cell lung (NSCLC) patients. METHODS In total, 294 Chinese patients with pathological diagnosis of Phase III-IV NSCLC were enrolled. 3-4 mL peripheral blood was collected and NGS-based analysis was carried out using a 20-gene panel. The analytical sensitivity and specificity of ctDNA NGS-based assay was validated using droplet digital PCR (ddPCR). RESULTS We have tested 570 sites from 286 samples using ddPCR, which included 108 positive sites and 462 negative sites from NGS results, and the concordance rate was 99.8% (418/419) for single-nucleotide variants (SNVs) and 96.7% (146/151) for insertions and deletions (InDels). The most frequent genes were TP53 (32%), EGFR (31.97%), KRAS (6.46%), PIK3CA (4.76%), and MET (4.08%). Exon 19 deletion (19del) was the most common alteration in EGFR and G12C was the most common alteration in KRAS. Furthermore, the detection rate of TP53 was higher in the male and patients with squamous cell carcinoma. We also found the prevalence of TP53 in L858R was higher than in 19del (61.29% vs. 40%; p = 0.1115). CONCLUSION The results indicate that the results of NGS-based ctDNA assay are highly consistent with ddPCR. In Chinese NSCLC patients, TP53 mutation was more frequently associated with male and squamous cell carcinoma. The prevalence of concomitant mutations in L858R may be different from that in 19del.
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Affiliation(s)
- Yanfeng Xi
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, Shanxi, China
| | - Zhongyuan Bai
- First Clinical Medical School, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Sihang Gao
- Department of Bioinformatics, Beijing USCI Medical Devices Co., Ltd., Beijing, 102699, China
| | - Jianghong Guo
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, Shanxi, China
| | - Zhen Zhang
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, Shanxi, China
| | - Hongling Zhang
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, Shanxi, China
| | - Li Qu
- Department of Bioinformatics, Beijing USCI Medical Devices Co., Ltd., Beijing, 102699, China
| | - Bing Xu
- Department of Bioinformatics, Beijing USCI Medical Devices Co., Ltd., Beijing, 102699, China
| | - Weiwei Wang
- Department of Bioinformatics, Beijing USCI Medical Devices Co., Ltd., Beijing, 102699, China
| | - Guangyu Shan
- Department of Bioinformatics, Beijing USCI Medical Devices Co., Ltd., Beijing, 102699, China
| | - Wei Cui
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, Shanxi, China.
| | - Wenqi Bai
- Department of Colorectal Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, 030013, Shanxi, China.
| | - Xiaoyong Ji
- Department of Bioinformatics, Beijing USCI Medical Devices Co., Ltd., Beijing, 102699, China.
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Dutta S, Tarafdar S, Mukhopadhyay P, Bhattacharyya NP, Ghosh S. Detection of driver mutations in plasma cell-free nucleic acids in differentiated thyroid neoplasm. Eur J Endocrinol 2023; 188:6976051. [PMID: 36744987 DOI: 10.1093/ejendo/lvac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/15/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023]
Abstract
IMPORTANCE This proof-of-concept paper demonstrates that driver mutations can be detected in plasma in differentiated thyroid tumors, and we were able to detect mutations in upto 80% malignant thyroid nodules. Additionally, cancer subtypes could also be predicted using a 8-gene panel. In almost 90% follicular adenoma, rat sarcoma virus (RAS) mutations were detectable. There was a strong agreement between driver mutations found in plasma samples, FNAC materials, and histopathology samples. This has potential as a noninvasive, preoperative diagnostic tool (particularly of clinical importance in indeterminate nodules) and may help in detection of residual tumor after surgery. Future research is warranted to test the role of this tool to detect tumor recurrence. OBJECTIVE Ultrasonographic (USG) evaluation and fine-needle aspiration (FNA) are cornerstone for evaluation of thyroid neoplasm. Molecular technique including detection of driver mutation from FNA cytology (FNAC) material is an established modality. In this study, we explored the feasibility of using plasma cell-free nucleic acids to identify known driver mutations in differentiated thyroid neoplasm. DESIGN Patients presenting with thyroid nodules underwent USG with Thyroid Image Reporting and Data Systems scoring and FNAC (Bethesda classification). All patients in Bethesda 3, 4, 5, 6 underwent surgery and histopathological confirmation. Patients in Bethesda 2 (cosmetic concerns, compressive symptoms) underwent surgery, and rest were presumed benign on the basis of USG, FNAC features, and clinical followup.). SETTING Endocrinology clinic. PARTICIPANTS Subjects with thyroid nodule. INTERVENTION(S) OR EXPOSURE(S) None. MAIN OUTCOME(S) AND MEASURE(S) Plasma sample, FNA, and histopathology material were evaluated for driver mutations (8-gene panel comprising BRAF-V600E, RET/PTC3, RET/PTC1, TERT promoter, HRAS, NRAS, KRAS, and PAX8-PPARG). RESULTS A total of 223 subjects were recruited; of these 154 were benign and 69 had differentiated thyroid cancer. We were able to detect driver mutation from plasma in 55 subjects (79.71%) of all malignant patients, and 11 patients in benign category had RAS mutation (follicular adenoma). Rest of the benign nodules did not have any detectable driver mutations. CONCLUSIONS AND RELEVANCE Plasma might be a viable noninvasive alternative source for detection of driver mutations (8-gene panel) in subjects with differentiated thyroid tumors and may have significant clinical utility.
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Affiliation(s)
- Susmita Dutta
- Department of Endocrinology, Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Soham Tarafdar
- Department of Endocrinology, Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Pradip Mukhopadhyay
- Department of Endocrinology, Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Nitai P Bhattacharyya
- Department of Endocrinology, Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Sujoy Ghosh
- Department of Endocrinology, Institute of Post Graduate Medical Education & Research, Kolkata, India
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Long C, Li K, Liu Z, Zhang N, Xing X, Xu L, Gai F, Che N. Real-world analysis of the prognostic value of EGFR mutation detection in plasma ctDNA from patients with advanced non-small cell lung cancer. Cancer Med 2023; 12:7982-7991. [PMID: 36621813 PMCID: PMC10134383 DOI: 10.1002/cam4.5582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/21/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The plasma sample has emerged as a promising surrogate sample for EGFR mutation detection in advanced non-small cell lung cancer (NSCLC). In clinical practice, whether EGFR variants in baseline plasma ctDNA of advanced NSCLC can predict prognosis in addition to guiding targeted therapy remains to be further explored. MATERIAL AND METHODS In total, 315 NSCLC patients were retrospectively enrolled. EGFR mutation data from tissue detected by ARMS-PCR and paired plasma samples within 1 month of admission detected by SuperARMS or ARMS-PCR were collected. The correlation between baseline plasma ctDNA EGFR mutation status and survival was compared. RESULTS EGFR mutation detection rates in tumor samples and plasma samples were 65.1% (205/315) and 43.8% (138/315). Referred to tissue results, the consistent rate of test ctDNA EGFR alteration by SuperARMS was higher than that detected by ARMS (79.5% vs. 69.0%, p = 0.04), either in stage I-IIIA patients (85.7% vs. 50.0%, p = 0.4) or stage IIIB-IV patients (79.1% vs. 69.4%, p = 0.04). Patients' treatment status and pathological subtype were the two factors that affected plasma ctDNA EGFR alteration detection accuracy. The concordance in non-adenocarcinoma patients was obviously higher than that in adenocarcinoma (p = 0.02), and the concordance in treatment naïve patients was significantly higher than that in relapse patients (p = 0.047). In treatment naïve patients, the median PFS (mPFS) in plasma ctDNA EGFR-positive patients was shorter than that in plasma ctDNA EGFR negative patients (7.0 vs. 10.0 months, p = 0.01). In relapsed patients, the mPFS in plasma ctDNA EGFR-positive patients was 9.0 months versus 11.0 months in plasma ctDNA EGFR negative patients (p = 0.1). CONCLUSIONS A plasma sample could be an alternative for a molecular test when tissue samples was unavailable. The SuperARMS-PCR detection method has high sensitivity in real-world clinical practice. Furthermore, in patients with stage IIIB-IV, baseline plasma ctDNA EGFR mutation positivity not only guides targeted therapy but also predicts a worse prognosis.
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Affiliation(s)
- Chaolian Long
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Kun Li
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zichen Liu
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Nana Zhang
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xuya Xing
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Liming Xu
- Amoy Diagnostics Co., Ltd, Xiamen, China
| | - Fei Gai
- Amoy Diagnostics Co., Ltd, Xiamen, China
| | - Nanying Che
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Ren Y, Cao L, You M, Ji J, Gong Y, Ren H, Xu F, Guo H, Hu J, Li Z. “SMART” digital nucleic acid amplification technologies for lung cancer monitoring from early to advanced stages. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Hou T, Zeng J, Xu H, Su S, Ye J, Li Y. Performance of different methods for detecting T790M mutation in the plasma of patients with advanced NSCLC after developing resistance to first‑generation EGFR‑TKIs in a real‑world clinical setting. Mol Clin Oncol 2022; 16:88. [PMID: 35251639 DOI: 10.3892/mco.2022.2521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 02/26/2021] [Indexed: 12/24/2022] Open
Affiliation(s)
- Tongtong Hou
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Jiahao Zeng
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Hanyan Xu
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Shanshan Su
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Junru Ye
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Yuping Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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Qi H, Xiong A, Jiang L, Van H, Xu J, Wu J, Zheng Q, Minervini F, Alonso DP, Yang Y, Wu L. Blood digital polymerase chain reaction as a potential method to detect human epidermal growth factor receptor 2 amplification in non-small cell lung cancer. Transl Lung Cancer Res 2022; 10:4235-4249. [PMID: 35004253 PMCID: PMC8674588 DOI: 10.21037/tlcr-21-860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/17/2021] [Indexed: 12/12/2022]
Abstract
Background This study aimed to verify the feasibility of human epidermal growth factor receptor-2 (HER2) amplification detection by digital polymerase chain reaction (dPCR) in non-small cell lung cancer (NSCLC) patients and explore whether HER2 amplification could be detected in circulating tumor DNA (ctDNA) by dPCR. Methods A total of 112 fresh biopsy tissues and 88 blood samples from NSCLC patients were collected. The serum ctDNA was obtained from blood samples. The copy number of the HER2 gene was evaluated by dPCR and next-generation sequencing (NGS). The sensitivity/specificity and survival analysis were performed by the receiver operating characteristic (ROC) curve. The survival analysis was performed by Kaplan-Meier (KM) curve and univariate Cox regression analysis was also conducted. Results ROC analysis showed a good prediction result for HER2 amplification in blood samples by dPCR. The survival analysis showed that the median overall survival (OS) in the HER2 negative group detected by blood dPCR was significantly different from the positive group. The results of multivariate Cox regression were the same as those of survival analysis. Conclusions Blood dPCR might be a potential method to detect HER2 amplification in NSCLC. Amplification of the HER2 gene detected by dPCR was correlated with OS in NSCLC.
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Affiliation(s)
- Hui Qi
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Anwen Xiong
- Department of Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Lei Jiang
- School of Medicine, Tongji University, Shanghai, China
| | - Hardy Van
- Alphamab Oncology Ltd., Suzhou, China
| | - June Xu
- Alphamab Oncology Ltd., Suzhou, China
| | - Jing Wu
- Genetron Health (Beijing) Co. Ltd., Beijing, China
| | | | - Fabrizio Minervini
- Department of Thoracic Surgery, Cantonal Hospital Lucerne, Lucerne, Switzerland
| | - Dinora Polanco Alonso
- Group of Translational Research in Respiratory Medicine, Hospital Universitari Arnau de Vilanova y Santa Maria, IRB Lleida, Lleida, Spain
| | - Yifu Yang
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Liang Wu
- Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Liu D, Yin H, Wang Y, Cao Y, Yin J, Zhang J, Yin H, Zhao X. Development of a highly sensitive digital PCR assay to quantify long non-coding RNA MYU in urine samples which exhibited great potential as an alternative diagnostic biomarker for prostate cancer. Transl Androl Urol 2021; 10:3815-3825. [PMID: 34804824 PMCID: PMC8575588 DOI: 10.21037/tau-21-820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/21/2021] [Indexed: 12/31/2022] Open
Abstract
Background The diagnostic methods of prostate cancer (PCa) present major drawbacks in that serum prostate specific antigen (PSA) testing lacks specificity for PCa and prostate needle biopsy is a painful and highly invasive procedure for patients. Thus, new alternative screening methods which are specific and non-invasive both in the early detection and in the clinical definitive diagnosis of PCa are in urgent need. Long non-coding RNA MYU has been shown to promote PCa cell proliferation and migration, and is significantly upregulated both at the cellular and tumor tissue level. Therefore, long non-coding RNA MYU may be a new potential diagnostic biomarker for PCa. Methods In the present study, we successfully developed a highly sensitive digital PCR assay to detect long non-coding RNA in clinical urine samples. dPCR was carried out using Qx200 ddPCR EvaGreen Supermix (Bio-Rad) according to the manufacturer’s instructions. Results Our results indicated that the digital PCR assay showed better linearity, repeatability, and reproducibility when compared with real-time quantitative PCR. In addition, we identified the normalized MYU level and used the digital PCR assay to measure it in 100 clinical urine samples. Our study showed that the normalized MYU level is a promising diagnostic biomarker for predicting and evaluating the malignancy of PCa. Conclusions Our findings presented a non-invasive liquid biopsy method to detect an alternative diagnostic parameter which can assist the diagnosis of PCa in clinical practice.
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Affiliation(s)
- Di Liu
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,JiHua Laboratory, Foshan, China
| | - Huming Yin
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yong Wang
- College of Biomedical Engineering, University of Science and Technology of China, Hefei, China
| | - Yang Cao
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian Yin
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,JiHua Laboratory, Foshan, China
| | - Jianping Zhang
- Department of Tuberculosis, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Huancai Yin
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,JiHua Laboratory, Foshan, China
| | - Xiaojun Zhao
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
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Shah P, Sands J, Normanno N. The expanding capability and clinical relevance of molecular diagnostic technology to identify and evaluate EGFR mutations in advanced/metastatic NSCLC. Lung Cancer 2021; 160:118-126. [PMID: 34500194 DOI: 10.1016/j.lungcan.2021.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 11/25/2022]
Abstract
Epidermal growth factor receptor (EGFR) mutation testing in advanced non-small-cell lung cancer (NSCLC) has evolved rapidly over the past decade, largely triggered by the introduction of the targeted EGFR tyrosine kinase inhibitors (TKIs). Initially used to detect common EGFR mutations and determine the most appropriate first-line therapy at diagnosis, testing methodologies have expanded to test for multiple mutations at multiple time points throughout the disease course. Here we review the current mutation testing approaches, including types of biopsies, and the available assays commonly used in the clinic. Specific application of these approaches in advanced NSCLC, including current guideline recommendations, and potential future developments are discussed.
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Affiliation(s)
- Parth Shah
- Dartmouth-Hitchcock Medical Centre, 1 Medical Center Dr, Lebanon, NH 03766, USA.
| | - Jacob Sands
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215, USA.
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Via Mariano Semmola 52, 80131 Naples, Italy.
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Super-ARMS: A new method for plasma ESR1 mutation detection. Clin Chim Acta 2021; 520:23-28. [PMID: 34048732 DOI: 10.1016/j.cca.2021.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/17/2021] [Accepted: 05/22/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND ESR1 mutation is an important mechanism of drug resistance and recurrence in hormone receptor-positive breast cancer patients during AI treatment. Patient could still benefit from treatment with fulvestrant after ESR1 mutated. OBJECTIVE At present, there is still no suitable method to detect ESR1 mutation in plasma as clinical promotion method. We aim to improve from ARMS-PCR to get a method with higher sensitivity but no additional cost is incurred. METHODS We designed new primers for ESR1. Then positive and negative standard sample was used for sensitivity and specificity tests. Lastly, we collected patient peripheral blood sample and analyzed the performance of Super-ARMS in plasma ctDNA samples. RESULTS A total of 207 patients were enrolled in this study, including 142 prime breast cancer (PBC) patients and 65 metastasis breast cancer(MBC) patients. The mutation rate was as high as 27.9%(12/43) in MBC patients with AI treatment. But only 2.97%(3/101) in PBC patients with AI and 0% in both MBC or PBC patient without AI. There was no significant difference in Super-ARMS results compared with DDPCR method. CONCLUSION Super-ARMS is a method that has sensitivity close to DDPCR and has the convenience and low price of ARMS-PCR for plasma ctDNA ESR1 mutation detection. It has obvious advantages compared with other method such NGS and DDPCR as clinical promotion method.
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A supersensitive silicon nanowire array biosensor for quantitating tumor marker ctDNA. Biosens Bioelectron 2021; 181:113147. [PMID: 33773219 DOI: 10.1016/j.bios.2021.113147] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/27/2021] [Accepted: 03/03/2021] [Indexed: 12/20/2022]
Abstract
Cancer has become one of the major diseases threatening human health and life. Circulating tumor DNA (ctDNA) testing, as a practical liquid biopsy technique, is a promising method for cancer diagnosis, targeted therapy and prognosis. Here, for the first time, a field effect transistor (FET) biosensor based on uniformly sized high-response silicon nanowire (SiNW) array was studied for real-time, label-free, super-sensitive detection of PIK3CA E542K ctDNA. High-response 120-SiNWs array was fabricated on a (111) silicon-on-insulator (SOI) by the complementary metal oxide semiconductor (CMOS)-compatible microfabrication technology. To detecting ctDNA, we modified the DNA probe on the SiNWs array through silanization. The experimental results demonstrated that the as-fabricated biosensor had significant superiority in ctDNA detection, which achieved ultralow detection limit of 10 aM and had a good linearity under the ctDNA concentration range from 0.1 fM to 100 pM. This biosensor can recognize complementary target ctDNA from one/two/full-base mismatched DNA with high selectivity. Furthermore, the fabricated SiNW-array FET biosensor successfully detected target ctDNA in human serum samples, indicating a good potential in clinical applications in the future.
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Siggillino A, Ulivi P, Pasini L, Reda MS, Chiadini E, Tofanetti FR, Baglivo S, Metro G, Crinó L, Delmonte A, Minotti V, Roila F, Ludovini V. Detection of EGFR Mutations in Plasma Cell-Free Tumor DNA of TKI-Treated Advanced-NSCLC Patients by Three Methodologies: Scorpion-ARMS, PNAClamp, and Digital PCR. Diagnostics (Basel) 2020; 10:diagnostics10121062. [PMID: 33297595 PMCID: PMC7762356 DOI: 10.3390/diagnostics10121062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Analysis of circulating cell-free tumor DNA (cftDNA) has emerged as a specific and sensitive blood-based approach to detect epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC) patients. Still, there is some debate on what should be the preferential clinical method for plasma-derived cftDNA analysis. We tested 31 NSCLC patients treated with anti-EGFR tyrosine kinase inhibitors (TKIs), at baseline and serially during therapy, by comparing three methodologies in detecting EGFR mutations (L858R, exon 19 deletion, and T790M) from plasma: scorpions-amplification refractory mutation system (ARMS) methodology by using EGFR Plasma RGQ PCR Kit-QIAGEN, peptide nucleic acid (PNA) clamp and PANA RealTyper integration by using PNAClamp EGFR-PANAGENE, and digital real time PCR by using QuantStudio 3D Digital PCR System-Thermo Fisher Scientific. Specificity was 100% for all three mutations, independently from the platform used. The sensitivity for L858R (42.86%) and T790M (100%) did not change based on the method, while the sensitivity for Del 19 differed markedly (Scorpion-ARMS 45%, PNAClamp 75%, and Digital PCR 85%). The detection rate was also higher (94.23%) as measured by Digital PCR, and when we monitored the evolution of EGFR mutations over time, it evidenced the extreme inter-patient heterogeneity in terms of levels of circulating mutated copies. In our study, Digital PCR showed the best correlation with tissue biopsy and the highest sensitivity to attain the potential clinical utility of monitoring plasma levels of EGFR mutations.
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Affiliation(s)
- Annamaria Siggillino
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (P.U.); (E.C.)
| | - Luigi Pasini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (P.U.); (E.C.)
- Correspondence:
| | - Maria Sole Reda
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Elisa Chiadini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (P.U.); (E.C.)
| | - Francesca Romana Tofanetti
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Sara Baglivo
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Giulio Metro
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Lucio Crinó
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (L.C.); (A.D.)
| | - Angelo Delmonte
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (L.C.); (A.D.)
| | - Vincenzo Minotti
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Fausto Roila
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
| | - Vienna Ludovini
- Medical Oncology Division, S. Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.S.); (M.S.R.); (F.R.T.); (S.B.); (G.M.); (V.M.); (F.R.); (V.L.)
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Cao Z, Wang J, Qin N, Li K, Lv J, Wang J, Yang X, Li X, Zhang H, Zhang Q, Long H, Shu C, Ma L, Zhang S. [Clinical Value of Droplet Digital PCR and Super-ARMS Detection of Epidermal Growth Factor Receptor Gene Mutation in Plasma Circulating Tumor DNA of Patients with Advanced Lung Adenocarcinoma]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:84-90. [PMID: 32093452 PMCID: PMC7049790 DOI: 10.3779/j.issn.1009-3419.2020.02.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND The patients with advanced lung adenocarcinoma should select targeted drugs based on the type of tumor epidermal growth factor receptor (EGFR) gene mutation. However, it is difficult to collect tumor tissue of advanced lung adenocarcinoma, and some experts agree that peripheral blood can be used as a substitute for tumor tissue as a test specimen. This paper aimed to investigate the clinical value of ddPCR and super-amplification refractory mutation system (ARMS) in detecting EGFR gene mutation in peripheral blood of patients with advanced lung adenocarcinoma. METHODS A total of 119 patients diagnosed in Beijing Chest Hospital Affiliated to Capital Medical University from February 2016 to February 2019 were collected, and the sensitivity and specificity of plasma ctDNA EGFR gene mutation detected by ddPCR and super-arms were compared. Some patients with positive EGFR gene mutations received oral treatment with first-line EGFR tyrosine kinase inhibitors (EGFR-TKI). The patients were divided into subgroups according to the test results. In group 1, both ddPCR and super-arms showed positive EGFR gene mutation results, with 21 cases. In group 2, ddPCR and super-arms detection of EGFR gene mutation were all negative, with 16 cases. In group 3, the ddPCR test was positive and the super-arms test was negative, with 5 cases. In group 4, the ddPCR test result was negative while the super-arms test result was positive. Since the number of patients in group 4 was 0, no statistics were included. Objective response rate (ORR) and disease control rate (DCR) were used to evaluate the short-term outcome, and progression-free survival (PFS) was compared with survival analysis to evaluate the long-term outcome. RESULTS EGFR mutations were detected in 58 (48.7%) of 119 patients with advanced lung adenocarcinoma. The coincidence rate between ddPCR and EGFR gene mutation in tumor tissues was 82.4% (Kappa=0.647, P<0.001), the sensitivity was 74.1%, and the specificity was 90.2%. However, the coincidence degree of super-arms test and tissue test was 71.4%, the sensitivity was only 58.6%, and the specificity was 83.6%. The ORR and DCR values in group 3 were lower than those in group 1 and 2, but there was no significant difference in ORR between groups (P>0.05). Survival analysis showed that the PFS of the three groups was compared. The difference was not statistically significant (χ²=2.221, P=0.329). CONCLUSIONS ddPCR, as a high sensitivity and specificity liquid gene detection method, can be used as a reliable method to detect the mutation of plasma ctDNA EGFR gene in patients with advanced lung adenocarcinoma. The results of plasma genetic testing can also be used as the basis for predicting the efficacy of EGFR-TKIs in patients.
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Affiliation(s)
- Zhe Cao
- Department of Cancer and Nuclear Medicine, School of Clinical Medicine, Hubei University of Science and Technology/Cancer Center, First Affiliated Hospital of Hubei University of Science and Technology, Xianning 437100, China
| | - Jing Wang
- Department of Medical Cosmetology, Xiamen Hospital of T.C.M, Xiamen 361001, China
| | - Na Qin
- Beijing Chest Hospital Affiliated to Capital Medical University/ Department of Oncology, Beijing Institute of Tuberculosis and Thoracic Oncology, Beijing 101149, China
| | - Kun Li
- Beijing Chest Hospital Affiliated to Capital Medical University/ Department of Pathology, Beijing Institute of Tuberculosis and Thoracic Oncology, Beijing 101149, China
| | - Jialin Lv
- Beijing Chest Hospital Affiliated to Capital Medical University/ Department of Oncology, Beijing Institute of Tuberculosis and Thoracic Oncology, Beijing 101149, China
| | - Jinghui Wang
- Beijing Chest Hospital Affiliated to Capital Medical University/ Department of Oncology, Beijing Institute of Tuberculosis and Thoracic Oncology, Beijing 101149, China
| | - Xinjie Yang
- Beijing Chest Hospital Affiliated to Capital Medical University/ Department of Oncology, Beijing Institute of Tuberculosis and Thoracic Oncology, Beijing 101149, China
| | - Xi Li
- Beijing Chest Hospital Affiliated to Capital Medical University/ Department of Oncology, Beijing Institute of Tuberculosis and Thoracic Oncology, Beijing 101149, China
| | - Hui Zhang
- Beijing Chest Hospital Affiliated to Capital Medical University/ Department of Oncology, Beijing Institute of Tuberculosis and Thoracic Oncology, Beijing 101149, China
| | - Quan Zhang
- Beijing Chest Hospital Affiliated to Capital Medical University/ Department of Oncology, Beijing Institute of Tuberculosis and Thoracic Oncology, Beijing 101149, China
| | - Hongqing Long
- Department of Cancer and Nuclear Medicine, School of Clinical Medicine, Hubei University of Science and Technology/Cancer Center, First Affiliated Hospital of Hubei University of Science and Technology, Xianning 437100, China
| | - Chengrong Shu
- Department of Cancer and Nuclear Medicine, School of Clinical Medicine, Hubei University of Science and Technology/Cancer Center, First Affiliated Hospital of Hubei University of Science and Technology, Xianning 437100, China
| | - Li Ma
- Beijing Chest Hospital Affiliated to Capital Medical University/ Department of Oncology, Beijing Institute of Tuberculosis and Thoracic Oncology, Beijing 101149, China
| | - Shucai Zhang
- Beijing Chest Hospital Affiliated to Capital Medical University/ Department of Oncology, Beijing Institute of Tuberculosis and Thoracic Oncology, Beijing 101149, China
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Plasma-based early screening and monitoring of EGFR mutations in NSCLC patients by a 3-color digital PCR assay. Br J Cancer 2020; 123:1437-1444. [PMID: 32782293 PMCID: PMC7592053 DOI: 10.1038/s41416-020-1024-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 12/30/2022] Open
Abstract
Background Noninvasive plasma-based detection of EGFR mutations using digital PCR promises a fast, sensitive and reliable approach to predicting the efficiency of EGFR-TKI. However, the low throughput and high cost of digital PCR restricts its clinical application. Methods We designed a digital PCR assay, which can simultaneously detect 39 mutations of exons 18–21 of the EGFR gene. To assess overall performance, retrospective FFPE tissues from 30 NSCLC patients and plasma from 33 NSCLC patients were collected and analysed. Results The LoD of the EGFR mutations was as low as 0.308 copies/μL, and the linear correlation between the detected and expected values at different concentrations (0.01–10%) was low as well. Compared to ARMS-PCR in FFPE, the accuracy values of the dEGFR39 assay in plasma from 33 patients was 87.88% (29/33, 95% CI 72.67–95.18%). While monitoring the 33 patients, the EGFR mutation load as assessed by dEGFR39 was associated with the objective response to treatment. Thirteen samples from eight patients were identified by dEGFR39 to harbour the T790M mutation over time; of these patients, only nine (69%) were detected using SuperARMS. Conclusion Our results indicate that dEGFR39 assay is reliable, sensitive and cost-efficient. This method is beneficial for profiling EGFR mutations for precision therapy and prognosis after TKI treatment, especially in patients with insufficient tissue biopsy samples.
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Tran VT, Phan TT, Nguyen ST, Tran BT, Ho TT, Pho SP, Nguyen TB, Pham TTB, Le AT, Le VT, Nguyen HT. Smoking habit and chemo-radiotherapy and/or surgery affect the sensitivity of EGFR plasma test in non-small cell lung cancer. BMC Res Notes 2020; 13:367. [PMID: 32746896 PMCID: PMC7398354 DOI: 10.1186/s13104-020-05209-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/28/2020] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE This study aimed to identify the influential factors for the sensitivity of epidermal growth factor receptor (EGFR) plasma test in non-small cell lung cancer (NSCLC). The mutations were detected in tumor tissue and matched plasma samples from 125 newly diagnosed adenocarcinoma, clinical-stage IIIB-IV patients, and compared the diagnostic values of EGFR plasma test between groups of clinical characteristics. The influential factors for the sensitivity were identified and assessed by logistic regression. RESULTS EGFR mutations were detected in 65 (52.0%) tumor tissue and 50 (40.0%) matched plasma samples (P = 0.028). Compared to the tissue method, the concordance rate, sensitivity, and specificity of the EGFR plasma test were 86.4%, 75.4%, and 98.3%, respectively. Notably, we found that sensitivity of the test is higher in non-smokers (84.1%) compared to smokers (57.1%, P = 0.018), and in treatment naïve subjects (85.7%) compared to whom undergone chemo-radiotherapy with/without surgery before testing (56.5%, P = 0.009). Furthermore, the highest sensitivity was attained in patients without these two factors (90.3%), whilst the lowest value was noted in those with both factors (40.0%, P = 0.004). The multivariable analysis confirmed that smoking habit and treatment history have independently negative impacts on sensitivity (OR = 0.24, P = 0.019, and OR = 0.36, P = 0.047, respectively).
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Affiliation(s)
- Vinh Thanh Tran
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
| | - Thang Thanh Phan
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam.
- Faculty of Biology-Biotechnology, University of Science, VNU-HCM, Ho Chi Minh City, 700000, Vietnam.
| | - Son Truong Nguyen
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
- Department of the Vice Minister, Ministry of Health, Hanoi City, 100000, Vietnam
| | - Bich-Thu Tran
- Faculty of Biology-Biotechnology, University of Science, VNU-HCM, Ho Chi Minh City, 700000, Vietnam
| | - Toan Trong Ho
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
| | - Suong Phuoc Pho
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
| | - Tran Bao Nguyen
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
| | - Tuyen Thi Bich Pham
- The Laboratory D Unit, Clinical Cancer Center, Cho Ray Hospital, 201B Nguyen Chi Thanh Street, Dist. 5, Ho Chi Minh City, 700000, Vietnam
| | - Anh Tuan Le
- Department of Chemo-Radiotherapy, Clinical Cancer Center, Cho Ray Hospital, Ho Chi Minh City, 700000, Vietnam
| | - Vu Thuong Le
- Department of Thoracic Disease, Cho Ray Hospital, Ho Chi Minh City, 700000, Vietnam
| | - Hang Thuy Nguyen
- Department of Clinical Pathology, Cho Ray Hospital, Ho Chi Minh City, 700000, Vietnam
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A self-powered bidirectional partition microfluidic chip with embedded microwells for highly sensitive detection of EGFR mutations in plasma of non-small cell lung cancer patients. Talanta 2020; 220:121426. [PMID: 32928434 DOI: 10.1016/j.talanta.2020.121426] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/12/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023]
Abstract
Circulating tumor DNA (ctDNA) is a promising biomarker for tumor genotyping and therapy monitoring. Herein, we developed a digital PCR chip with embedded microwell and bidirectional partition network for highly sensitive ctDNA analysis. The embedded microwell contributes to increasing microreaction density (up to 7000 microwells/cm2) and reducing evaporation during amplification. The bidirectional partition network can achieve fast and random distribution of targets, ensuring the precise quantification of nucleic acid. We used plasmids, artificial samples and 32 clinical blood samples from non-small cell lung cancer patients to test the performance of this platform. The results demonstrated that our chip has not only comparable quantification performance to commercial counterpart but also the ability to detect EGFR mutations with as low as 0.01% mutation rate and 20 alter molecules in 27 ng genomic DNA. The identification of EGFR mutations in plasma using developed chip exhibited 85.71% sensitivity and 94.44% specificity for L858R mutation and 100% sensitivity and 86.96% specificity for T790 M mutation. Moreover, the monitoring of mutant allele in plasma was accomplished in this work. In conclusion, the developed chip has a potential in lung tumor genotyping and therapy monitoring for precision medicine, even other tumors.
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Lee SH, Kim EY, Kim T, Chang YS. Compared to plasma, bronchial washing fluid shows higher diagnostic yields for detecting EGFR-TKI sensitizing mutations by ddPCR in lung cancer. Respir Res 2020; 21:142. [PMID: 32517757 PMCID: PMC7281949 DOI: 10.1186/s12931-020-01408-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The rate of diagnosis of advanced lung adenocarcinoma must be improved. In this study, we compared the detection rates of EGFR-tyrosine kinase inhibitor-sensitizing mutations (mEGFRs) in bronchial washing fluid (BWF) and the plasma of patients with lung adenocarcinoma using the tissue genotype as the standard reference. METHODS Paired blood and BWF specimens were collected from 73 patients with lung cancer. The tumor EGFR mutation status was determined by genotyping of the plasma and BWF samples using droplet digital PCR (ddPCR). RESULTS The study cohort included 26, 10, 10, and 27 patients with stage I, II, III, and IV disease. Of the 73 cases, 35 had a wild-type EGFR, and 19 had the L858R substitution and exon 19 deletion mutations. The areas under the receiver operator characteristic curves for sensitivity vs. specificity of ddPCR were 0.895 [95% confidence interval (CI): 0.822-0.969] for BWF and 0.686 (95% CI: 0.592-0.780) for plasma (p < 0.001). The fractional abundance was higher in BWF of the mEGFR-positive cases than in the plasma (p = 0.004), facilitating easy threshold setting and discrimination between mEGFR-positive and negative cases. When genotyping results obtained using plasma and BWF were compared for early lung cancer (stages I-IIIA), the diagnostic yields were significantly higher for BWF ddPCR, and the same tendency was observed for the advanced stages, suggesting that the BWF data may reflect the genotype status in early-stage patients. CONCLUSIONS The mEGFR genotyping results obtained using BWF showed a higher diagnostic efficacy than did those obtained using the plasma. Thus, BWF-based genotyping may be a useful substitute for that using plasma in lung cancer.
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Affiliation(s)
- Sang Hoon Lee
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eun Young Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Taehee Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yoon Soo Chang
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
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Detection of Meningeal Metastasis in the Cerebrospinal Fluid in Lung Adenocarcinoma: Case Report. Clin Lung Cancer 2020; 21:e493-e496. [PMID: 32418825 DOI: 10.1016/j.cllc.2020.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/15/2020] [Accepted: 04/03/2020] [Indexed: 11/22/2022]
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Bai S, Xu B, Zhang Y, Zhang Y, Dang H, Yang S, Zuo C, Zhang L, Li J, Xie G. Tuning the specificity of DNA probes using bulge-loops for low-abundance SNV detection. Biosens Bioelectron 2020; 154:112092. [DOI: 10.1016/j.bios.2020.112092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 12/15/2022]
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Chen X, Wang L, Lou J. Nanotechnology Strategies for the Analysis of Circulating Tumor DNA: A Review. Med Sci Monit 2020; 26:e921040. [PMID: 32200389 PMCID: PMC7111132 DOI: 10.12659/msm.921040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Circulating tumor DNA (ctDNA) describes the fragmented DNA released from tumor cells into the blood. The ctDNA may have the same genetic changes as the primary tumor. Currently, ctDNA has become a popular biomarker for diagnosis, treatment, real-time clinical response monitoring, and prognosis, for solid tumors. Detection of ctDNA is minimally invasive, and repeat sampling can easily be performed. However, due to its low quality and short DNA fragment length, ctDNA detection still faces challenges and requires highly sensitive analytical techniques. Recently, liquid biopsies for the analysis of circulating tumor cells (CTCs) and circulating tumor-derived exosomes have been studied, and nanotechnology techniques have rapidly developed. Compared to traditional analytical methods, these nanotechnology-based platforms have the advantages of sensitivity, multiplex detection, simplicity, miniaturization, and automation, which support their potential use in clinical practice. This review aims to discuss the recent nanotechnological strategies for ctDNA analysis and the design of reliable techniques for ctDNA detection and to identify the potential clinical applications.
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Affiliation(s)
- Xiaomin Chen
- Nano Biomedical Research Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China (mainland).,Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China (mainland)
| | - Lin Wang
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China (mainland)
| | - Jiatao Lou
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China (mainland)
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Li C, He Q, Liang H, Cheng B, Li J, Xiong S, Zhao Y, Guo M, Liu Z, He J, Liang W. Diagnostic Accuracy of Droplet Digital PCR and Amplification Refractory Mutation System PCR for Detecting EGFR Mutation in Cell-Free DNA of Lung Cancer: A Meta-Analysis. Front Oncol 2020; 10:290. [PMID: 32195189 PMCID: PMC7063461 DOI: 10.3389/fonc.2020.00290] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Epidermal growth factor receptor (EGFR) mutation testing in plasma cell-free DNA (cfDNA) from advanced lung cancer patients is an emerging clinical tool. This meta-analysis was designed to determine the diagnostic accuracy of two common PCR systems, droplet digital PCR (ddPCR) and amplification refractory mutation system PCR (ARMS-PCR), for detecting EGFR mutation in cfDNA. Materials and methods: A systematic search was carried out based on PubMed, Web of science, Embase and the Cochrane library. Data from eligible studies were extracted and pooled to calculate the sensitivity, specificity, diagnostic odds ratio (DOR), area under the summary receiver-operating characteristic curve (AUROC), using tissue biopsy results as the standard method. Subgroup analyses were performed regarding EGFR mutation type, tumor stage, and EGFR-TKI treatment. Results: Twenty-five studies involving 4,881 cases were included. The plasma testing sensitivity, specificity, DOR, and AUROC, compared with the matched tumor tissues, were 72.1%, 95.6%, 38.5, 0.89 for ddPCR, and 65.3%, 98.2%, 52.8, 0.71 for ARMS-PCR, respectively, through indirect comparison, significant differences were found in sensitivity (P = 0.003) and specificity (P = 0.007). Furthermore, significant difference was found in sensitivity between tumor stage subgroups (IIIB–IV subgroup vs. IA–IV subgroup) in ARMS-PCR (73.7 vs. 64.2%, P = 0.008), but not in ddPCR (72.5 vs. 71.2%, P = 0.756). Conclusions: This study demonstrates that ddPCR and ARMS-PCR have a high specificity with a practical sensitivity for detecting EGFR mutation in cfDNA, which supports their application as a supplement or a conditional-alternative to tissue biopsy in clinical practice for genotyping. It seems that ddPCR has a higher sensitivity than ARMS-PCR, especially in early stages.
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Affiliation(s)
- Caichen Li
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qihua He
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hengrui Liang
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bo Cheng
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianfu Li
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shan Xiong
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yi Zhao
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Minzhang Guo
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhichao Liu
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianxing He
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenhua Liang
- China State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Wu W, Cao Z, Zhang W, Zhang L, Hou L, Wu C. Comparison of the SuperARMS and ARMS for detecting EGFR mutations in liquid-based cytology specimens from NSCLC patients. Diagn Pathol 2020; 15:9. [PMID: 32005253 PMCID: PMC6995041 DOI: 10.1186/s13000-019-0910-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Non-surgical cytological specimens are adequate not only for accurate histological subtyping but also for molecular profiling. A modified amplification refractory mutation system polymerase chain reaction (ARMS PCR), known as SuperARMS PCR, was improved by optimizing the primers designation, which provides a higher sensitivity and specificity approach for free plasma DNA detection. It is unclear whether SuperARMS PCR detects epidermal growth factor receptor (EGFR) mutations in cytology samples. The aim of this study was to compare the EGFR mutations detected by ARMS PCR and SuperARMS PCR in cytology samples derived from advanced non-small cell lung cancer (NSCLC) patients. METHODS From March 2016 to March 2018, a total of 234 cytological samples were obtained from primary or metastatic lesions of NSCLC, including 144 fine-needle aspirations (FNAs), 36 endobroncheal ultrasonography (EBUS) FNAs, 36 transbronchial needle aspirations (TBNAs) and 18 pleural effusion (PLEs). EGFR mutations were simultaneously detected using an ADx-ARMS EGFR kit (Amoy Diagnostics CO., ltd., Xiamen, China) and an ADx-SuperARMS EGFR kit (Amoy Diagnostics CO., ltd., Xiamen, China). Digital droplet PCR (ddPCR) and next-generation sequencing (NGS) were further used to verify the EGFR mutant inconsistent samples. RESULTS All of the 234 patients with advanced or recurrent NSCLC were diagnosed and assessed by two cytopathologists, and their EGFR mutation statuses were successfully detected by ARMS and SuperARMS. Importantly, the SuperARMS and ARMS methods showed a highly concordant result of 94.0% (220/234) (95%CI: 85.0, 95.0%). The positive rate of the SuperARMS was higher than the ARMS in the cytology samples for EGFR detection (46.2% vs. 40.2%). The specific EGFR mutation sites in 16 samples (6.8%) were not completely consistent between the SuperARMS and ARMS. A total of 14 patients showed EGFR mutations when detected by SuperARMS, but by ARMS there were EGFR wild-type. Two patients were detected as having one more EGFR mutation site by SuperARMS than by ARMS. ddPCR and NGS were used to further confirm the EGFR mutations in these inconsistent samples. Eight samples had the same mutation results as the SuperARMS, and 6 samples were not verified because the remaining DNA was insufficient. A total of 78 EGFR mutation patients received Tyrosine Kinase Inhibitor (TKI) treatment. The overall objective response rate (ORR) was 88.5% (69/78) for EGFR TKI treatment. CONCLUSION SuperARMS showed a high sensitivity and specificity for EGFR detection and thus, is expected to become a routine test in the clinic to be used as a widely available, easy-to-operate and sensitive method for EGFR mutation detection in liquid-based cytology samples.
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Affiliation(s)
| | | | - Wei Zhang
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 200433, Shanghai, People's Republic of China
| | - Liping Zhang
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 200433, Shanghai, People's Republic of China
| | - Likun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 200433, Shanghai, People's Republic of China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 200433, Shanghai, People's Republic of China.
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23
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Nguyen HT, Tran DH, Ngo QD, Pham HAT, Tran TT, Tran VU, Pham TVN, Le TK, Le NAT, Nguyen NM, Vo BT, Nguyen LT, Nguyen TCV, Bui QTN, Nguyen HN, Luong BA, Le LGH, Do DM, Do TTT, Hoang AV, Dinh KT, Phan MD, Tran LS, Giang H, Nguyen HN. Evaluation of a Liquid Biopsy Protocol using Ultra-Deep Massive Parallel Sequencing for Detecting and Quantifying Circulation Tumor DNA in Colorectal Cancer Patients. Cancer Invest 2020; 38:85-93. [DOI: 10.1080/07357907.2020.1713350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Duc Huy Tran
- University Medical Center, Ho Chi Minh City, Vietnam
| | - Quoc Dat Ngo
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Hong-Anh Thi Pham
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Thanh-Truong Tran
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Vu-Uyen Tran
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | | | - Trung Kien Le
- University Medical Center, Ho Chi Minh City, Vietnam
| | | | - Ngoc Mai Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Binh Thanh Vo
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Luan Thanh Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Thien-Chi Van Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Quynh Tram Nguyen Bui
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Huu-Nguyen Nguyen
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Bac An Luong
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Duc Minh Do
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Thanh-Thuy Thi Do
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Anh Vu Hoang
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | | | - Minh-Duy Phan
- Gene Solutions, Ho Chi Minh City, Vietnam
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | | | - Hoa Giang
- Gene Solutions, Ho Chi Minh City, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
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24
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Tran LS, Pham HAT, Tran VU, Tran TT, Dang ATH, Le DT, Nguyen SL, Nguyen NV, Nguyen TV, Vo BT, Dao HTT, Nguyen NH, Tran TH, Nguyen CV, Pham PC, Dang-Mai AT, Dinh-Nguyen TK, Phan VH, Do TTT, Truong Dinh K, Do HN, Phan MD, Giang H, Nguyen HN. Ultra-deep massively parallel sequencing with unique molecular identifier tagging achieves comparable performance to droplet digital PCR for detection and quantification of circulating tumor DNA from lung cancer patients. PLoS One 2019; 14:e0226193. [PMID: 31841547 PMCID: PMC6913927 DOI: 10.1371/journal.pone.0226193] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/21/2019] [Indexed: 12/24/2022] Open
Abstract
The identification and quantification of actionable mutations are of critical importance for effective genotype-directed therapies, prognosis and drug response monitoring in patients with non-small-cell lung cancer (NSCLC). Although tumor tissue biopsy remains the gold standard for diagnosis of NSCLC, the analysis of circulating tumor DNA (ctDNA) in plasma, known as liquid biopsy, has recently emerged as an alternative and noninvasive approach for exploring tumor genetic constitution. In this study, we developed a protocol for liquid biopsy using ultra-deep massively parallel sequencing (MPS) with unique molecular identifier tagging and evaluated its performance for the identification and quantification of tumor-derived mutations from plasma of patients with advanced NSCLC. Paired plasma and tumor tissue samples were used to evaluate mutation profiles detected by ultra-deep MPS, which showed 87.5% concordance. Cross-platform comparison with droplet digital PCR demonstrated comparable detection performance (91.4% concordance, Cohen's kappa coefficient of 0.85 with 95% CI = 0.72-0.97) and great reliability in quantification of mutation allele frequency (Intraclass correlation coefficient of 0.96 with 95% CI = 0.90-0.98). Our results highlight the potential application of liquid biopsy using ultra-deep MPS as a routine assay in clinical practice for both detection and quantification of actionable mutation landscape in NSCLC patients.
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Affiliation(s)
- Le Son Tran
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
| | - Hong-Anh Thi Pham
- Gene Solutions, Ho Chi Minh, Vietnam
- Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam
| | - Vu-Uyen Tran
- Gene Solutions, Ho Chi Minh, Vietnam
- Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam
| | - Thanh-Truong Tran
- Gene Solutions, Ho Chi Minh, Vietnam
- Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam
| | | | | | | | | | | | - Binh Thanh Vo
- Gene Solutions, Ho Chi Minh, Vietnam
- Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam
| | - Hong-Thuy Thi Dao
- Gene Solutions, Ho Chi Minh, Vietnam
- Graduate program of Genetics, Ho Chi Minh city University of Science, Ho Chi Minh city, Vietnam
| | | | - Tam Huu Tran
- Center for Standardization and QC in Medical Lab of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | | | - Van Hieu Phan
- Center for Forensic Science, Ho Chi Minh City, Vietnam
| | | | | | | | - Minh-Duy Phan
- Gene Solutions, Ho Chi Minh, Vietnam
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Hoa Giang
- Gene Solutions, Ho Chi Minh, Vietnam
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
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25
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Cervena K, Vodicka P, Vymetalkova V. Diagnostic and prognostic impact of cell-free DNA in human cancers: Systematic review. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:100-129. [DOI: 10.1016/j.mrrev.2019.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
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26
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Franczak C, Filhine-Tresarrieu P, Gilson P, Merlin JL, Au L, Harlé A. Technical considerations for circulating tumor DNA detection in oncology. Expert Rev Mol Diagn 2019; 19:121-135. [DOI: 10.1080/14737159.2019.1568873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Claire Franczak
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy, France
| | | | - Pauline Gilson
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Jean-Louis Merlin
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Lewis Au
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Alexandre Harlé
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
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27
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Wang H, Zhang L, Si X, Zhang X, Wang M. Re-biopsy status among Chinese non-small-cell lung cancer patients who progressed after icotinib therapy. Onco Targets Ther 2018; 11:7513-7519. [PMID: 30464499 PMCID: PMC6208793 DOI: 10.2147/ott.s174075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Objective Acquired T790M mutations account for 50%–60% of tyrosine kinase inhibitor (TKI)-resistant mechanisms in EGFR mutation-positive (m+) non-small-cell lung cancer (NSCLC) patients, and re-biopsy is recommended to detect these mutations. We investigated the re-biopsy status and the T790M incidence rate in patients after treatment with icotinib, which is the first-generation EGFR-TKI widely used in China. Patients and methods Target patients had EGFRm+NSCLC, who were progressed after icotinib therapy. The primary end point was the re-biopsy rate (number of cases in which re-biopsies were performed successfully/total number of patients progressed after icotinib therapy). Secondary end points included the T790M mutation incidence rate, differences between the first biopsy and re-biopsy, and details of why re-biopsy was not performed in relevant patients. Results A total of 77 adenocarcinoma patients were evaluated (median age, 58 years). Tissue re-biopsy was successful in 41 patients (53.2%). Compared with the first biopsy, percutaneous tissue biopsies increased from 51.2% to 70.7% (P=0.008), while bronchoscopy biopsies and the surgical rate decreased from 19.5% to 14.6% (P<0.001) and 17.1% to 7.3% (P<0.001), respectively. Primary lung lesions were more common in the first biopsy than in re-biopsy (80.5% vs 65.9%, P=0.008), but metastatic lesions were more often selected for re-biopsy (14/41 [34.1%], including metastases in the bone, lymph nodes, and liver). The incidence rate of T790M was 56.1% (23/41). The reasons for not performing re-biopsies included lesion sizes and/or locations unsuitable for biopsy (n=17), a positive circulating tumor DNA (ctDNA) result (n=3), patient unwillingness (n=7), older age or severe comorbidity (n=4), and poor health (n=5). No severe complications were found. Conclusion In this real-world study, the re-biopsy rate was 53.2% and the incidence rate of T790M mutations was 56.1%. Further efforts are needed to increase the re-biopsy rate in patients who progress after icotinib therapy.
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Affiliation(s)
- Hanping Wang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Dongcheng District, Beijing 100730, China,
| | - Li Zhang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Dongcheng District, Beijing 100730, China,
| | - Xiaoyan Si
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Dongcheng District, Beijing 100730, China,
| | - Xiaotong Zhang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Dongcheng District, Beijing 100730, China,
| | - Mengzhao Wang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Dongcheng District, Beijing 100730, China,
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28
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Utility of circulating tumor DNA in cancer diagnostics with emphasis on early detection. BMC Med 2018; 16:166. [PMID: 30285732 PMCID: PMC6167864 DOI: 10.1186/s12916-018-1157-9] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/17/2018] [Indexed: 02/06/2023] Open
Abstract
Various recent studies have focused on analyzing tumor genetic material released into the blood stream, known as circulating tumor DNA (ctDNA). Herein, we describe current research on the application of ctDNA to cancer management, including prognosis determination, monitoring for treatment efficacy/relapse, treatment selection, and quantification of tumor size and disease burden. Specifically, we examine the utility of ctDNA for early cancer diagnostics focusing on the development of a blood test to detect cancer in asymptomatic individuals by sequencing and analyzing mutations in ctDNA. Next, we discuss the prospect of using ctDNA to test for cancer, and present our calculations based on previously published empirical findings in cancer and prenatal diagnostics. We show that very early stage (asymptomatic) tumors are not likely to release enough ctDNA to be detectable in a typical blood draw of 10 mL. Data are also presented showing that mutations in circulating free DNA can be found in healthy individuals and will likely be very difficult to distinguish from those associated with cancer.We conclude that the ctDNA test, in addition to its high cost and complexity, will likely suffer from the same issues of low sensitivity and specificity as traditional biomarkers when applied to population screening and early (asymptomatic) cancer diagnosis.
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29
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Finotti A, Allegretti M, Gasparello J, Giacomini P, Spandidos DA, Spoto G, Gambari R. Liquid biopsy and PCR-free ultrasensitive detection systems in oncology (Review). Int J Oncol 2018; 53:1395-1434. [PMID: 30085333 PMCID: PMC6086621 DOI: 10.3892/ijo.2018.4516] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023] Open
Abstract
In oncology, liquid biopsy is used in the detection of next-generation analytes, such as tumor cells, cell-free nucleic acids and exosomes in peripheral blood and other body fluids from cancer patients. It is considered one of the most advanced non-invasive diagnostic systems to enable clinically relevant actions and implement precision medicine. Medical actions include, but are not limited to, early diagnosis, staging, prognosis, anticipation (lead time) and the prediction of therapy responses, as well as follow-up. Historically, the applications of liquid biopsy in cancer have focused on circulating tumor cells (CTCs). More recently, this analysis has been extended to circulating free DNA (cfDNA) and microRNAs (miRNAs or miRs) associated with cancer, with potential applications for development into multi-marker diagnostic, prognostic and therapeutic signatures. Liquid biopsies avoid some key limitations of conventional tumor tissue biopsies, including invasive tumor sampling, under-representation of tumor heterogeneity and poor description of clonal evolution during metastatic dissemination, strongly reducing the need for multiple sampling. On the other hand, this approach suffers from important drawbacks, i.e., the fragmentation of cfDNA, the instability of RNA, the low concentrations of certain analytes in body fluids and the confounding presence of normal, as well as aberrant DNAs and RNAs. For these reasons, the analysis of cfDNA has been mostly focused on mutations arising in, and pathognomonicity of, tumor DNA, while the analysis of cfRNA has been mostly focused on miRNA patterns strongly associated with neoplastic transformation/progression. This review lists some major applicative areas, briefly addresses how technology is bypassing liquid biopsy limitations, and places a particular emphasis on novel, PCR-free platforms. The ongoing collaborative efforts of major international consortia are reviewed. In addition to basic and applied research, we will consider technological transfer, including patents, patent applications and available information on clinical trials aimed at verifying the potential of liquid biopsy in cancer.
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Affiliation(s)
- Alessia Finotti
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
| | - Matteo Allegretti
- Oncogenomics and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
| | - Patrizio Giacomini
- Oncogenomics and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Crete, Greece
| | - Giuseppe Spoto
- Department of Chemistry, Catania University, 95125 Catania, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
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30
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Gong J, Li Y, Lin T, Feng X, Chu L. Multiplex real-time PCR assay combined with rolling circle amplification (MPRP) using universal primers for non-invasive detection of tumor-related mutations. RSC Adv 2018; 8:27375-27381. [PMID: 35540013 PMCID: PMC9083282 DOI: 10.1039/c8ra05259j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/23/2018] [Indexed: 12/01/2022] Open
Abstract
With the continuous development and application of targeted drugs, it is particularly desirable to find a non-invasive diagnostic approach to screen patients for precision treatment. Specifically, detection of multiple cancer-related mutations is very important for targeted therapy and prediction of drug resistance. Although numerous advanced PCR methods have been developed to discriminate single nucleotide polymorphisms, their drawbacks significantly limit their application, such as low sensitivity and throughput, complicated operations, and expensive costs. In order to overcome these challenges, in this study, we developed a method combining multiplex and sensitive real-time PCR assay with rolling circle amplification. This allows specific and sensitive discrimination of the single nucleotide mutation and provides convenient multiplex detection by real-time PCR assay. The clinical potential of the MPRP assay was further demonstrated by comparing samples from 8 patients with a digital PCR assay. The coincident results between these two methods indicated that the MPRP assay can provide a specific, sensitive, and convenient method for multiplex detection of cancer-related mutations. The MPRP system for SNP discrimination was developed, which showed high specificity and sensitivity for multiplex detection of tumor-related mutations.![]()
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Affiliation(s)
| | - Yishuai Li
- Department of Thoracic Surgery
- Hebei Chest Hospital
- China
| | - Ting Lin
- Apexbio Biotech Co., LTD
- Beijing 100176
- China
| | | | - Li Chu
- Hebei Medical University
- China
- Department of Pharmacology
- Hebei University of Chinese Medicine
- China
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