301
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Circulating Tumor DNA Detection in Early-Stage Non-Small Cell Lung Cancer Patients by Targeted Sequencing. Sci Rep 2016; 6:31985. [PMID: 27555497 PMCID: PMC4995492 DOI: 10.1038/srep31985] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/22/2016] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor DNA (ctDNA) isolated from peripheral blood has recently been shown to be an alternative source to detect gene mutations in primary tumors; however, most previous studies have focused on advanced stage cancers, and few have evaluated ctDNA detection in early-stage lung cancer. In the present study, blood and tumor samples were collected prospectively from 58 early-stage non-small lung cancer (NSCLC) patients (stages IA, IB, and IIA) and a targeted sequencing approach was used to detect somatic driver mutations in matched tumor DNA (tDNA) and plasma ctDNA. We identified frequent driver mutations in plasma ctDNA and tDNA in EGFR, KRAS, PIK3CA, and TP53, and less frequent mutations in other genes, with an overall study concordance of 50.4% and sensitivity and specificity of 53.8% and 47.3%, respectively. Cell-free (cfDNA) concentrations were found to be significantly associated with some clinical features, including tumor stage and subtype. Importantly, the presence of cfDNA had a higher positive predictive value than that of currently used protein tumor biomarkers. This study demonstrates the feasibility of identifying plasma ctDNA mutations in the earliest stage lung cancer patients via targeted sequencing, demonstrating a potential utility of targeted sequencing of ctDNA in the clinical management of NSCLC.
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302
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Ignatiadis M, Lee M, Jeffrey SS. Circulating Tumor Cells and Circulating Tumor DNA: Challenges and Opportunities on the Path to Clinical Utility. Clin Cancer Res 2016; 21:4786-800. [PMID: 26527805 DOI: 10.1158/1078-0432.ccr-14-1190] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent technological advances have enabled the detection and detailed characterization of circulating tumor cells (CTC) and circulating tumor DNA (ctDNA) in blood samples from patients with cancer. Often referred to as a "liquid biopsy," CTCs and ctDNA are expected to provide real-time monitoring of tumor evolution and therapeutic efficacy, with the potential for improved cancer diagnosis and treatment. In this review, we focus on these opportunities as well as the challenges that should be addressed so that these tools may eventually be implemented into routine clinical care.
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Affiliation(s)
- Michail Ignatiadis
- Department of Medical Oncology and Breast Cancer Translational Research Laboratory J. C. Heuson, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Mark Lee
- Google[x] Life Sciences, Google, Inc, Mountain View, California
| | - Stefanie S Jeffrey
- Department of Surgery, Stanford University School of Medicine, Stanford, California.
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303
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Neueste technologische Entwicklungen für die Analyse von zirkulierender Tumor-DNA. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zusammenfassung
Die Analyse von zirkulierender Tumor-DNA, zusammen mit der Analyse von zirkulierenden Tumorzellen auch oft Liquid Biopsy genannt, ist ein sich rasch entwickelndes Feld in der medizinischen Forschung. Obwohl es von der Entdeckung der zellfreien DNA bis hin zur Erkenntnis, dass sie sich als Biomarker eignet, Jahrzehnte gedauert hat, wurde der klinische Nutzen der ctDNA hinsichtlich der Überwachung des Therapieansprechens, der Identifizierung von Resistenzmechanismen und neu aufkommenden Therapiezielen sowie der Detektion von minimaler Resterkrankung mittlerweile in unzähligen Studien bewiesen.
Aufgrund der hohen Variabilität, mit der ctDNA in der Zirkulation vorkommt, sowie der starken Fragmentierung, stellt die ctDNA aber einen schwierigen Analyten dar. In den letzten Jahren haben erhebliche technologische Fortschritte dazu beigetragen, dass eine Routineanwendung der ctDNA-Analysen tatsächlich realisierbar wird, sofern eine Reihe von regulatorischen Hürden überwunden wird.
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304
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Han JY, Choi JJ, Kim JY, Han YL, Lee GK. PNA clamping-assisted fluorescence melting curve analysis for detecting EGFR and KRAS mutations in the circulating tumor DNA of patients with advanced non-small cell lung cancer. BMC Cancer 2016; 16:627. [PMID: 27519791 PMCID: PMC4983013 DOI: 10.1186/s12885-016-2678-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 08/05/2016] [Indexed: 01/12/2023] Open
Abstract
Background Circulating cell-free DNA (cfDNA) is emerging as a surrogate sample type for mutation analyses. To improve the clinical utility of cfDNA, we developed a sensitive peptide nucleic acid (PNA)-based method for analyzing EGFR and KRAS mutations in the plasma cfDNA of patients with advanced non-small cell lung cancer (NSCLC). Methods Baseline tissue and plasma samples were collected from treatment-naïve advanced NSCLC patients participated in a randomized phase II study, which was registered with ClinicalTrials.gov at Feb. 2009 (NCT01003964). EGFR and KRAS mutations in the plasma cfDNA were analyzed retrospectively using a PNA clamping-assisted fluorescence melting curve analysis. The results were compared with those obtained from tissue analysis performed using the direct sequencing. Exploratory analyses were performed to determine survival predicted by the plasma and tissue mutation status. Results Mutation analyses in matched tissue and plasma samples were available for 194 patients for EGFR and 135 patients for KRAS. The mutation concordance rates were 82.0 % (95 % confidence interval [CI], 76.5–87.4) for EGFR and 85.9 % (95 % CI, 80.1–91.8) for KRAS. The plasma EGFR mutation test sensitivity and specificity were 66.7 % (95 % CI, 60.0–73.3) and 87.4 % (95 % CI, 82.7–92.1), respectively, and the plasma KRAS mutation test sensitivity and specificity were 50.0 % (95 % CI, 41.6–58.4) and 89.4 % (95 % CI, 84.2–94.6), respectively. The predictive value of the plasma EGFR and KRAS mutation status with respect to survival was comparable with that of the tissue mutation status. Conclusions These data suggest that plasma EGFR and KRAS mutations can be analyzed using PNA-based real-time PCR methods and used as an alternative to tumor genotyping for NSCLC patients when tumor tissue is not available. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2678-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ji-Youn Han
- Lung Cancer Branch, Research Institute, National Cancer Center, Goyang, Korea. .,Center for Lung Cancer, Hospital, National Cancer Center, 323 Ilsan-ro, Ilsan-dong-gu, Goyang, Gyeonggi, 10408, Korea.
| | | | - Jin Young Kim
- Lung Cancer Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - You Lim Han
- Lung Cancer Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Geon Kook Lee
- Lung Cancer Branch, Research Institute, National Cancer Center, Goyang, Korea
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305
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Urinary circulating DNA detection for dynamic tracking of EGFR mutations for NSCLC patients treated with EGFR-TKIs. Clin Transl Oncol 2016; 19:332-340. [PMID: 27468867 DOI: 10.1007/s12094-016-1534-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/20/2016] [Indexed: 10/21/2022]
Abstract
PURPOSE Changes in EGFR profiles of non small cell lung cancer (NSCLC) patients correlates to clinical outcome. Extracting quality tumor tissue remains a challenge for molecular profiling. Our study aims to ascertain the clinical relevance of urinary cell free DNA as an alternative tumor material source. METHODS 150 patients with activating EGFR mutation and received EGFR-TKIs were recruited to participate in the serial monitoring study. Matched primary tumor samples were taken together with blood and urine specimens before the initiation of TKIs. The EGFR mutation testing was performed and quantified using ddPCR. For serial time point measurements, urine and blood samples were extracted at 1-month intervals for duration of 9 months. RESULTS Urinary ctDNA yielded a close agreement of 88 % on EGFR mutation status when compared to primary tissue at baseline. Almost all samples detected via urine specimens were uncovered in plasma samples. Analysis of urinary cell free DNA at different time points showed a strong correlation to treatment efficacy. Interestingly, a secondary EGFR mutation T790M was detected for 53 % of the patients during monitoring. The results were corroborated with the plasma ctDNA analysis. The T790M+ group had a reduced median survival when compared to the wildtype group. CONCLUSION Urinary cell free DNA may be a potential alternative to conventional primary tissue based EGFR mutation testing. Our findings showed that the assay sensitivity was comparable to results from blood plasma. Urinary samples being noninvasive and readily available have clinical utility for monitoring of EGFR TKI treatment.
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306
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Reckamp KL, Melnikova VO, Karlovich C, Sequist LV, Camidge DR, Wakelee H, Perol M, Oxnard GR, Kosco K, Croucher P, Samuelsz E, Vibat CR, Guerrero S, Geis J, Berz D, Mann E, Matheny S, Rolfe L, Raponi M, Erlander MG, Gadgeel S. A Highly Sensitive and Quantitative Test Platform for Detection of NSCLC EGFR Mutations in Urine and Plasma. J Thorac Oncol 2016; 11:1690-700. [PMID: 27468937 DOI: 10.1016/j.jtho.2016.05.035] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/24/2016] [Indexed: 01/19/2023]
Abstract
INTRODUCTION In approximately 60% of patients with NSCLC who are receiving EGFR tyrosine kinase inhibitors, resistance develops through the acquisition of EGFR T790M mutation. We aimed to demonstrate that a highly sensitive and quantitative next-generation sequencing analysis of EGFR mutations from urine and plasma specimens is feasible. METHODS Short footprint mutation enrichment next-generation sequencing assays were used to interrogate EGFR activating mutations and the T790M resistance mutation in urine or plasma specimens from patients enrolled in TIGER-X (NCT01526928), a phase 1/2 clinical study of rociletinib in previously treated patients with EGFR mutant-positive advanced NSCLC. RESULTS Of 63 patients, 60 had evaluable tissue specimens. When the tissue result was used as a reference, the sensitivity of EGFR mutation detection in urine was 72% (34 of 47 specimens) for T790M, 75% (12 of 16) for L858R, and 67% (28 of 42) for exon 19 deletions. With specimens that met a recommended volume of 90 to 100 mL, the sensitivity was 93% (13 of 14 specimens) for T790M, 80% (four of five) for L858R, and 83% (10 of 12) for exon 19 deletions. A comparable sensitivity of EGFR mutation detection was observed in plasma: 93% (38 of 41 specimens) for T790M, 100% (17 of 17) for L858R, and 87% (34 of 39) for exon 19 deletions. Together, urine and plasma testing identified 12 additional T790M-positive cases that were either undetectable or inadequate by tissue test. In nine patients monitored while receiving treatment with rociletinib, a rapid decrease in urine T790M levels was observed by day 21. CONCLUSIONS DNA derived from NSCLC tumors can be detected with high sensitivity in urine and plasma, enabling diagnostic detection and monitoring of therapeutic response from these noninvasive "liquid biopsy" samples.
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Affiliation(s)
- Karen L Reckamp
- City of Hope Comprehensive Cancer Center, Duarte, California.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - David Berz
- Beverly Hills Cancer Center, Beverly Hills, CA; City of Hope, Duarte, California
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307
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Bruno R, Giordano M, Giannini R, Alì G, Puppo G, Ribechini A, Chella A, Fontanini G. Aberrant expression of anaplastic lymphoma kinase in lung adenocarcinoma: Analysis of circulating free tumor RNA using one-step reverse transcription-polymerase chain reaction. Mol Med Rep 2016; 14:2238-42. [PMID: 27430882 DOI: 10.3892/mmr.2016.5479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/02/2016] [Indexed: 11/06/2022] Open
Abstract
Lung adenocarcinoma patients harboring anaplastic lymphoma kinase (ALK) gene rearrangements respond well to approved ALK inhibitors. However, to date, limited evidence is available regarding whether using circulating free tumor mRNA to identify aberrant ALK expression is possible, and its feasibility remains to be clearly addressed. The present study evaluated ALK expression by a one-step reverse transcription‑polymerase chain reaction (PCR) assay on the circulating free tumor mRNA from 12 lung adenocarcinoma patients. Additionally, the present study tested for ALK rearrangements by fluorescence in situ hybridization (FISH) and immunohistochemistry. A molecular genetic characterization was performed on tumor tissues and plasma samples. Aberrant ALK expression was detected in 2/12 patients using mRNA purified from plasma specimens and the results agreed with the FISH and immunohistochemistry findings of solid biopsy samples. The detection of aberrant ALK expression on circulating free tumor RNA may be feasible using a one‑step real‑time PCR assay and may be particularly helpful when a solid biopsy sample is not available.
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Affiliation(s)
- Rossella Bruno
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, I‑56126 Pisa, Italy
| | - Mirella Giordano
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, I‑56126 Pisa, Italy
| | - Riccardo Giannini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, I‑56126 Pisa, Italy
| | - Greta Alì
- Unit of Pathological Anatomy, University Hospital of Pisa, I‑56100 Pisa, Italy
| | - Gianfranco Puppo
- Unit of Pneumology, University Hospital of Pisa, I‑56100 Pisa, Italy
| | - Alessandro Ribechini
- Endoscopic Section of Pneumology, University Hospital of Pisa, I‑56100 Pisa, Italy
| | - Antonio Chella
- Unit of Pneumology, University Hospital of Pisa, I‑56100 Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, I‑56126 Pisa, Italy
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308
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Multiplex Detection of Rare Mutations by Picoliter Droplet Based Digital PCR: Sensitivity and Specificity Considerations. PLoS One 2016; 11:e0159094. [PMID: 27416070 PMCID: PMC4945036 DOI: 10.1371/journal.pone.0159094] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/27/2016] [Indexed: 01/01/2023] Open
Abstract
In cancer research, the accuracy of the technology used for biomarkers detection is remarkably important. In this context, digital PCR represents a highly sensitive and reproducible method that could serve as an appropriate tool for tumor mutational status analysis. In particular, droplet-based digital PCR approaches have been developed for detection of tumor-specific mutated alleles within plasmatic circulating DNA. Such an approach calls for the development and validation of a very significant quantity of assays, which can be extremely costly and time consuming. Herein, we evaluated assays for the detection and quantification of various mutations occurring in three genes often misregulated in cancers: the epidermal growth factor receptor (EGFR), the v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) and the Tumoral Protein p53 (TP53) genes. In particular, commercial competitive allele-specific TaqMan® PCR (castPCR™) technology, as well as TaqMan® and ZEN™ assays, have been evaluated for EGFR p.L858R, p.T790M, p.L861Q point mutations and in-frame deletions Del19. Specificity and sensitivity have been determined on cell lines DNA, plasmatic circulating DNA of lung cancer patients or Horizon Diagnostics Reference Standards. To show the multiplexing capabilities of this technology, several multiplex panels for EGFR (several three- and four-plexes) have been developed, offering new "ready-to-use" tests for lung cancer patients.
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309
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EGFR Mutation Analysis of Circulating Tumor DNA Using an Improved PNA-LNA PCR Clamp Method. Can Respir J 2016; 2016:5297329. [PMID: 27478396 PMCID: PMC4961805 DOI: 10.1155/2016/5297329] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 12/23/2022] Open
Abstract
Introduction. Rebiopsies have become more crucial in non-small cell lung cancer (NSCLC). Instead of invasive biopsies, development of collecting biological data of the tumor from blood samples is expected. We conducted a prospective study to assess the feasibility of detection of epidermal growth factor receptor (EGFR) mutation in plasma samples. Method. NSCLC patients harboring EGFR activating mutations, who were going to receive EGFR-tyrosine kinase inhibitors (TKIs) as first-line treatment, were enrolled in this study. Plasma EGFR activating mutations and the T790M resistance mutation were analyzed by an improved PNA-LNA PCR clamp method, characterized by a 10-fold or more sensitivity compared with the original methods. Result. Six patients with wild-type EGFR and 24 patients with EGFR mutations were enrolled in this study. Pretreatment plasma samples achieved sensitivity of 79%. The 6 patients with wild-type EGFR were all negative for plasma EGFR mutations. At the time of disease progression, plasma T790M mutation was detected in 8 of 16 cases. Absence of T790M before and during TKI treatment and disappearance of activating mutations during TKI treatment were considered as predictors of EGFR-TKIs efficacy. Conclusion. We were able to detect EGFR mutations in plasma samples by using an improved PNA-LNA PCR clamp method.
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310
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Liquid biopsy: will it be the 'magic tool' for monitoring response of solid tumors to anticancer therapies? Curr Opin Oncol 2016; 27:560-7. [PMID: 26335664 DOI: 10.1097/cco.0000000000000223] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW The aim of this review is to highlight the recent advances (in the past 12 months) concerning circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) in oncology. RECENT FINDINGS The value of CTCs as a prognostic biomarker is now well validated in breast, colon, and prostate cancer, but no trial has yet demonstrated that modifying treatment according to CTCs is superior to standard of care. Ongoing trials are addressing the clinical utility of CTCs. Moreover, there is emerging evidence about the potential of CTCs as a tumor tissue source to analyze protein and RNA expression, DNA mutations and drug sensitivity. ctDNA is a specific biomarker associated with tumor burden, and small studies have shown an association with worse outcome; prospective clinical studies on the prognostic and predictive value of ctDNA are needed. ctDNA can be used for tumor molecular profiling, with the potential advantage to encompass the spectrum of mutations present in the tumor. SUMMARY CTCs and ctDNA are promising new biomarkers in oncology, with potential clinical applications for monitoring and for comprehensive molecular profiling of cancer. For each assay, demonstration of analytical and clinical validity, as well as clinical utility in prospective clinical trials is needed before implementation in clinical practice.
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311
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Trombetta D, Sparaneo A, Fabrizio FP, Muscarella LA. Liquid biopsy and NSCLC. Lung Cancer Manag 2016; 5:91-104. [PMID: 30643553 DOI: 10.2217/lmt-2016-0006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/20/2016] [Indexed: 12/18/2022] Open
Abstract
In the era of high-throughput molecular screening and personalized medicine, difficulty in determining whether cancer mutations are truly 'actionable' remains a gray zone in NSCLC. The most important prerequisite to perform such investigations is the tumor tissue retrieval via biopsy at diagnosis and after occurrence of resistance. Blood-based liquid biopsy as circulating tumor cells, circulating tumor DNA and exosomes can offer a fast and non-invasive method to elucidate the genetic heterogeneity of patients, the screening and patient stratification and give a dynamic surveillance for tumor progression and monitor treatments response. Here we prospectively discuss the three main approaches in the blood-biopsy field of lung cancer patients and its clinical applications in patient management. We also outline some of the analytical challenges that remain for liquid biopsy techniques in demonstrating that it could represent a true and actionable picture in lung cancer management for the implementation into clinical routine.
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Affiliation(s)
- Domenico Trombetta
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
| | - Angelo Sparaneo
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
| | - Federico Pio Fabrizio
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
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312
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Levy B, Hu ZI, Cordova KN, Close S, Lee K, Becker D. Clinical Utility of Liquid Diagnostic Platforms in Non-Small Cell Lung Cancer. Oncologist 2016; 21:1121-30. [PMID: 27388233 DOI: 10.1634/theoncologist.2016-0082] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/27/2016] [Indexed: 11/17/2022] Open
Abstract
UNLABELLED : A firmer understanding of the genomic landscape of lung cancer has recently led to targeted, therapeutic advances in non-small cell lung cancer. Historically, the reference standard for the diagnosis and genetic interrogation for advanced-stage patients has been tissue acquisition via computed tomography-guided core or fine needle aspiration biopsy. However, this process can frequently put the patient at risk and remains complicated by sample availability and tumor heterogeneity. In addition, the time required to complete the diagnostic assays can negatively affect clinical care. Technological advances in recent years have led to the development of blood-based diagnostics or "liquid biopsies" with great potential to quickly diagnose and genotype lung cancer using a minimally invasive technique. Recent studies have suggested that molecular alterations identified in cell-free DNA (cfDNA) or circulating tumor DNA can serve as an accurate molecular proxy of tumor biology and reliably predict the response to tyrosine kinase therapy. In addition, several trials have demonstrated the high accuracy of microRNA (miRNA) platforms in discerning cancerous versus benign nodules in high-risk, screened patients. Despite the promise of these platforms, issues remain, including varying sensitivities and specificities between competing platforms and a lack of standardization of techniques and downstream processing. In the present report, the clinical applications of liquid biopsy technologies, including circulating tumor cells, proteomics, miRNA, and cfDNA for NSCLC, are reviewed and insight is provided into the diagnostic and therapeutic implications and challenges of these platforms. IMPLICATIONS FOR PRACTICE Although tumor biopsies remain the reference standard for the diagnosis and genotyping of non-small cell lung cancer, they remain fraught with logistical complexities that can delay treatment decisions and affect clinical care. Liquid diagnostic platforms, including cell-free DNA, proteomic signatures, RNA (mRNA and microRNA), and circulating tumor cells, have the potential to overcome many of these barriers, including rapid and accurate identification of de novo and resistant genetic alterations, real-time monitoring of treatment responses, prognosis of outcomes, and identification of minimal residual disease. The present report provides insights into new liquid diagnostic platforms in non-small cell lung cancer and discusses the promise and challenges of their current and future clinical use.
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Affiliation(s)
- Benjamin Levy
- Icahn School of Medicine, Mount Sinai Health System, New York, New York, USA
| | - Zishuo I Hu
- Icahn School of Medicine, Mount Sinai Health System, New York, New York, USA
| | | | | | - Karen Lee
- Icahn School of Medicine, Mount Sinai Health System, New York, New York, USA
| | - Daniel Becker
- Veterans Affairs Hospital, New York University, New York, New York, USA
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313
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Kato K, Uchida J, Kukita Y, Kumagai T, Nishino K, Inoue T, Kimura M, Oba S, Imamura F. Numerical indices based on circulating tumor DNA for the evaluation of therapeutic response and disease progression in lung cancer patients. Sci Rep 2016; 6:29093. [PMID: 27381430 PMCID: PMC4933907 DOI: 10.1038/srep29093] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/14/2016] [Indexed: 12/18/2022] Open
Abstract
Monitoring of disease/therapeutic conditions is an important application of circulating tumor DNA (ctDNA). We devised numerical indices, based on ctDNA dynamics, for therapeutic response and disease progression. 52 lung cancer patients subjected to the EGFR-TKI treatment were prospectively collected, and ctDNA levels represented by the activating and T790M mutations were measured using deep sequencing. Typically, ctDNA levels decreased sharply upon initiation of EGFR-TKI, however this did not occur in progressive disease (PD) cases. All 3 PD cases at initiation of EGFR-TKI were separated from other 27 cases in a two-dimensional space generated by the ratio of the ctDNA levels before and after therapy initiation (mutation allele ratio in therapy, MART) and the average ctDNA level. For responses to various agents after disease progression, PD/stable disease cases were separated from partial response cases using MART (accuracy, 94.7%; 95% CI, 73.5–100). For disease progression, the initiation of ctDNA elevation (initial positive point) was compared with the onset of objective disease progression. In 11 out of 28 eligible patients, both occurred within ±100 day range, suggesting a detection of the same change in disease condition. Our numerical indices have potential applicability in clinical practice, pending confirmation with designed prospective studies.
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Affiliation(s)
- Kikuya Kato
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Junji Uchida
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Yoji Kukita
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Takako Inoue
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Madoka Kimura
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Shigeyuki Oba
- Graduate School of Informatics, Kyoto University, Kyoto, Japan
| | - Fumio Imamura
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
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314
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Comparison of plasma and tissue samples in epidermal growth factor receptor mutation by ARMS in advanced non-small cell lung cancer. Gene 2016; 591:58-64. [PMID: 27370697 DOI: 10.1016/j.gene.2016.06.053] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 06/13/2016] [Accepted: 06/24/2016] [Indexed: 01/31/2023]
Abstract
OBJECTIVE The aim of this study was to assess the effectiveness and accuracy of blood-based circulating-free tumor DNA on testing epidermal growth factor receptor (EGFR) gene mutations. METHODS In total, 219 non-small cell lung cancer patients in stages III-IV were enrolled into this study. All patients had tissue samples and matched plasma DNA samples. EGFR gene mutations were detected by the Amplification Refractory Mutation System (ARMS). We compared the mutations in tumor tissue samples with matched plasma samples and determined the correlation between EGFR mutation status and clinical pathologic characteristics. RESULT The overall concordance rate of EGFR mutation status between the 219 matched plasma and tissue samples was 82% (179/219). The sensitivity and specificity for the ARMS EGFR mutation test in the plasma compared with tumor tissue were 60% (54/90) and 97% (125/129), respectively. The positive predictive value was 93% (54/58) and the negative predictive value was 78% (125/161). The median overall survival was longer for those with EGFR mutations than for those without EGFR mutations both in tissue samples (23.98 vs. 12.16months; P<0.001) and in plasma (19.96 vs. 13.63months; P=0.009). For the 68 patients treated with EGFR- tyrosine kinase inhibitors (TKIs), the median progression-free survival (PFS) was significantly prolonged in the EGFR mutant group compared to the non-mutation group in tumor tissue samples (12.26months vs. 2.40months, P<0.001). In plasma samples, the PFS of the mutant group was longer than that of the non-mutant group. However, there was no significant difference between the two groups (10.88months vs. 9.89months, P=0.411). CONCLUSIONS The detection of EGFR mutations in plasma using ARMS is relatively sensitive and highly specific. However, EGFR mutation status tested by ARMS in plasma cannot replace a tumor tissue biopsy. Positive EGFR mutation results detected in plasma are fairly reliable, but negative results are hampered by a high rate of false negatives.
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315
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Oxnard GR, Thress KS, Alden RS, Lawrance R, Paweletz CP, Cantarini M, Yang JCH, Barrett JC, Jänne PA. Association Between Plasma Genotyping and Outcomes of Treatment With Osimertinib (AZD9291) in Advanced Non-Small-Cell Lung Cancer. J Clin Oncol 2016; 34:3375-82. [PMID: 27354477 DOI: 10.1200/jco.2016.66.7162] [Citation(s) in RCA: 640] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have demonstrated potent activity against TKI resistance mediated by EGFR T790M. We studied whether noninvasive genotyping of cell-free plasma DNA (cfDNA) is a useful biomarker for prediction of outcome from a third-generation EGFR-TKI, osimertinib. METHODS Plasma was collected from all patients in the first-in-man study of osimertinib. Patients who were included had acquired EGFR-TKI resistance and evidence of a common EGFR-sensitizing mutation. Genotyping of cell-free plasma DNA was performed by using BEAMing. Plasma genotyping accuracy was assessed by using tumor genotyping from a central laboratory as reference. Objective response rate (ORR) and progression-free survival (PFS) were analyzed in all T790M-positive or T790M-negative patients. RESULTS Sensitivity of plasma genotyping for detection of T790M was 70%. Of 58 patients with T790M-negative tumors, T790M was detected in plasma of 18 (31%). ORR and median PFS were similar in patients with T790M-positive plasma (ORR, 63%; PFS, 9.7 months) or T790M-positive tumor (ORR, 62%; PFS, 9.7 months) results. Although patients with T790M-negative plasma had overall favorable outcomes (ORR, 46%; median PFS, 8.2 months), tumor genotyping distinguished a subset of patients positive for T790M who had better outcomes (ORR, 69%; PFS, 16.5 months) as well as a subset of patients negative for T790M with poor outcomes (ORR, 25%; PFS, 2.8 months). CONCLUSION In this retrospective analysis, patients positive for T790M in plasma have outcomes with osimertinib that are equivalent to patients positive by a tissue-based assay. This study suggests that, upon availability of validated plasma T790M assays, some patients could avoid a tumor biopsy for T790M genotyping. As a result of the 30% false-negative rate of plasma genotyping, those with T790M-negative plasma results still need a tumor biopsy to determine presence or absence of T790M.
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Affiliation(s)
- Geoffrey R Oxnard
- Geoffrey R. Oxnard, Ryan S. Alden, Cloud P. Paweletz, and Pasi A. Jänne, Dana-Farber Cancer Institute, Boston; Kenneth S. Thress and J. Carl Barrett, AstraZeneca, Waltham, MA; Rachael Lawrance and Mireille Cantarini, AstraZeneca, Macclesfield, United Kingdom; and James Chih-Hsin Yang, National Taiwan University and National Taiwan University Hospital, Taipei, Taiwan.
| | - Kenneth S Thress
- Geoffrey R. Oxnard, Ryan S. Alden, Cloud P. Paweletz, and Pasi A. Jänne, Dana-Farber Cancer Institute, Boston; Kenneth S. Thress and J. Carl Barrett, AstraZeneca, Waltham, MA; Rachael Lawrance and Mireille Cantarini, AstraZeneca, Macclesfield, United Kingdom; and James Chih-Hsin Yang, National Taiwan University and National Taiwan University Hospital, Taipei, Taiwan
| | - Ryan S Alden
- Geoffrey R. Oxnard, Ryan S. Alden, Cloud P. Paweletz, and Pasi A. Jänne, Dana-Farber Cancer Institute, Boston; Kenneth S. Thress and J. Carl Barrett, AstraZeneca, Waltham, MA; Rachael Lawrance and Mireille Cantarini, AstraZeneca, Macclesfield, United Kingdom; and James Chih-Hsin Yang, National Taiwan University and National Taiwan University Hospital, Taipei, Taiwan
| | - Rachael Lawrance
- Geoffrey R. Oxnard, Ryan S. Alden, Cloud P. Paweletz, and Pasi A. Jänne, Dana-Farber Cancer Institute, Boston; Kenneth S. Thress and J. Carl Barrett, AstraZeneca, Waltham, MA; Rachael Lawrance and Mireille Cantarini, AstraZeneca, Macclesfield, United Kingdom; and James Chih-Hsin Yang, National Taiwan University and National Taiwan University Hospital, Taipei, Taiwan
| | - Cloud P Paweletz
- Geoffrey R. Oxnard, Ryan S. Alden, Cloud P. Paweletz, and Pasi A. Jänne, Dana-Farber Cancer Institute, Boston; Kenneth S. Thress and J. Carl Barrett, AstraZeneca, Waltham, MA; Rachael Lawrance and Mireille Cantarini, AstraZeneca, Macclesfield, United Kingdom; and James Chih-Hsin Yang, National Taiwan University and National Taiwan University Hospital, Taipei, Taiwan
| | - Mireille Cantarini
- Geoffrey R. Oxnard, Ryan S. Alden, Cloud P. Paweletz, and Pasi A. Jänne, Dana-Farber Cancer Institute, Boston; Kenneth S. Thress and J. Carl Barrett, AstraZeneca, Waltham, MA; Rachael Lawrance and Mireille Cantarini, AstraZeneca, Macclesfield, United Kingdom; and James Chih-Hsin Yang, National Taiwan University and National Taiwan University Hospital, Taipei, Taiwan
| | - James Chih-Hsin Yang
- Geoffrey R. Oxnard, Ryan S. Alden, Cloud P. Paweletz, and Pasi A. Jänne, Dana-Farber Cancer Institute, Boston; Kenneth S. Thress and J. Carl Barrett, AstraZeneca, Waltham, MA; Rachael Lawrance and Mireille Cantarini, AstraZeneca, Macclesfield, United Kingdom; and James Chih-Hsin Yang, National Taiwan University and National Taiwan University Hospital, Taipei, Taiwan
| | - J Carl Barrett
- Geoffrey R. Oxnard, Ryan S. Alden, Cloud P. Paweletz, and Pasi A. Jänne, Dana-Farber Cancer Institute, Boston; Kenneth S. Thress and J. Carl Barrett, AstraZeneca, Waltham, MA; Rachael Lawrance and Mireille Cantarini, AstraZeneca, Macclesfield, United Kingdom; and James Chih-Hsin Yang, National Taiwan University and National Taiwan University Hospital, Taipei, Taiwan
| | - Pasi A Jänne
- Geoffrey R. Oxnard, Ryan S. Alden, Cloud P. Paweletz, and Pasi A. Jänne, Dana-Farber Cancer Institute, Boston; Kenneth S. Thress and J. Carl Barrett, AstraZeneca, Waltham, MA; Rachael Lawrance and Mireille Cantarini, AstraZeneca, Macclesfield, United Kingdom; and James Chih-Hsin Yang, National Taiwan University and National Taiwan University Hospital, Taipei, Taiwan
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316
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Matikas A, Syrigos KN, Agelaki S. Circulating Biomarkers in Non-Small-Cell Lung Cancer: Current Status and Future Challenges. Clin Lung Cancer 2016; 17:507-516. [PMID: 27373516 DOI: 10.1016/j.cllc.2016.05.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 12/18/2022]
Abstract
Despite recent advances, non-small-cell lung cancer remains a devastating disease and carries a grim prognosis. Major contributing factors include difficulties in diagnosing the disease early in its course during the asymptomatic stage and the poor understanding of the biology underlying disease progression. Liquid biopsies, noninvasive blood tests that detect circulating biomarkers such as circulating tumor cells and tumor-derived nucleic acid fragments, are in a rapidly evolving field of research that could provide answers to both of these unmet needs. Herein, we review the relevant data concerning the diagnostic, predictive, and prognostic significance of 3 distinct but potentially complementary circulating biomarkers in non-small-cell lung cancer: circulating tumor cells, cell-free DNA, and microRNAs.
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Affiliation(s)
- Alexios Matikas
- Department of Medical Oncology, University General Hospital of Heraklion, Heraklion, Crete, Greece
| | - Konstantinos N Syrigos
- Oncology Unit, 3rd Department of Internal Medicine, Sotiria General Hospital, National & Kapodistrian University, Athens School of Medicine, Athens, Greece
| | - Sofia Agelaki
- Department of Medical Oncology, University General Hospital of Heraklion, Heraklion, Crete, Greece; Laboratory of Translational Oncology, University of Crete, School of Medicine, Heraklion, Crete, Greece.
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317
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Sholl LM, Aisner DL, Allen TC, Beasley MB, Cagle PT, Capelozzi VL, Dacic S, Hariri LP, Kerr KM, Lantuejoul S, Mino-Kenudson M, Raparia K, Rekhtman N, Roy-Chowdhuri S, Thunnissen E, Tsao M, Vivero M, Yatabe Y. Liquid Biopsy in Lung Cancer: A Perspective From Members of the Pulmonary Pathology Society. Arch Pathol Lab Med 2016; 140:825-9. [PMID: 27195432 DOI: 10.5858/arpa.2016-0163-sa] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Liquid biopsy has received extensive media coverage and has been called the holy grail of cancer detection. Attempts at circulating tumor cell and genetic material capture have been progressing for several years, and recent financially and technically feasible improvements of cell capture devices, plasma isolation techniques, and highly sensitive polymerase chain reaction- and sequencing-based methods have advanced the possibility of liquid biopsy of solid tumors. Although practical use of circulating RNA-based testing has been hindered by the need to fractionate blood to enrich for RNAs, the detection of circulating tumor cells has profited from advances in cell capture technology. In fact, the US Food and Drug Administration has approved one circulating tumor cell selection platform, the CellSearch System. Although the use of liquid biopsy in a patient population with a genomically defined solid tumor may potentially be clinically useful, it currently does not supersede conventional pretreatment tissue diagnosis of lung cancer. Liquid biopsy has not been validated for lung cancer diagnosis, and its lower sensitivity could lead to significant diagnostic delay if liquid biopsy were to be used in lieu of tissue biopsy. Ultimately, notwithstanding the enthusiasm encompassing liquid biopsy, its clinical utility remains unproven.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yasushi Yatabe
- From the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts (Drs Sholl and Vivero); the Department of Pathology, University of Colorado Cancer Center, Denver (Dr Aisner); the Department of Pathology, The University of Texas Medical Branch, Galveston (Dr Allen); the Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York (Dr Beasley); the Department of Pathology, Weill Cornell Medical College, New York, New York, and the Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas (Dr Cagle); the Department of Pathology, University of Sao Paulo Medical School, Sao Paulo, Brazil (Dr Capelozzi); the Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Dr Dacic); the Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston (Drs Hariri and Mino-Kenudson); the Department of Pathology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Foresterhill, Aberdeen, Scotland, United Kingdom (Dr Kerr); the Department of Biopathology, Centre Léon Bérard, Lyon, France, and J Fourier University-INSERM U 823-Institut A Bonniot, Grenoble, France (Dr Lantuejoul); the Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois (Dr Raparia); the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York (Dr Rekhtman); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Roy-Chowdhuri); the Department of Pathology, VU Medical Center, Amsterdam, the Netherlands (Dr Thunnissen); the Department of Pathology, University Health Network/Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada (Dr Tsao); and the Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan (Dr Yatabe)
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318
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Karlovich C, Goldman JW, Sun JM, Mann E, Sequist LV, Konopa K, Wen W, Angenendt P, Horn L, Spigel D, Soria JC, Solomon B, Camidge DR, Gadgeel S, Paweletz C, Wu L, Chien S, O’Donnell P, Matheny S, Despain D, Rolfe L, Raponi M, Allen AR, Park K, Wakelee H. Assessment of EGFR Mutation Status in Matched Plasma and Tumor Tissue of NSCLC Patients from a Phase I Study of Rociletinib (CO-1686). Clin Cancer Res 2016; 22:2386-95. [PMID: 26747242 PMCID: PMC6886231 DOI: 10.1158/1078-0432.ccr-15-1260] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/11/2015] [Indexed: 12/14/2022]
Abstract
PURPOSE The evaluation of plasma testing for the EGFR resistance mutation T790M in NSCLC patients has not been broadly explored. We investigated the detection of EGFR activating and T790M mutations in matched tumor tissue and plasma, mostly from patients with acquired resistance to first-generation EGFR inhibitors. EXPERIMENTAL DESIGN Samples were obtained from two studies, an observational study and a phase I trial of rociletinib, a mutant-selective inhibitor of EGFR that targets both activating mutations and T790M. Plasma testing was performed with the cobas EGFR plasma test and BEAMing. RESULTS The positive percent agreement (PPA) between cobas plasma and tumor results was 73% (55/75) for activating mutations and 64% (21/33) for T790M. The PPA between BEAMing plasma and tumor results was 82% (49/60) for activating mutations and 73% (33/45) for T790M. Presence of extrathoracic (M1b) versus intrathoracic (M1a/M0) disease was found to be strongly associated with ability to identify EGFR mutations in plasma (P < 0.001). Rociletinib objective response rates (ORR) were 52% [95% confidence interval (CI), 31 - 74%] for cobas tumor T790M-positive and 44% (95% CI, 25 - 63%) for BEAMing plasma T790M-positive patients. A drop in plasma-mutant EGFR levels to ≤10 molecules/mL was seen by day 21 of treatment in 7 of 8 patients with documented partial response. CONCLUSIONS These findings suggest the cobas and BEAMing plasma tests can be useful tools for noninvasive assessment and monitoring of the T790M resistance mutation in NSCLC, and could complement tumor testing by identifying T790M mutations missed because of tumor heterogeneity or biopsy inadequacy. Clin Cancer Res; 22(10); 2386-95. ©2016 AACR.
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Affiliation(s)
| | | | - Jong-Mu Sun
- Samsung Medical Center Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Elaina Mann
- Clovis Oncology Inc., San Francisco, California
| | | | | | - Wei Wen
- Roche Molecular Systems, Pleasanton, California
| | | | - Leora Horn
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | - David Spigel
- Sarah Cannon Research Institute, Nashville; Tennessee
| | | | | | | | - Shirish Gadgeel
- Karmanos Cancer Institute/Wayne State University, Detroit, Michigan
| | | | - Lin Wu
- Roche Molecular Systems, Pleasanton, California
| | - Sean Chien
- Roche Molecular Systems, Pleasanton, California
| | | | | | | | | | | | | | - Keunchil Park
- Samsung Medical Center Sungkyunkwan University School of Medicine, Seoul, Korea
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319
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Wei Z, Shah N, Deng C, Xiao X, Zhong T, Li X. Circulating DNA addresses cancer monitoring in non small cell lung cancer patients for detection and capturing the dynamic changes of the disease. SPRINGERPLUS 2016; 5:531. [PMID: 27186495 PMCID: PMC4844578 DOI: 10.1186/s40064-016-2141-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/12/2016] [Indexed: 11/18/2022]
Abstract
Purpose Monitoring of key markers for lung cancer detection and tracking of acquired drug resistance is critical for the management of the disease. We aim to ascertain the value of monitoring both total cell free DNA concentrations and mutant EGFR DNA content within diverse groups of individuals most vulnerable to the disease. Methods We proposed longitudinal monitoring of circulating DNA using digital PCR. Circulating DNA present in peripheral blood can be obtained non-invasively and provide timely disease status update. 25 heavy smokers and 50 patients undergoing TKI therapy were recruited. Peripheral blood specimens were taken at different time points and their circulating DNA were analyzed and quantified. Results Significant higher concentrations of total cell free DNA were detected when compared with healthy high-risk individuals. Levels were stable throughout the treatment cycles, which makes it potentially a useful tool for patient stratification. Concurrent mutant T790M DNA detection of lung cancer patients at baseline achieved 82 % concordance with matched tissue analysis. Samples initially negative for the T790M gene mutation that became positive during treatment were corroborated with a repeat biopsy. The results showed its usefulness for serial monitoring. Conclusion Monitoring of circulating DNA addresses the need for disease detection and shows the ability to capture the dynamic changes of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2141-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhangjing Wei
- Department of Diagnostic Medicine, JingMen NO.1 People's Hospital, JingMen, People's Republic of China
| | - Nirej Shah
- Department of Clinical Medicine, JingChu University of Technology, JingMen, People's Republic of China
| | - Chong Deng
- Department of Diagnostic Medicine, JingMen NO.1 People's Hospital, JingMen, People's Republic of China
| | - Xuehui Xiao
- Department of Diagnostic Medicine, JingMen NO.1 People's Hospital, JingMen, People's Republic of China
| | - Tenglang Zhong
- Department of Diagnostic Medicine, JingMen NO.1 People's Hospital, JingMen, People's Republic of China
| | - Xiansong Li
- Department of Neurosurgery, JingZhou Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Renmin Road 1, JingZhou, 434020 People's Republic of China
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320
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Integrated digital error suppression for improved detection of circulating tumor DNA. Nat Biotechnol 2016; 34:547-555. [PMID: 27018799 PMCID: PMC4907374 DOI: 10.1038/nbt.3520] [Citation(s) in RCA: 717] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 02/26/2016] [Indexed: 01/06/2023]
Abstract
High-throughput sequencing of circulating tumor DNA (ctDNA) promises to facilitate personalized cancer therapy. However, low quantities of cell-free DNA (cfDNA) in the blood and sequencing artifacts currently limit analytical sensitivity. To overcome these limitations, we introduce an approach for integrated digital error suppression (iDES). Our method combines in silico elimination of highly stereotypical background artifacts with a molecular barcoding strategy for the efficient recovery of cfDNA molecules. Individually, these two methods each improve the sensitivity of cancer personalized profiling by deep sequencing (CAPP-Seq) by ~3 fold, and synergize when combined to yield ~15-fold improvements. As a result, iDES-enhanced CAPP-Seq facilitates noninvasive variant detection across hundreds of kilobases. Applied to clinical non-small cell lung cancer (NSCLC) samples, our method enabled biopsy-free profiling of EGFR kinase domain mutations with 92% sensitivity and 96% specificity and detection of ctDNA down to 4 in 105 cfDNA molecules. We anticipate that iDES will aid the noninvasive genotyping and detection of ctDNA in research and clinical settings.
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321
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Santarpia M, Karachaliou N, González-Cao M, Altavilla G, Giovannetti E, Rosell R. Feasibility of cell-free circulating tumor DNA testing for lung cancer. Biomark Med 2016; 10:417-30. [PMID: 26974841 DOI: 10.2217/bmm.16.6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Tumor tissue genotyping is used routinely for lung cancer to identify specific targetable oncogenic alterations, including EGFR mutations and ALK rearrangements. However, tumor tissue from a single biopsy is often insufficient for molecular testing, may offer a limited evaluation because of tumor heterogeneity and can be difficult to obtain. Cell-free circulating tumor DNA has been widely investigated as a potential surrogate for tissue biopsy for noninvasive assessment of tumor-related genomic alterations. New techniques have improved EGFR mutations detection in ctDNA, thus supporting the use of this liquid biopsy for predicting response to EGFR tyrosine kinase inhibitors (TKIs) and monitoring the emergence of resistance. The serial evaluation of ctDNA during treatment is feasible and can be used to track tumor changes in real time and for a wide range of clinically useful applications.
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Affiliation(s)
- Mariacarmela Santarpia
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina, Italy
| | - Niki Karachaliou
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Maria González-Cao
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain
| | - Giuseppe Altavilla
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina, Italy
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.,Cancer Pharmacology Lab, AIRC Start-Up Unit, University of Pisa, Pisa, Italy
| | - Rafael Rosell
- Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain.,Pangaea Biotech, Barcelona, Spain.,Cancer Biology & Precision Medicine Program, Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain.,Germans Trias i Pujol Health Sciences Institute & Hospital, Campus Can Ruti, Badalona, Barcelona, Spain.,Molecular Oncology Research (MORe) Foundation, Barcelona, Spain
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322
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Fenizia F, De Luca A, Pasquale R, Sacco A, Forgione L, Lambiase M, Iannaccone A, Chicchinelli N, Franco R, Rossi A, Morabito A, Rocco G, Piccirillo MC, Normanno N. EGFR mutations in lung cancer: from tissue testing to liquid biopsy. Future Oncol 2016; 11:1611-23. [PMID: 26043215 DOI: 10.2217/fon.15.23] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
ABSTRACT The presence of EGFR mutations predicts the sensitivity to EGF receptor (EGFR)-tyrosine kinase inhibitors in a molecularly defined subset of non-small-cell lung carcinoma (NSCLC) patients. For this reason, EGFR testing of NSCLC is required to provide personalized treatment options and better outcomes for NSCLC patients. As surgery specimens are not available in the majority of NSCLC, other currently available DNA sources are small biopsies and cytological samples, providing however limited and low-quality material. In order to address this issue, the use of surrogate sources of DNA, such as blood, serum and plasma samples, which often contains circulating free tumor DNA or circulating tumor cells, is emerging as a new strategy for tumor genotyping.
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Affiliation(s)
- Francesca Fenizia
- 1Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS, Mercogliano (AV), Italy
| | | | - Raffaella Pasquale
- 1Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS, Mercogliano (AV), Italy
| | - Alessandra Sacco
- 1Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS, Mercogliano (AV), Italy
| | - Laura Forgione
- 1Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS, Mercogliano (AV), Italy
| | - Matilde Lambiase
- 1Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS, Mercogliano (AV), Italy
| | - Alessia Iannaccone
- 1Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS, Mercogliano (AV), Italy
| | | | - Renato Franco
- 3Surgical Pathology Unit, Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS, Naples, Italy
| | - Antonio Rossi
- 4Division of Medical Oncology, 'S.G. Moscati' Hospital, Avellino, Italy
| | - Alessandro Morabito
- 5Medical Oncology Unit, Thoraco-Pulmonary Department, Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS, Naples, Italy
| | - Gaetano Rocco
- 6Thoracic Surgery, Thoraco-Pulmonary Department, Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS, Naples, Italy
| | | | - Nicola Normanno
- 1Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM)-Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS, Mercogliano (AV), Italy
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323
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Sherwood JL, Corcoran C, Brown H, Sharpe AD, Musilova M, Kohlmann A. Optimised Pre-Analytical Methods Improve KRAS Mutation Detection in Circulating Tumour DNA (ctDNA) from Patients with Non-Small Cell Lung Cancer (NSCLC). PLoS One 2016; 11:e0150197. [PMID: 26918901 PMCID: PMC4769175 DOI: 10.1371/journal.pone.0150197] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/10/2016] [Indexed: 12/29/2022] Open
Abstract
Introduction Non-invasive mutation testing using circulating tumour DNA (ctDNA) is an attractive premise. This could enable patients without available tumour sample to access more treatment options. Materials & Methods Peripheral blood and matched tumours were analysed from 45 NSCLC patients. We investigated the impact of pre-analytical variables on DNA yield and/or KRAS mutation detection: sample collection tube type, incubation time, centrifugation steps, plasma input volume and DNA extraction kits. Results 2 hr incubation time and double plasma centrifugation (2000 x g) reduced overall DNA yield resulting in lowered levels of contaminating genomic DNA (gDNA). Reduced “contamination” and increased KRAS mutation detection was observed using cell-free DNA Blood Collection Tubes (cfDNA BCT) (Streck), after 72 hrs following blood draw compared to EDTA tubes. Plasma input volume and use of different DNA extraction kits impacted DNA yield. Conclusion This study demonstrated that successful ctDNA recovery for mutation detection in NSCLC is dependent on pre-analytical steps. Development of standardised methods for the detection of KRAS mutations from ctDNA specimens is recommended to minimise the impact of pre-analytical steps on mutation detection rates. Where rapid sample processing is not possible the use of cfDNA BCT tubes would be advantageous.
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Affiliation(s)
- James L. Sherwood
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
- * E-mail:
| | - Claire Corcoran
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Helen Brown
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Alan D. Sharpe
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Milena Musilova
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Alexander Kohlmann
- Personalised Healthcare & Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, United Kingdom
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324
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Hart CD, Galardi F, Pestrin M, De Luca F, Risi E, Di Leo A. Using CTCs for pharmacogenomic analysis. Pharmacol Res 2016; 106:92-100. [PMID: 26921662 DOI: 10.1016/j.phrs.2016.02.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/18/2016] [Accepted: 02/19/2016] [Indexed: 12/31/2022]
Abstract
In the era of precision medicine in oncology, pharmacogenomic assessment is a vital step in delivering personalized care. Increasing evidence points towards the importance of assessing molecular features of the advanced disease, rather than relying on the primary tumor sample, in order to appreciate the evolution of the tumor and to target relevant features. Circulating tumor cells (CTCs) represent a novel method of tumor sampling, as they offer a contemporaneous picture of the current disease state without the need for invasive needle biopsy. As they may derive from any number of metastatic sites, the potential to capture the heterogeneity of the disease is increased. Improvements in CTC capture, enrichment and isolation technology now allow sophisticated interrogation of these cells, such that pharmacogenomic assessment of CTCs is now possible, and the clinical potential is being explored. We review current and potential uses for CTCs for pharmacogenomic analysis.
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Affiliation(s)
- Christopher D Hart
- Sandro Pitigliani Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Prato 59100, Italy; Breast Cancer Translational Research Unit, Hospital of Prato, Via Suor Niccolina 20, Prato 59100, Italy
| | - Francesca Galardi
- Breast Cancer Translational Research Unit, Hospital of Prato, Via Suor Niccolina 20, Prato 59100, Italy
| | - Marta Pestrin
- Sandro Pitigliani Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Prato 59100, Italy; Breast Cancer Translational Research Unit, Hospital of Prato, Via Suor Niccolina 20, Prato 59100, Italy
| | - Francesca De Luca
- Breast Cancer Translational Research Unit, Hospital of Prato, Via Suor Niccolina 20, Prato 59100, Italy
| | - Emanuela Risi
- Sandro Pitigliani Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Prato 59100, Italy; Breast Cancer Translational Research Unit, Hospital of Prato, Via Suor Niccolina 20, Prato 59100, Italy
| | - Angelo Di Leo
- Sandro Pitigliani Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Prato 59100, Italy; Breast Cancer Translational Research Unit, Hospital of Prato, Via Suor Niccolina 20, Prato 59100, Italy.
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325
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Guisier F, Salaün M, Lachkar S, Lamy A, Piton N, Obstoy B, Sabourin JC, Thiberville L. Molecular analysis of peripheral non-squamous non-small cell lung cancer sampled by radial EBUS. Respirology 2016; 21:718-26. [DOI: 10.1111/resp.12737] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/22/2015] [Accepted: 11/13/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Florian Guisier
- Clinique Pneumologique; Rouen University Hospital; Rouen France
- CIC-INSERM 1404; Rouen University Hospital; Rouen France
- EA 4108, LITIS QuantiF laboratory; University of Rouen; Rouen France
| | - Mathieu Salaün
- Clinique Pneumologique; Rouen University Hospital; Rouen France
- CIC-INSERM 1404; Rouen University Hospital; Rouen France
- EA 4108, LITIS QuantiF laboratory; University of Rouen; Rouen France
| | - Samy Lachkar
- Clinique Pneumologique; Rouen University Hospital; Rouen France
- CIC-INSERM 1404; Rouen University Hospital; Rouen France
| | - Aude Lamy
- Genetic Somatic Tumor Laboratory and Pathology Department; Rouen University Hospital; Rouen France
| | - Nicolas Piton
- Genetic Somatic Tumor Laboratory and Pathology Department; Rouen University Hospital; Rouen France
| | - Bérengère Obstoy
- Clinique Pneumologique; Rouen University Hospital; Rouen France
- CIC-INSERM 1404; Rouen University Hospital; Rouen France
| | - Jean-Christophe Sabourin
- Genetic Somatic Tumor Laboratory and Pathology Department; Rouen University Hospital; Rouen France
- INSERM U1079, IRIB; Rouen University Hospital; Rouen France
| | - Luc Thiberville
- Clinique Pneumologique; Rouen University Hospital; Rouen France
- CIC-INSERM 1404; Rouen University Hospital; Rouen France
- EA 4108, LITIS QuantiF laboratory; University of Rouen; Rouen France
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326
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Riva F, Dronov OI, Khomenko DI, Huguet F, Louvet C, Mariani P, Stern MH, Lantz O, Proudhon C, Pierga JY, Bidard FC. Clinical applications of circulating tumor DNA and circulating tumor cells in pancreatic cancer. Mol Oncol 2016; 10:481-93. [PMID: 26856794 DOI: 10.1016/j.molonc.2016.01.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/12/2016] [Accepted: 01/18/2016] [Indexed: 02/07/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most frequent pancreatic cancer type and is characterized by a dismal prognosis due to late diagnosis, local tumor invasion, frequent distant metastases and poor sensitivity to current therapy. In this context, circulating tumor cells and circulating tumor DNA constitute easily accessible blood-borne tumor biomarkers that may prove their clinical interest for screening, early diagnosis and metastatic risk assessment of PDAC. Moreover these markers represent a tool to assess PDAC mutational landscape. In this review, together with key biological findings, we summarize the clinical results obtained using "liquid biopsies" at the different stages of the disease, for early and metastatic diagnosis as well as monitoring during therapy.
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Affiliation(s)
- Francesca Riva
- Institut Curie, PSL Research University, SiRIC, Laboratory of Circulating Tumor Biomarkers, Paris, France; San Gerardo Hospital, Department of Medical Oncology, Monza, Italy
| | - Oleksii I Dronov
- Bogomolets National Medical University, Department of General Surgery No. 1, Kiev, Ukraine
| | - Dmytro I Khomenko
- Bogomolets National Medical University, Department of General Surgery No. 1, Kiev, Ukraine
| | - Florence Huguet
- Hopital Tenon, Pierre and Marie Curie Paris VI University, Department of Radiation Oncology, Paris, France
| | - Christophe Louvet
- Institut Mutualiste Montsouris, Department of Medical Oncology, Paris, France
| | - Pascale Mariani
- Institut Curie, PSL Research University, Department of Surgery, Paris, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, INSERM U830, Paris, France
| | - Olivier Lantz
- Institut Curie, PSL Research University, INSERM U932, Paris, France
| | - Charlotte Proudhon
- Institut Curie, PSL Research University, SiRIC, Laboratory of Circulating Tumor Biomarkers, Paris, France
| | - Jean-Yves Pierga
- Institut Curie, PSL Research University, SiRIC, Laboratory of Circulating Tumor Biomarkers, Paris, France; Institut Curie, PSL Research University, Department of Medical Oncology, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Francois-Clement Bidard
- Institut Curie, PSL Research University, SiRIC, Laboratory of Circulating Tumor Biomarkers, Paris, France; Institut Curie, PSL Research University, Department of Medical Oncology, Paris, France.
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327
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Pietrasz D, Pécuchet N, Fabre E, Blons H, Chevalier L, Taly V, Laurent-Puig P, Bachet JB. [What future for circulating tumor DNA? Current data and prospects in colorectal, non-small cell lung and pancreatic cancers]. Bull Cancer 2016; 103:55-65. [PMID: 26790710 DOI: 10.1016/j.bulcan.2015.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 10/29/2015] [Accepted: 10/30/2015] [Indexed: 12/23/2022]
Abstract
Ten years after the discovery of the predictive value of KRAS status for anti-EGFR antibodies, other genes involved in oncogenesis and therapeutic responses were identified and are now systematically sought. Molecular diagnosis often requires invasive procedures, sometimes iatrogenic, and is limited by feasibility problems, quantity and quality of samples. Identifying these mutations from blood biomarkers would reduce costs and diagnostic delay. The circulating tumor DNA (ctDNA) is one of the most promising blood biomarkers. In this review, we report and discuss the latest results obtained with ctDNA in colorectal cancer, non-small cell lung cancer, and adenocarcinoma of the pancreas. If the methods highlighting appear very heterogeneous, the correlation between mutations found in tumor and those identified in the blood exceeds 95 % specificity in numerous studies. The detection sensitivity is in turn strongly related to tumor stage patients. The presence of ctDNA appears as a prognostic factor for progression-free survival and overall survival. Finally, recent studies have shown that the changing rate ctDNA during systemic treatments had a predictive value for therapeutic efficacy. These results allow to consider the use of ctDNA in monitoring patients to identify early recurrence or progression.
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Affiliation(s)
- Daniel Pietrasz
- Université Paris Sorbonne Cité, centre universitaire des Saints-Pères, CNRS SNC5014, Inserm UMR-S1147 MEPPOT, 75006 Paris, France; Assistance publique-Hôpitaux de Paris, groupe hospitalier Pitié-Salpêtrière, service de chirurgie digestive et hépato-biliaire, 75013 Paris, France
| | - Nicolas Pécuchet
- Université Paris Sorbonne Cité, centre universitaire des Saints-Pères, CNRS SNC5014, Inserm UMR-S1147 MEPPOT, 75006 Paris, France; Assistance publique-Hôpitaux de Paris, hôpital européen Georges-Pompidou, service d'oncologie médicale, 75015 Paris, France
| | - Elizabeth Fabre
- Université Paris Sorbonne Cité, centre universitaire des Saints-Pères, CNRS SNC5014, Inserm UMR-S1147 MEPPOT, 75006 Paris, France; Assistance publique-Hôpitaux de Paris, hôpital européen Georges-Pompidou, service d'oncologie médicale, 75015 Paris, France
| | - Hélène Blons
- Université Paris Sorbonne Cité, centre universitaire des Saints-Pères, CNRS SNC5014, Inserm UMR-S1147 MEPPOT, 75006 Paris, France; Assistance publique-Hôpitaux de Paris, hôpital européen Georges-Pompidou, pôle de biologie, 75015 Paris, France
| | - Line Chevalier
- Assistance publique-Hôpitaux de Paris, groupe hospitalier Pitié-Salpêtrière, pôle 3I, service d'hépatogastroentérologie, 75013 Paris, France
| | - Valérie Taly
- Université Paris Sorbonne Cité, centre universitaire des Saints-Pères, CNRS SNC5014, Inserm UMR-S1147 MEPPOT, 75006 Paris, France
| | - Pierre Laurent-Puig
- Université Paris Sorbonne Cité, centre universitaire des Saints-Pères, CNRS SNC5014, Inserm UMR-S1147 MEPPOT, 75006 Paris, France; Assistance publique-Hôpitaux de Paris, hôpital européen Georges-Pompidou, pôle de biologie, 75015 Paris, France
| | - Jean-Baptiste Bachet
- Université Paris Sorbonne Cité, centre universitaire des Saints-Pères, CNRS SNC5014, Inserm UMR-S1147 MEPPOT, 75006 Paris, France; Assistance publique-Hôpitaux de Paris, groupe hospitalier Pitié-Salpêtrière, pôle 3I, service d'hépatogastroentérologie, 75013 Paris, France; Université Sorbonne, université Pierre-et-Marie-Curie, Paris 06, 75005 Paris, France.
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328
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Balgkouranidou I, Chimonidou M, Milaki G, Tsaroucha E, Kakolyris S, Georgoulias V, Lianidou E. SOX17 promoter methylation in plasma circulating tumor DNA of patients with non-small cell lung cancer. ACTA ACUST UNITED AC 2016; 54:1385-93. [DOI: 10.1515/cclm-2015-0776] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/01/2015] [Indexed: 12/11/2022]
Abstract
AbstractSOX17 belongs to the high-mobility group-box transcription factor superfamily and down-regulates the Wnt pathway. The aim of our study was to evaluate the prognostic significance ofWe examined the methylation status ofIn operable NSCLC,Our results show that
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329
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Pécuchet N, Legras A, Laurent-Puig P, Blons H. Place du NGS (Next Generation Sequencing) et de l’ADN tumoral circulant dans le testing moléculaire des cancers bronchiques. Ann Pathol 2016; 36:80-93. [DOI: 10.1016/j.annpat.2015.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 11/12/2015] [Indexed: 02/05/2023]
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330
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Tsui DWY, Berger MF. Profiling Non-Small Cell Lung Cancer: From Tumor to Blood. Clin Cancer Res 2015; 22:790-2. [PMID: 26671996 DOI: 10.1158/1078-0432.ccr-15-2514] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 11/11/2015] [Indexed: 11/16/2022]
Abstract
Circulating cell-free tumor DNA has shown great promise for noninvasive genomic profiling to guide the administration of targeted therapies in non-small cell lung cancer. With advancements in molecular technology, it is now possible to interrogate multiple clinically actionable genetic drivers in the blood with a single assay.
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Affiliation(s)
- Dana W Y Tsui
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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331
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Remon J, Gorham J, Besse B, Sculier JP. Circulating free DNA, new dynamic marker in nonsmall cell lung cancer patients? Eur Respir J 2015; 46:1548-50. [DOI: 10.1183/13993003.01482-2015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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332
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Bianchi F. Molecular profile of liquid biopsies: next generation biomarkers to improve lung cancer treatment. Ecancermedicalscience 2015; 9:598. [PMID: 26635902 PMCID: PMC4664509 DOI: 10.3332/ecancer.2015.598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Indexed: 12/19/2022] Open
Abstract
Molecular profiling of liquid biopsies is now emerging as pivotal for cancer biomarker discovery. The low-invasive nature of the approach used for collecting biospecimens (i.e. blood, urine, saliva, etc.) may allow a widespread application of novel molecular diagnostics based on liquid biopsies. This is relevant, for example, in cancer screening programmes where it is essential to reduce costs and the complexity of screening tests in order to increase study compliance and effectiveness. Here, I discuss recent advances in biomarkers for the early cancer detection and prediction of chemotherapy response based on the molecular profiling of liquid biopsies.
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Affiliation(s)
- Fabrizio Bianchi
- Molecular Medicine Program, European Institute of Oncology, Milan 20141, Italy
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333
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Circulating tumor DNA identified by targeted sequencing in advanced-stage non-small cell lung cancer patients. Cancer Lett 2015; 370:324-31. [PMID: 26582655 DOI: 10.1016/j.canlet.2015.11.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/13/2015] [Accepted: 11/04/2015] [Indexed: 12/18/2022]
Abstract
Non-small cell lung cancers (NSCLC) have unique mutation patterns, and some of these mutations may be used to predict prognosis or guide patient treatment. Mutation profiling before and during treatment often requires repeated tumor biopsies, which is not always possible. Recently, cell-free, circulating tumor DNA (ctDNA) isolated from blood plasma has been shown to contain genetic mutations representative of those found in the primary tumor tissue DNA (tDNA), and these samples can readily be obtained using non-invasive techniques. However, there are still no standardized methods to identify mutations in ctDNA. In the current study, we used a targeted sequencing approach with a semi-conductor based next-generation sequencing (NGS) platform to identify gene mutations in matched tDNA and ctDNA samples from 42 advanced-stage NSCLC patients from China. We identified driver mutations in matched tDNA and ctDNA in EGFR, KRAS, PIK3CA, and TP53, with an overall concordance of 76%. In conclusion, targeted sequencing of plasma ctDNA may be a feasible option for clinical monitoring of NSCLC in the near future.
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334
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Polivka J, Pesta M, Janku F. Testing for oncogenic molecular aberrations in cell-free DNA-based liquid biopsies in the clinic: are we there yet? Expert Rev Mol Diagn 2015; 15:1631-44. [PMID: 26559503 DOI: 10.1586/14737159.2015.1110021] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The optimal choice of cancer therapy depends upon analysis of the tumor genome for druggable molecular alterations. The spatial and temporal intratumor heterogeneity of cancers creates substantial challenges, as molecular profile depends on time and site of tumor tissue collection. To capture the entire molecular profile, multiple biopsies from primary and metastatic sites at different time points would be required, which is not feasible for ethical or economic reasons. Molecular analysis of circulating cell-free DNA offers a novel, minimally invasive method that can be performed at multiple time-points and plausibly better represents the prevailing molecular profile of the cancer. Molecular analysis of this cell-free DNA offers multiple clinically useful applications, such as identification of molecular targets for cancer therapy, monitoring of tumor molecular profile in real time, detection of emerging molecular aberrations associated with resistance to particular therapy, determination of cancer prognosis and diagnosis of cancer recurrence or progression.
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Affiliation(s)
- Jiri Polivka
- a Department of Histology and Embryology and Biomedical Centre, Faculty of Medicine in Plzen , Charles University in Prague , Plzen , Czech Republic.,b Department of Neurology , Faculty Hospital Plzen , Plzen , Czech Republic
| | - Martin Pesta
- c Department of Biology, Faculty of Medicine in Plzen , Charles University in Prague , Plzen , Czech Republic
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335
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Hollingsworth SJ, Biankin AV. The Challenges of Precision Oncology Drug Development and Implementation. Public Health Genomics 2015; 18:338-48. [PMID: 26555355 DOI: 10.1159/000441557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The drivers of precision medicine are clear: for patients (and physicians)--more options, durable clinical benefit, reduced exposure to non-effective drugs and potential to leverage current scientific and technological advances; for the pharmaceutical industry--the potential to tackle core challenges in discovering and developing better and more efficacious medicines, to reduce rates of attrition in drug development and to reduce development costs; for healthcare systems and payers--improved efficiency through the provision of effective care and avoiding ineffective treatments. Oncology has been at the vanguard, the improvements gained in patient survival notable. However, the increasing number of molecular subgroups requires an equally increasing number (and new generation) of highly selective agents targeting inevitably lower incidence molecular segments. Innovative trial designs (umbrella/basket studies) are emerging as a patient-centric approach to drug development, and the rise in public-private partnerships, cross-industry, government and non-profit sector collaborations is enabling implementation of complex clinical trial designs. This poses significant challenges for healthcare systems and regulatory approval. Further substantial evolution of policy and processes, particularly regulatory requirements for approval for new therapeutics, are required.
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336
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Vallée A, Audigier-Valette C, Herbreteau G, Merrien J, Tessonnier L, Théoleyre S, Denis MG. Rapid clearance of circulating tumor DNA during treatment with AZD9291 of a lung cancer patient presenting the resistance EGFR T790M mutation. Lung Cancer 2015; 91:73-4. [PMID: 26612314 DOI: 10.1016/j.lungcan.2015.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 11/04/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Audrey Vallée
- Laboratoire de Biochimie, Plateforme de Génétique Moléculaire des Cancers, CHU de Nantes, France
| | | | - Guillaume Herbreteau
- Laboratoire de Biochimie, Plateforme de Génétique Moléculaire des Cancers, CHU de Nantes, France
| | - Julien Merrien
- Service de Pneumologie, CHITS Toulon Sainte Musse, France
| | | | - Sandrine Théoleyre
- Laboratoire de Biochimie, Plateforme de Génétique Moléculaire des Cancers, CHU de Nantes, France
| | - Marc G Denis
- Laboratoire de Biochimie, Plateforme de Génétique Moléculaire des Cancers, CHU de Nantes, France.
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337
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Guo K, Zhang Z, Han L, Han J, Wang J, Zhou Y, Liu H, Tong L, Li X, Yan X. Detection of epidermal growth factor receptor mutation in plasma as a biomarker in Chinese patients with early-stage non-small cell lung cancer. Onco Targets Ther 2015; 8:3289-96. [PMID: 26609241 PMCID: PMC4644181 DOI: 10.2147/ott.s94297] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Purpose This preplanned exploratory analysis was conducted to reveal the true status of correlation between tissue and plasma detection for early-stage non-small cell lung cancer (NSCLC) epidermal growth factor receptor (EGFR) mutations, knowing that specific subgroups of NSCLC patients may be potential candidates for EGFR mutation analysis by using plasma samples. Materials and methods Tissue samples were surgically resected from 198 patients with stage I–IV NSCLC, where stage IA to IIIA accounted for 92.4%. EGFR mutations in all these tissues were positive. Paired plasma EGFR mutations were detected by real-time polymerase chain reaction; concentration of cell-free DNA (cfDNA) in plasma was measured by ultraviolet spectrophotometry. Results EGFR-activating mutation was detected in 34 plasma samples, and their mutation types were matched with that in tissue. The sensitivity of EGFR mutation for the 198 paired tissue and plasma samples was 17.2%. The sensitivity positively correlated with disease stage and negatively correlated with tumor differentiation. The sensitivity of stage IA, IB, IIA, IIB, and IIIA was 1.6%, 7.9%, 11.1%, 20%, and 33.3%, respectively; the sensitivity of high differentiation was 0% versus 36.8% for poor differentiation. There was no correlation between plasma cfDNA concentration and patient characteristics. Conclusion We recommend using plasma cfDNA as a biomarker in stage IIIA or poorly differentiated tumors for gene diagnosis, especially in patients whose tissue samples cannot be obtained by surgery. Plasma samples can really reflect the patients’ EGFR mutation types and may contain comprehensive genotypic information that comes from different parts of the tumor than tissue specimens. The concentration of plasma cfDNA does not vary with patient characteristics.
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Affiliation(s)
- Kai Guo
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - ZhiPei Zhang
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - Lu Han
- Department of Ultrasound, Xijing Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - Jing Han
- Department of Ophthalmology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - Jian Wang
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - YongAn Zhou
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - HongGang Liu
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - LiPing Tong
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - XiaoFei Li
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
| | - XiaoLong Yan
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, People's Republic of China
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338
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Li BT, Drilon A, Johnson ML, Hsu M, Sima CS, McGinn C, Sugita H, Kris MG, Azzoli CG. A prospective study of total plasma cell-free DNA as a predictive biomarker for response to systemic therapy in patients with advanced non-small-cell lung cancers. Ann Oncol 2015; 27:154-9. [PMID: 26487589 DOI: 10.1093/annonc/mdv498] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/08/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND While previous studies have reported on the prognostic value of total plasma cell-free deoxyribonucleic acid (cfDNA) in lung cancers, few have prospectively evaluated its predictive value for systemic therapy response. PATIENTS AND METHODS We conducted a prospective study to evaluate the association between changes in total cfDNA and radiologic response to systemic therapy in patients with stage IIIB/IV non-small-cell lung cancers (NSCLCs). Paired blood collections for cfDNA and computed tomography (CT) assessments by RECIST v1.0 were performed at baseline and 6-12 weeks after therapy initiation. Total cfDNA levels were measured in plasma using quantitative real-time polymerase chain reaction. Associations between changes in cfDNA and radiologic response, progression-free survival (PFS), and overall survival (OS) were measured using Kruskal-Wallis and Kaplan-Meier estimates. RESULTS A total of 103 patients completed paired cfDNA and CT response assessments. Systemic therapy administered included cytotoxic chemotherapy in 57% (59/103), molecularly targeted therapy in 17% (17/103), and combination therapy in 26% (27/103). Median change in cfDNA from baseline to response assessment did not significantly differ by radiologic response categories of progression of disease, stable disease and partial response (P = 0.10). However, using radiologic response as continuous variable, there was a weak positive correlation between change in radiologic response and change in cfDNA (Spearman's correlation coefficient 0.21, P = 0.03). Baseline cfDNA levels were not associated with PFS [hazard ratio (HR) = 1.06, 95% confidence interval (CI) 0.93-1.20, P = 0.41] or OS (HR = 1.04, 95% CI 0.93-1.17, P = 0.51), neither were changes in cfDNA. CONCLUSIONS In this large prospective study, changes in total cfDNA over time did not significantly predict radiologic response from systemic therapy in patients with advanced NSCLC. Pretreatment levels of total cfDNA were not prognostic of survival. Total cfDNA level is not a highly specific predictive biomarker and future investigations in cfDNA should focus on tumor-specific genomic alterations using expanded capabilities of next-generation sequencing.
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Affiliation(s)
- B T Li
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, and Weill Cornell Medical College, New York, USA Sydney Medical School, University of Sydney, Sydney, Australia
| | - A Drilon
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, and Weill Cornell Medical College, New York, USA
| | - M L Johnson
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, and Weill Cornell Medical College, New York, USA
| | - M Hsu
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | - C S Sima
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York
| | - C McGinn
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, and Weill Cornell Medical College, New York, USA
| | - H Sugita
- Department of Biochemistry, Keck School of Medicine, University of Southern California, Los Angeles
| | - M G Kris
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, and Weill Cornell Medical College, New York, USA
| | - C G Azzoli
- Thoracic Oncology Program, Massachusetts General Hospital Cancer Center, Boston, USA
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339
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Lanman RB, Mortimer SA, Zill OA, Sebisanovic D, Lopez R, Blau S, Collisson EA, Divers SG, Hoon DSB, Kopetz ES, Lee J, Nikolinakos PG, Baca AM, Kermani BG, Eltoukhy H, Talasaz A. Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA. PLoS One 2015; 10:e0140712. [PMID: 26474073 PMCID: PMC4608804 DOI: 10.1371/journal.pone.0140712] [Citation(s) in RCA: 510] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/28/2015] [Indexed: 12/18/2022] Open
Abstract
Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital SequencingTM is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient’s cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing.
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Affiliation(s)
- Richard B. Lanman
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California, United States of America
- * E-mail:
| | - Stefanie A. Mortimer
- Department of Research and Bioinformatics, Guardant Health, Inc., Redwood City, California, United States of America
| | - Oliver A. Zill
- Department of Research and Bioinformatics, Guardant Health, Inc., Redwood City, California, United States of America
| | - Dragan Sebisanovic
- Department of Research and Bioinformatics, Guardant Health, Inc., Redwood City, California, United States of America
| | - Rene Lopez
- Department of Research and Bioinformatics, Guardant Health, Inc., Redwood City, California, United States of America
| | - Sibel Blau
- Rainier Hematology Oncology, Northwest Medical Specialties, Puyallup, Washington, United States of America
| | - Eric A. Collisson
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, California, United States of America
| | - Stephen G. Divers
- Genesis Cancer Center, Hot Springs, Arkansas, United States of America
| | - Dave S. B. Hoon
- Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, California, United States of America
| | - E. Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jeeyun Lee
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Petros G. Nikolinakos
- Department of Hematology and Medical Oncology, University Cancer and Blood Center, Athens, Georgia, United States of America
| | - Arthur M. Baca
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California, United States of America
| | - Bahram G. Kermani
- Department of Research and Bioinformatics, Guardant Health, Inc., Redwood City, California, United States of America
| | - Helmy Eltoukhy
- Administration, Guardant Health, Inc., Redwood City, California, United States of America
| | - AmirAli Talasaz
- Department of Research and Bioinformatics, Guardant Health, Inc., Redwood City, California, United States of America
- Administration, Guardant Health, Inc., Redwood City, California, United States of America
- * E-mail:
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340
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Biankin AV, Piantadosi S, Hollingsworth SJ. Patient-centric trials for therapeutic development in precision oncology. Nature 2015; 526:361-70. [PMID: 26469047 DOI: 10.1038/nature15819] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/14/2015] [Indexed: 12/26/2022]
Abstract
An enhanced understanding of the molecular pathology of disease gained from genomic studies is facilitating the development of treatments that target discrete molecular subclasses of tumours. Considerable associated challenges include how to advance and implement targeted drug-development strategies. Precision medicine centres on delivering the most appropriate therapy to a patient on the basis of clinical and molecular features of their disease. The development of therapeutic agents that target molecular mechanisms is driving innovation in clinical-trial strategies. Although progress has been made, modifications to existing core paradigms in oncology drug development will be required to realize fully the promise of precision medicine.
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Affiliation(s)
- Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland G61 1BD, UK
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
- Department of Surgery, Bankstown Hospital, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
| | - Steven Piantadosi
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90095, USA
| | - Simon J Hollingsworth
- Innovative Medicines &Early Development Oncology, AstraZeneca, Cambridge Science Park, Cambridge CB4 0FZ, UK
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341
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Paweletz CP, Sacher AG, Raymond CK, Alden RS, O'Connell A, Mach SL, Kuang Y, Gandhi L, Kirschmeier P, English JM, Lim LP, Jänne PA, Oxnard GR. Bias-Corrected Targeted Next-Generation Sequencing for Rapid, Multiplexed Detection of Actionable Alterations in Cell-Free DNA from Advanced Lung Cancer Patients. Clin Cancer Res 2015; 22:915-22. [PMID: 26459174 DOI: 10.1158/1078-0432.ccr-15-1627-t] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/29/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Tumor genotyping is a powerful tool for guiding non-small cell lung cancer (NSCLC) care; however, comprehensive tumor genotyping can be logistically cumbersome. To facilitate genotyping, we developed a next-generation sequencing (NGS) assay using a desktop sequencer to detect actionable mutations and rearrangements in cell-free plasma DNA (cfDNA). EXPERIMENTAL DESIGN An NGS panel was developed targeting 11 driver oncogenes found in NSCLC. Targeted NGS was performed using a novel methodology that maximizes on-target reads, and minimizes artifact, and was validated on DNA dilutions derived from cell lines. Plasma NGS was then blindly performed on 48 patients with advanced, progressive NSCLC and a known tumor genotype, and explored in two patients with incomplete tumor genotyping. RESULTS NGS could identify mutations present in DNA dilutions at ≥ 0.4% allelic frequency with 100% sensitivity/specificity. Plasma NGS detected a broad range of driver and resistance mutations, including ALK, ROS1, and RET rearrangements, HER2 insertions, and MET amplification, with 100% specificity. Sensitivity was 77% across 62 known driver and resistance mutations from the 48 cases; in 29 cases with common EGFR and KRAS mutations, sensitivity was similar to droplet digital PCR. In two cases with incomplete tumor genotyping, plasma NGS rapidly identified a novel EGFR exon 19 deletion and a missed case of MET amplification. CONCLUSIONS Blinded to tumor genotype, this plasma NGS approach detected a broad range of targetable genomic alterations in NSCLC with no false positives including complex mutations like rearrangements and unexpected resistance mutations such as EGFR C797S. Through use of widely available vacutainers and a desktop sequencing platform, this assay has the potential to be implemented broadly for patient care and translational research.
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Affiliation(s)
- Cloud P Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Adrian G Sacher
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Ryan S Alden
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Allison O'Connell
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stacy L Mach
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yanan Kuang
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Leena Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Paul Kirschmeier
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jessie M English
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lee P Lim
- Resolution Bioscience, Bellevue, Washington
| | - Pasi A Jänne
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts. Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Geoffrey R Oxnard
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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342
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Thress KS, Brant R, Carr TH, Dearden S, Jenkins S, Brown H, Hammett T, Cantarini M, Barrett JC. EGFR mutation detection in ctDNA from NSCLC patient plasma: A cross-platform comparison of leading technologies to support the clinical development of AZD9291. Lung Cancer 2015; 90:509-15. [PMID: 26494259 DOI: 10.1016/j.lungcan.2015.10.004] [Citation(s) in RCA: 399] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/28/2015] [Accepted: 10/04/2015] [Indexed: 12/19/2022]
Abstract
OBJECTIVES To assess the ability of different technology platforms to detect epidermal growth factor receptor (EGFR) mutations, including T790M, from circulating tumor DNA (ctDNA) in advanced non-small cell lung cancer (NSCLC) patients. MATERIALS AND METHODS A comparison of multiple platforms for detecting EGFR mutations in plasma ctDNA was undertaken. Plasma samples were collected from patients entering the ongoing AURA trial (NCT01802632), investigating the safety, tolerability, and efficacy of AZD9291 in patients with EGFR-sensitizing mutation-positive NSCLC. Plasma was collected prior to AZD9291 dosing but following clinical progression on a previous EGFR-tyrosine kinase inhibitor (TKI). Extracted ctDNA was analyzed using two non-digital platforms (cobas(®) EGFR Mutation Test and therascreen™ EGFR amplification refractory mutation system assay) and two digital platforms (Droplet Digital™ PCR and BEAMing digital PCR [dPCR]). RESULTS Preliminary assessment (38 samples) was conducted using all four platforms. For EGFR-TKI-sensitizing mutations, high sensitivity (78-100%) and specificity (93-100%) were observed using tissue as a non-reference standard. For the T790M mutation, the digital platforms outperformed the non-digital platforms. Subsequent assessment using 72 additional baseline plasma samples was conducted using the cobas(®) EGFR Mutation Test and BEAMing dPCR. The two platforms demonstrated high sensitivity (82-87%) and specificity (97%) for EGFR-sensitizing mutations. For the T790M mutation, the sensitivity and specificity were 73% and 67%, respectively, with the cobas(®) EGFR Mutation Test, and 81% and 58%, respectively, with BEAMing dPCR. Concordance between the platforms was >90%, showing that multiple platforms are capable of sensitive and specific detection of EGFR-TKI-sensitizing mutations from NSCLC patient plasma. CONCLUSION The cobas(®) EGFR Mutation Test and BEAMing dPCR demonstrate a high sensitivity for T790M mutation detection. Genomic heterogeneity of T790M-mediated resistance may explain the reduced specificity observed with plasma-based detection of T790M mutations versus tissue. These data support the use of both platforms in the AZD9291 clinical development program.
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Affiliation(s)
- Kenneth S Thress
- Translational Science, Oncology iMED, AstraZeneca, 35 Gatehouse Drive, Waltham, MA 02451, USA.
| | - Roz Brant
- Translational Science, Oncology iMED, AstraZeneca, Alderley Park, Macclesfield SK10 4TF, UK
| | - T Hedley Carr
- Translational Science, Oncology iMED, AstraZeneca, Milton Road, Cambridge CB4 0FZ, UK
| | - Simon Dearden
- Personalised Healthcare & Biomarkers, AstraZeneca, Milton Road, Cambridge CB4 0FZ, UK
| | - Suzanne Jenkins
- Personalised Healthcare & Biomarkers, AstraZeneca, Alderley Park, Macclesfield SK10 4TF, UK
| | - Helen Brown
- Personalised Healthcare & Biomarkers, AstraZeneca, Milton Road, Cambridge CB4 0FZ, UK
| | - Tracey Hammett
- Early Clinical Development, Alderley Park, Macclesfield SK10 4TF, UK
| | | | - J Carl Barrett
- Translational Science, Oncology iMED, AstraZeneca, 35 Gatehouse Drive, Waltham, MA 02451, USA
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343
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Sundaresan TK, Sequist LV, Heymach JV, Riely GJ, Jänne PA, Koch WH, Sullivan JP, Fox DB, Maher R, Muzikansky A, Webb A, Tran HT, Giri U, Fleisher M, Yu HA, Wei W, Johnson BE, Barber TA, Walsh JR, Engelman JA, Stott SL, Kapur R, Maheswaran S, Toner M, Haber DA. Detection of T790M, the Acquired Resistance EGFR Mutation, by Tumor Biopsy versus Noninvasive Blood-Based Analyses. Clin Cancer Res 2015; 22:1103-10. [PMID: 26446944 PMCID: PMC4775471 DOI: 10.1158/1078-0432.ccr-15-1031] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/01/2015] [Indexed: 12/21/2022]
Abstract
PURPOSE The T790M gatekeeper mutation in the EGFR is acquired by some EGFR-mutant non-small cell lung cancers (NSCLC) as they become resistant to selective tyrosine kinase inhibitors (TKI). As third-generation EGFR TKIs that overcome T790M-associated resistance become available, noninvasive approaches to T790M detection will become critical to guide management. EXPERIMENTAL DESIGN As part of a multi-institutional Stand-Up-To-Cancer collaboration, we performed an exploratory analysis of 40 patients with EGFR-mutant tumors progressing on EGFR TKI therapy. We compared the T790M genotype from tumor biopsies with analysis of simultaneously collected circulating tumor cells (CTC) and circulating tumor DNA (ctDNA). RESULTS T790M genotypes were successfully obtained in 30 (75%) tumor biopsies, 28 (70%) CTC samples, and 32 (80%) ctDNA samples. The resistance-associated mutation was detected in 47% to 50% of patients using each of the genotyping assays, with concordance among them ranging from 57% to 74%. Although CTC- and ctDNA-based genotyping were each unsuccessful in 20% to 30% of cases, the two assays together enabled genotyping in all patients with an available blood sample, and they identified the T790M mutation in 14 (35%) patients in whom the concurrent biopsy was negative or indeterminate. CONCLUSIONS Discordant genotypes between tumor biopsy and blood-based analyses may result from technological differences, as well as sampling different tumor cell populations. The use of complementary approaches may provide the most complete assessment of each patient's cancer, which should be validated in predicting response to T790M-targeted inhibitors.
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Affiliation(s)
- Tilak K Sundaresan
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory J Riely
- Department of Medicine, Thoracic Oncology Service, Division of Solid Tumor Oncology, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medical College, New York, New York
| | - Pasi A Jänne
- Department of Medicine, Harvard Medical School, Boston, Massachusetts. Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Walter H Koch
- Roche Molecular Systems, Inc., Pleasanton, California
| | - James P Sullivan
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Douglas B Fox
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Robert Maher
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Andrew Webb
- EKF Molecular Diagnostics, Ltd., Cardiff, United Kingdom
| | - Hai T Tran
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Uma Giri
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Martin Fleisher
- Clinical Chemistry Service, Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medical College, New York, New York
| | - Helena A Yu
- Department of Medicine, Thoracic Oncology Service, Division of Solid Tumor Oncology, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medical College, New York, New York
| | - Wen Wei
- Roche Molecular Systems, Inc., Pleasanton, California
| | - Bruce E Johnson
- Department of Medicine, Harvard Medical School, Boston, Massachusetts. Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Thomas A Barber
- BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - John R Walsh
- BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Jeffrey A Engelman
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Shannon L Stott
- Department of Medicine, Harvard Medical School, Boston, Massachusetts. BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Ravi Kapur
- BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Department of Surgery, Harvard Medical School, Boston, Massachusetts
| | - Mehmet Toner
- BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts. Department of Surgery, Harvard Medical School, Boston, Massachusetts
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts. Howard Hughes Medical Institute, Chevy Chase, Maryland.
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344
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D'Arcangelo M, Margetts J, Greystoke A. The use of circulating biomarkers in early clinical trials in patients with cancer. Biomark Med 2015; 9:1011-23. [PMID: 26441037 DOI: 10.2217/bmm.15.51] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The development of targeted therapies has changed the approach to early oncological clinical trial design. Identification of patient populations most likely to derive benefit and the biologically effective dose are now as important as determination of the maximum tolerated dose. Completion of the 'pharmacological audit trail' highlights drugs most likely to progress through to license, so resources can be allocated appropriately. Key to the success of this changing model is the validation/qualification of circulating biomarkers. These might provide a readily accessible and dynamic picture of drug effect, tumor response and toxicity with minimum risk to patients. This review article examines circulating biomarkers currently used in early oncological clinical trials. It considers the evidence for their employment, limitations and challenges for future development.
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Affiliation(s)
- Manolo D'Arcangelo
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK.,Northern Centre for Cancer Care, Freeman Hospital, Newcastle upon Tyne, UK
| | - Jane Margetts
- Northern Centre for Cancer Care, Freeman Hospital, Newcastle upon Tyne, UK
| | - Alastair Greystoke
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK.,Northern Centre for Cancer Care, Freeman Hospital, Newcastle upon Tyne, UK
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345
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Bordi P, Del Re M, Danesi R, Tiseo M. Circulating DNA in diagnosis and monitoring EGFR gene mutations in advanced non-small cell lung cancer. Transl Lung Cancer Res 2015; 4:584-97. [PMID: 26629427 PMCID: PMC4630520 DOI: 10.3978/j.issn.2218-6751.2015.08.09] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 08/11/2015] [Indexed: 01/06/2023]
Abstract
Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are current treatments for advanced non-small cell lung cancer (NSCLC) harboring activating EGFR gene mutations. Histological or cytological samples are the standard tumor materials for EGFR mutation analysis. However, the accessibility of tumor samples is not always possible and satisfactory in advanced NSCLC patients. Moreover, totality of EGFR mutated NSCLC patients will develop resistance to EGFR-TKIs. Repeat biopsies to study genetic evolution as a result of therapy are difficult, invasive and may be confounded by intra-tumor heterogeneity. Thus, exploring accurate and less invasive techniques to (I) diagnosis EGFR mutation if tissue is not available or not appropriate for molecular analysis and to (II) monitor EGFR-TKI treatment are needed. Circulating DNA fragments carrying tumor specific sequence alterations [circulating cell-free tumor DNA (cftDNA)] are found in the cell-free fraction of blood, representing a variable and generally small fraction of the total circulating DNA. cftDNA has a high degree of specificity to detect EGFR gene mutations in NSCLC. Studies have shown the feasibility of using cftDNA to diagnosis of EGFR activating gene mutations and also to monitor tumor dynamics in NSCLC patients treated with EGFR-TKIs. These evidences suggested that non-invasive techniques based on blood samples had a great potential in EGFR mutated NSCLC patients. In this review, we summarized these non-invasive approaches and relative scientific data now available, considering their possible applications in clinical practice of NSCLC treatment.
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346
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Lin CC, Huang WL, Wei F, Su WC, Wong DT. Emerging platforms using liquid biopsy to detect EGFR mutations in lung cancer. Expert Rev Mol Diagn 2015; 15:1427-40. [PMID: 26420338 DOI: 10.1586/14737159.2015.1094379] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Advances in target therapies for lung cancer have enabled detection of gene mutations, specifically those of EGFR. Assays largely depend on the acquisition of tumor tissue biopsy, which is invasive and may not reflect the genomic profile of the tumor at treatment due to tumor heterogeneity or changes that occur during treatment through acquired resistance. Liquid biopsy, a blood test that detects evidence of cancer cells or tumor DNA, has generated considerable interest for its ability to detect EGFR mutations. However, its clinical application is limited by complicated collection methods and the need for technique-dependent platforms. Recently, simpler techniques for EGFR mutant detection in urine or saliva samples have been developed. This review focuses on advances in liquid biopsy and discusses its potential for clinical implementation in lung cancer.
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Affiliation(s)
- Chien-Chung Lin
- a 1 Department of Internal Medicine, Institute of Clinical Medicine, National Cheng Kung University, Hospital, College of Medicine , Tainan, Taiwan
| | - Wei-Lun Huang
- a 1 Department of Internal Medicine, Institute of Clinical Medicine, National Cheng Kung University, Hospital, College of Medicine , Tainan, Taiwan
| | - Fang Wei
- b 2 UCLA - Dentistry, 73-034 CHS UCLA School of Dentistry , 10833 Le Conte Avenue, Los Angeles, California 90095, USA
| | - Wu-Chou Su
- a 1 Department of Internal Medicine, Institute of Clinical Medicine, National Cheng Kung University, Hospital, College of Medicine , Tainan, Taiwan
| | - David T Wong
- b 2 UCLA - Dentistry, 73-034 CHS UCLA School of Dentistry , 10833 Le Conte Avenue, Los Angeles, California 90095, USA
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347
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Jiang T, Ren S, Zhou C. Role of circulating-tumor DNA analysis in non-small cell lung cancer. Lung Cancer 2015; 90:128-34. [PMID: 26415994 DOI: 10.1016/j.lungcan.2015.09.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 09/13/2015] [Indexed: 01/04/2023]
Abstract
The discovery of actionable driver mutations such as epidermal growth factor receptor (EGFR) and microtubule-associated protein-like 4 anaplastic lymphoma kinase (EML4-ALK) and their highly responses to EGFR and ALK tyrosine kinase inhibitors (TKIs) in patients with advanced non-small-cell lung cancer (NSCLC) allowed precise medicine into reality. However, a substantial part of patients still have no sufficient tissue to perform genomic analysis. As a promising noninvasive biomarker and potential surrogate for the entire tumor genome, circulating tumor DNA (ctDNA) has been applied to the detection of driver gene mutations and epigenetic alteration and monitoring of tumor burden, acquired resistance, tumor heterogeneity and early diagnosis. Since precise therapy is a strategy that optimal therapy is decided based on simultaneous tumor genome information, ctDNA, as a liquid biopsy, may help to perform dynamic genetic surveillance. In this paper we will perspectively discuss the biology and identification of ctDNA in the blood of NSCLC patients and its clinical applications in patient management.
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Affiliation(s)
- Tao Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, PR China.
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348
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Midha A, Dearden S, McCormack R. EGFR mutation incidence in non-small-cell lung cancer of adenocarcinoma histology: a systematic review and global map by ethnicity (mutMapII). Am J Cancer Res 2015; 5:2892-911. [PMID: 26609494 PMCID: PMC4633915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 07/27/2015] [Indexed: 06/05/2023] Open
Abstract
Mutations in the epidermal growth factor receptor (EGFR) gene are commonly observed in non-small-cell lung cancer (NSCLC), particularly in tumors of adenocarcinoma (ADC) histology (NSCLC/ADC). Robust data exist regarding the prevalence of EGFR mutations in Western and Asian patients with NSCLC/ADC, yet there is a lack of data for patients of other ethnicities. This review collated available data with the aim of creating a complete, global picture of EGFR mutation frequency in patients with NSCLC/ADC by ethnicity. Worldwide literature reporting EGFR mutation frequency in patients with NSCLC/ADC was reviewed, to create a map of the world populated with EGFR mutation frequency by country (a 'global EGFR mutMap'). A total of 151 worldwide studies (n=33162 patients with NSCLC/ADC, of which 9749 patients had EGFR mutation-positive NSCLC/ADC) were included. There was substantial variation in EGFR mutation frequency between studies, even when grouped by geographic region or individual country. As expected, the Asia-Pacific NSCLC/ADC subgroup had the highest EGFR mutation frequency (47% [5958/12819; 87 studies; range 20%-76%]) and the lowest EGFR mutation frequency occurred in the Oceania NSCLC/ADC subgroup (12% [69/570; 4 studies; range 7%-36%]); however, comparisons between regions were limited due to the varying sizes of the patient populations studied. In all regional (geographic) subgroups where data were available, EGFR mutation frequency in NSCLC/ADC was higher in women compared with men, and in never-compared with ever-smokers. This review provides the foundation for a global map of EGFR mutation frequency in patients with NSCLC/ADC. The substantial lack of data from several large geographic regions of the world, notably Africa, the Middle East, Central Asia, and Central and South America, highlights a potential lack of routine mutation testing and the need for further investigations in these regions.
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Affiliation(s)
- Anita Midha
- Tissue Diagnostics Group, AstraZenecaMacclesfield, UK
| | - Simon Dearden
- Personalised Healthcare and Biomarkers, AstraZenecaMacclesfield, UK
| | - Rose McCormack
- Personalised Healthcare and Biomarkers, AstraZenecaMacclesfield, UK
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349
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Pasquale R, Fenizia F, Esposito Abate R, Sacco A, Esposito C, Forgione L, Rachiglio AM, Bevilacqua S, Montanino A, Franco R, Rocco G, Botti G, Denis MG, Morabito A, De Luca A, Normanno N. Assessment of high-sensitive methods for the detection of EGFR mutations in circulating free tumor DNA from NSCLC patients. Pharmacogenomics 2015; 16:1135-48. [PMID: 26249748 DOI: 10.2217/pgs.15.45] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
AIM We assessed the ability of the Therascreen(®) kit (plasma-Therascreen) and of a peptide nucleic acids (PNA)-clamp approach to detect EGFR mutations in plasma-derived circulating-free tumor DNA (cftDNA) from non-small-cell lung cancer patients. MATERIALS & METHODS cftDNA from 96 patients was analyzed for exon 19 deletions and the p.L858R mutation, using both plasma-Therascreen and PNA-clamp-based assays. RESULTS None of the 70 EGFR wild-type patients showed EGFR mutations in cftDNA with both techniques (specificity: 100%). In 17/26 EGFR-mutant patients, plasma-Therascreen analysis confirmed the mutation identified in the primary tumor (analytical sensitivity: 65.4%). Similar results were obtained with the PNA-clamp method. CONCLUSION Both approaches were specific and sensitive for EGFR mutational analysis of cftDNA in non-small-cell lung cancer patients.
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Affiliation(s)
- Raffaella Pasquale
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Francesca Fenizia
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Riziero Esposito Abate
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandra Sacco
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Claudia Esposito
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Laura Forgione
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Anna Maria Rachiglio
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Simona Bevilacqua
- Cell Biology & Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Agnese Montanino
- Thoraco-Pulmonary Medical Oncology, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Renato Franco
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Gaetano Rocco
- Thoracic Surgery, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Gerardo Botti
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Marc G Denis
- Department of Biochemistry, Nantes University Hospital, Nantes, France
| | - Alessandro Morabito
- Thoraco-Pulmonary Medical Oncology, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Antonella De Luca
- Cell Biology & Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Nicola Normanno
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy.,Cell Biology & Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
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Non-invasive approaches to monitor EGFR-TKI treatment in non-small-cell lung cancer. J Hematol Oncol 2015; 8:95. [PMID: 26227959 PMCID: PMC4521383 DOI: 10.1186/s13045-015-0193-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 07/20/2015] [Indexed: 01/10/2023] Open
Abstract
Tyrosine kinase inhibitors of epidermal growth factor receptor (EGFR-TKIs) are standard treatments for advanced non-small-cell lung cancer (NSCLC) patients harboring activating epidermal growth factor receptor (EGFR) mutations. Nowadays, tumor tissues acquired by surgery or biopsy are the routine materials for EGFR mutation analysis. However, the accessibility of tumor tissues is not always satisfactory in advanced NSCLC. Moreover, a high proportion of NSCLC patients will eventually develop resistance to EGFR-TKIs. Invasive procedures, such as surgery or biopsy, are impractical to be performed repeatedly to assess the evolution of EGFR-TKI resistance. Thus, exploring some convenient and less invasive techniques to monitor EGFR-TKI treatment is urgently needed. Circulating cell-free tumor DNA (ctDNA) has a high degree of specificity to detect EGFR mutations in NSCLC. Besides, ctDNA is capable of monitoring the disease progression during EGFR-TKI treatment. Certain serum microRNAs that correlate with EGFR signaling pathway, such as miR-21 and miR-10b, have been demonstrated to be helpful in evaluating the efficiency of EGFR-TKI therapeutics. A commercialized serum-based proteomic test, named VeriStrat test, has shown an outstanding ability to predict the clinical outcome of NSCLC patients receiving EGFR-TKIs. Analysis of EGFR mutations in circulating tumor cells (CTCs) is feasible, and CTCs represent a promising material to predict EGFR-TKI-treatment efficacy and resistance. These evidences suggested that non-invasive techniques based on serum or plasma samples had a great potential for monitoring EGFR-TKI treatment in NSCLC. In this review, we summarized these non-invasive approaches and considered their possible applications in EGFR-TKI-treatment monitoring.
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