101
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Palmirotta R, Lovero D, Cafforio P, Felici C, Mannavola F, Pellè E, Quaresmini D, Tucci M, Silvestris F. Liquid biopsy of cancer: a multimodal diagnostic tool in clinical oncology. Ther Adv Med Oncol 2018; 10:1758835918794630. [PMID: 30181785 PMCID: PMC6116068 DOI: 10.1177/1758835918794630] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/28/2018] [Indexed: 12/17/2022] Open
Abstract
Over the last decades, the concept of precision medicine has dramatically renewed
the field of medical oncology; the introduction of patient-tailored therapies
has significantly improved all measurable outcomes. Liquid biopsy is a
revolutionary technique that is opening previously unexpected perspectives. It
consists of the detection and isolation of circulating tumor cells, circulating
tumor DNA and exosomes, as a source of genomic and proteomic information in
patients with cancer. Many technical hurdles have been resolved thanks to newly
developed techniques and next-generation sequencing analyses, allowing a broad
application of liquid biopsy in a wide range of settings. Initially correlated
to prognosis, liquid biopsy data are now being studied for cancer diagnosis,
hopefully including screenings, and most importantly for the prediction of
response or resistance to given treatments. In particular, the identification of
specific mutations in target genes can aid in therapeutic decisions, both in the
appropriateness of treatment and in the advanced identification of secondary
resistance, aiming to early diagnose disease progression. Still application is
far from reality but ongoing research is leading the way to a new era in
oncology. This review summarizes the main techniques and applications of liquid
biopsy in cancer.
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Affiliation(s)
- Raffaele Palmirotta
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Domenica Lovero
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Paola Cafforio
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Felici
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Mannavola
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Eleonora Pellè
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Davide Quaresmini
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Marco Tucci
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Franco Silvestris
- Section of Clinical and Molecular Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro, Bari, 70124, Italy
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102
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Kessler MD, Pawar NR, Martin SS, Antalis TM, O'Connor TD. Improving Cancer Detection and Treatment with Liquid Biopsies and ptDNA. Trends Cancer 2018; 4:643-654. [PMID: 30149882 DOI: 10.1016/j.trecan.2018.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 07/07/2018] [Accepted: 07/09/2018] [Indexed: 12/30/2022]
Abstract
Liquid biopsy, or the capacity to noninvasively isolate and analyze plasma tumor DNA (ptDNA) using blood samples, represents an important tool for modern oncology that enables increasingly safe, personalized, and robust cancer diagnosis and treatment. Here, we review advances in the development and implementation of liquid biopsy approaches, and we focus on the capacity of liquid biopsy to noninvasively detect oncological disease and enhance early detection strategies. In addition to noting the distinctions between mutation-targeted and mutation-agnostic approaches, we discuss the potential for genomic analysis and longitudinal testing to identify somatic lesions early and to guide intervention at more manageable disease stages.
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Affiliation(s)
- Michael D Kessler
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore MD 21201, USA.
| | - Nisha R Pawar
- Department of Medicine, University of Maryland School of Medicine, Baltimore MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore MD 21201, USA
| | - Stuart S Martin
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore MD 21201, USA; Department of Physiology, University of Maryland School of Medicine, Baltimore MD 21201, USA
| | - Toni M Antalis
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore MD 21201, USA; Department of Physiology, University of Maryland School of Medicine, Baltimore MD 21201, USA
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore MD 21201, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore MD 21201, USA
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103
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The liquid biopsy in the management of colorectal cancer patients: Current applications and future scenarios. Cancer Treat Rev 2018; 70:1-8. [PMID: 30053724 DOI: 10.1016/j.ctrv.2018.07.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/17/2018] [Indexed: 02/06/2023]
Abstract
The term liquid biopsy refers to the analysis of biomarkers in any body fluid, including blood, urine and cerebrospinal fluid. In cancer, liquid biopsy testing allows the analysis of tumor-derived DNA, RNA, miRNA and proteins that can be either cell-free or contained in circulating tumor cells (CTC), extracellular vesicles (EVs) or platelets. A number of studies suggest that liquid biopsy testing could have a relevant role in the management of colorectal cancer (CRC) patients at different stages of the disease. Analysis of cell-free DNA (cfDNA), CTC and/or miRNA can provide relevant information for the early diagnosis of CRC and the identification of minimal residual disease and, more generally, the evaluation of the risk of recurrence in early CRC patients. In addition, liquid biopsy testing might allow the assessment of prognostic and predictive biomarkers in metastatic CRC patients, and the monitoring of the response to treatment and of the clonal evolution of the disease. While a number of elegant studies have shown the potential of liquid biopsy in CRC, the possibility to use this approach in the daily clinical practice is still limited. The use of non-standardized methods, the small cohorts of patients analyzed, the lack of demonstration of a clear clinical benefit are the main limitations of the studies with liquid biopsy in CRC reported up to now. The potential of this approach and the steps that need still to be taken to translate these preliminary findings in the clinic are discussed in this review.
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104
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Hu T, Shen H, Huang H, Song M, Yang Z, Zhou Y, Zhao G. Urinary circulating DNA profiling in non-small cell lung cancer patients following treatment shows prognostic potential. J Thorac Dis 2018; 10:4137-4146. [PMID: 30174858 DOI: 10.21037/jtd.2018.06.50] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Disease relapse in non-small cell lung cancer (NSCLC) requires close monitoring for early detection. The aim of the current study examines the use of urinary circulating DNA for patients after first line therapies. Methods EGFR positive NSCLC patients in stages I-III were profiled using digital droplet PCR (ddPCR). Urinary circulating DNA was collected prior to treatment and all monitored patients had detectable EGFR mutations. Post treatment urinary DNA measurements were taken at multiple time intervals. Results were matched to disease-free survival. Results Among the 213 patients recruited, 130 had matched EGFR profiles to corresponding tumor tissues. Concentrations of mutant DNA varied with different patients and mean concentration was 220±237 copies/mL. Measurements taken post-treatment showed a significant number of patients with undetectable EGFR mutations in their urine samples. Other patients registered a significant decline in urinary DNA concentrations. For measurements taken post treatment (6-month), we observed a significant increase of positively identified EGFR mutations in urine samples. In the patient group with higher urinary DNA concentration, 91% of the cohort experienced recurrence. Conclusions Our results indicated that urinary DNA measurements can potentially be useful for disease monitoring of minimal residual disease (MRD) in NSCLC. This can complement current serial radiographic imaging to provide early detection for lung cancer relapse.
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Affiliation(s)
- Tianjun Hu
- Department of Thoracic Surgery, Ningbo No. 2 Hospital, Ningbo 315010, China
| | - Haibo Shen
- Department of Thoracic Surgery, Ningbo No. 2 Hospital, Ningbo 315010, China
| | - Hongbo Huang
- Department of Thoracic Surgery, Ningbo No. 2 Hospital, Ningbo 315010, China
| | - Meijun Song
- Department of Emergency Medicine, Ningbo No. 2 Hospital, Ningbo 315010, China
| | - Zhenghua Yang
- Department of Thoracic Surgery, Ningbo No. 2 Hospital, Ningbo 315010, China
| | - Yingjie Zhou
- Department of Thoracic Surgery, Ningbo No. 2 Hospital, Ningbo 315010, China
| | - Guofang Zhao
- Department of Thoracic Surgery, Ningbo No. 2 Hospital, Ningbo 315010, China
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105
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ctDNA and CTCs in Liquid Biopsy - Current Status and Where We Need to Progress. Comput Struct Biotechnol J 2018; 16:190-195. [PMID: 29977481 PMCID: PMC6024152 DOI: 10.1016/j.csbj.2018.05.002] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 12/12/2022] Open
Abstract
We discuss the current status of liquid biopsy and its advantages and challenges with a focus on pre-analytical sample handling, technologies and workflows. The potential of circulating tumor cells and circulating tumor DNA is pointed out and an overview of corresponding technologies is given.
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106
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Abstract
CDKN2A is a tumor suppressor gene and is frequently inactivated in human cancers by hypermethylation of its promoter. However, the role and diagnostic value of CDKN2A methylation in esophageal cancer (EC) remains controversial. Therefore, we performed a meta-analysis, including data from 42 articles (2656 ECs, 612 precancerous lesions, and 2367 controls). A significant increase in the frequency of CDKN2A methylation was identified during EC carcinogenesis: cancer vs. controls, odds ratio (OR) = 12.60 (95 % CI, 8.90–17.85); cancer vs. precancerous lesions, OR = 2.89 (95% CI, 2.20–3.79); and precancerous lesions vs. controls, OR = 7.38, 95% (CI, 4.31–12.66). CDKN2A promoter methylation was associated with EC tumor grade (OR = 1.79; 95% CI, 1.20–2.67) and clinical stage (OR = 2.56; 95% CI, 1.33–4.92). Additionally, the sensitivity, specificity, and area under the summary receiver operating characteristic curve (AUC) for diagnosis of EC based on CDKN2A methylation were 0.52 (95% CI, 0.44–0.59), 0.96 (95% CI, 0.93–0.98), and 0.83 (95% CI, 0.79–0.86), respectively. AUCs for blood and tissue sample subgroups were 0.90 and 0.82, respectively. Our findings indicate that CDKN2A methylation has a vital role in EC tumorigenesis and could be a biomarker for early diagnosis of EC.
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107
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Tikkanen T, Leroy B, Fournier JL, Risques RA, Malcikova J, Soussi T. Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing. Hum Mutat 2018; 39:925-933. [PMID: 29696732 DOI: 10.1002/humu.23543] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/13/2018] [Accepted: 04/23/2018] [Indexed: 12/12/2022]
Abstract
Accurate annotation of genomic variants in human diseases is essential to allow personalized medicine. Assessment of somatic and germline TP53 alterations has now reached the clinic and is required in several circumstances such as the identification of the most effective cancer therapy for patients with chronic lymphocytic leukemia (CLL). Here, we present Seshat, a Web service for annotating TP53 information derived from sequencing data. A flexible framework allows the use of standard file formats such as Mutation Annotation Format (MAF) or Variant Call Format (VCF), as well as common TXT files. Seshat performs accurate variant annotations using the Human Genome Variation Society (HGVS) nomenclature and the stable TP53 genomic reference provided by the Locus Reference Genomic (LRG). In addition, using the 2017 release of the UMD_TP53 database, Seshat provides multiple statistical information for each TP53 variant including database frequency, functional activity, or pathogenicity. The information is delivered in standardized output tables that minimize errors and facilitate comparison of mutational data across studies. Seshat is a beneficial tool to interpret the ever-growing TP53 sequencing data generated by multiple sequencing platforms and it is freely available via the TP53 Website, http://p53.fr or directly at http://vps338341.ovh.net/.
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Affiliation(s)
| | | | | | - Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jitka Malcikova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Thierry Soussi
- Sorbonne Université, UPMC Univ Paris, Paris, France.,Department of Oncology-Pathology, Cancer Center Karolinska (CCK), Karolinska Institutet, Stockholm, Sweden.,INSERM, Centre de Recherche des Cordeliers, U1138, Paris, France
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108
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Šlekienė L, Stakišaitis D, Balnytė I, Valančiūtė A. Sodium Valproate Inhibits Small Cell Lung Cancer Tumor Growth on the Chicken Embryo Chorioallantoic Membrane and Reduces the p53 and EZH2 Expression. Dose Response 2018; 16:1559325818772486. [PMID: 29760602 PMCID: PMC5944146 DOI: 10.1177/1559325818772486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 12/30/2022] Open
Abstract
The study aims to test the effect of different sodium valproate (NaVP) doses on small cell lung cancer NCI-H146 cells tumor in chicken embryo chorioallantoic membrane (CAM) model. Xenografts were investigated in the following groups: nontreated control and 5 groups treated with different NaVP doses (2, 3, 4, 6, and 8 mmol/L). Invasion of tumors into CAM in the nontreated group reached 76%. Tumors treated with 8 mmol/L NaVP doses significantly differed in tumor invasion frequency from the control and those treated with 2 mmol/L (P < .01). The calculated probability of 50% tumor noninvasion into CAM was when tumors were treated with 4 mmol/L of NaVP. Number of p53-positive cells in tumors was significantly reduced when treated with NaVP doses from 3 to 8 mmol/L as compared with control; number of EZH2-positive cells in control significantly differed from all NaVP-treated groups. No differences in p53- and EZH2-positive cell numbers were found among 4, 6, and 8 mmol/L NaVP-treated groups. Invaded tumors had an increased N-cadherin and reduced E-cadherin expression. The results indicate the increasing NaVP dose to be able to inhibit tumors progression. Expression of p53 and EZH2 may be promising target markers of therapeutic efficacy evaluation.
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Affiliation(s)
- Lina Šlekienė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Donatas Stakišaitis
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania.,Laboratory of Molecular Oncology, National Cancer Institute, Vilnius, Lithuania
| | - Ingrida Balnytė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Angelija Valančiūtė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
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109
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What Does This Mutation Mean? The Tools and Pitfalls of Variant Interpretation in Lymphoid Malignancies. Int J Mol Sci 2018; 19:ijms19041251. [PMID: 29677173 PMCID: PMC5979354 DOI: 10.3390/ijms19041251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/09/2018] [Accepted: 04/14/2018] [Indexed: 01/21/2023] Open
Abstract
High throughput sequencing (HTS) is increasingly important in determining cancer diagnoses, with subsequent prognostic and therapeutic implications. The biology of cancer is becoming increasingly deciphered and it is clear that therapy needs to be individually tailored. Whilst translational research plays an important role in lymphoid malignancies, few guidelines exist to guide biologists and routine laboratories through this constantly evolving field. In this article, we review the challenges of interpreting HTS in lymphoid malignancies and provide a toolkit to interpret single nucleotide variants obtained from HTS. We define the pre-analytical issues such as sequencing DNA obtained from formalin-fixed and paraffin-embedded tissue (FFPE), the acquisition of germline DNA, or the bioinformatic pitfalls, the analytical issues encountered and how to manage them. We describe the main constitutional and cancer databases, their characteristics and limitations, with an emphasis on variant interpretation in lymphoid malignancies. Finally, we discuss the challenges of predictions that one can make using in silico or in vitro modelling, pharmacogenomic screening, and the limits of those prediction tools. This description of the current status in genomic interpretation highlights the need for new large databases and international collaboration in the lymphoma field.
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110
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Santarpia M, Liguori A, D'Aveni A, Karachaliou N, Gonzalez-Cao M, Daffinà MG, Lazzari C, Altavilla G, Rosell R. Liquid biopsy for lung cancer early detection. J Thorac Dis 2018; 10:S882-S897. [PMID: 29780635 DOI: 10.21037/jtd.2018.03.81] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecularly targeted therapies and immune checkpoint inhibitors have markedly improved the therapeutic management of advanced lung cancer. However, it still remains the leading cause of cancer-related mortality worldwide, with disease stage at diagnosis representing the main prognostic factor. Detection of lung cancer at an earlier stage of disease, potentially susceptible of curative resection, can be critical to improve patients survival. Low-dose computed tomography (LDCT) screening of high-risk patients has been demonstrated to reduce mortality from lung cancer, but can be also associated with high false-positive rate, thus often resulting in unnecessary interventions for patients. Novel sensitive and specific biomarkers for identification of high-risk subjects and early detection that can be used alternatively and/or complement current routine diagnostic procedures are needed. Liquid biopsy has recently demonstrated its clinical usefulness in advanced NSCLC as a surrogate of tissue biopsy for noninvasive assessment of specific genomic alterations, thereby providing prognostic and predictive information. Different biosources from liquid biopsy, including cell free circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes and tumor-educated platelets (TEPs), have also been widely investigated for their potential role in lung cancer diagnosis. This review will provide an overview on the circulating biomarkers being evaluated for lung cancer detection, mainly focusing on results from most recent studies, the techniques developed to perform their assessment in blood and other biologic fluids and challenges in their clinical applications.
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Affiliation(s)
- Mariacarmela Santarpia
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Alessia Liguori
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Alessandro D'Aveni
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Niki Karachaliou
- Institute of Oncology Rosell (IOR), University Hospital Sagrat Cor, Barcelona, Spain
| | - Maria Gonzalez-Cao
- Department of Oncology, Institute of Oncology Rosell (IOR), Quirón-Dexeus University Institute, Barcelona, Spain
| | - Maria Grazia Daffinà
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Chiara Lazzari
- Department of Oncology, Division of Experimental Medicine, IRCCS San Raffaele, Milan, Italy
| | - Giuseppe Altavilla
- Medical Oncology Unit, Department of Human Pathology of Adult and Evolutive Age "G. Barresi", University of Messina, Messina, Italy
| | - Rafael Rosell
- Cancer Biology and Precision Medicine Program, Germans Trias i Pujol University Hospital, Badalona, Spain.,Catalan Institute of Oncology, Germans Trias i Pujol University Hospital, Badalona, Spain
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111
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Zhao H, Chen KZ, Hui BG, Zhang K, Yang F, Wang J. Role of circulating tumor DNA in the management of early-stage lung cancer. Thorac Cancer 2018. [PMID: 29528556 PMCID: PMC5928385 DOI: 10.1111/1759-7714.12622] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Lung cancer is one of the most common cancers and the predominant cause of cancer‐related death in the world. The low accuracy of early detection techniques and high risk of relapse greatly contribute to poor prognosis. An accurate clinical tool that can assist in diagnosis and surveillance is urgently needed. Circulating tumor DNA (ctDNA) is free DNA shed from tumor cells and isolated from peripheral blood. The genomic profiles of ctDNA have been shown to closely match those of the corresponding tumors. With the development of approaches with high sensitivity and specificity, ctDNA plays a vital role in the management of lung cancer as a result of its reproducible, non‐invasive, and easy‐to‐obtain characteristics. However, most previous studies have focused on advanced lung cancer. Few studies have investigated ctDNA in the early stages of the disease. In this review, we focus on ctDNA obtained from patients in the early stage of lung cancer, provide a summary of the related literature to date, and describe the main approaches to ctDNA and the clinical applications.
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Affiliation(s)
- Heng Zhao
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
| | - Ke-Zhong Chen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
| | - Ben-Gang Hui
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
| | - Kai Zhang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
| | - Jun Wang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China
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112
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Merker JD, Oxnard GR, Compton C, Diehn M, Hurley P, Lazar AJ, Lindeman N, Lockwood CM, Rai AJ, Schilsky RL, Tsimberidou AM, Vasalos P, Billman BL, Oliver TK, Bruinooge SS, Hayes DF, Turner NC. Circulating Tumor DNA Analysis in Patients With Cancer: American Society of Clinical Oncology and College of American Pathologists Joint Review. Arch Pathol Lab Med 2018; 142:1242-1253. [PMID: 29504834 DOI: 10.5858/arpa.2018-0901-sa] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
PURPOSE.— Clinical use of analytical tests to assess genomic variants in circulating tumor DNA (ctDNA) is increasing. This joint review from the American Society of Clinical Oncology and the College of American Pathologists summarizes current information about clinical ctDNA assays and provides a framework for future research. METHODS.— An Expert Panel conducted a literature review on the use of ctDNA assays for solid tumors, including preanalytical variables, analytical validity, interpretation and reporting, and clinical validity and utility. RESULTS.— The literature search identified 1338 references. Of those, 390, plus 31 references supplied by the Expert Panel, were selected for full-text review. There were 77 articles selected for inclusion. CONCLUSIONS.— The evidence indicates that testing for ctDNA is optimally performed on plasma collected in cell stabilization or EDTA tubes, with EDTA tubes processed within 6 hours of collection. Some ctDNA assays have demonstrated clinical validity and utility with certain types of advanced cancer; however, there is insufficient evidence of clinical validity and utility for the majority of ctDNA assays in advanced cancer. Evidence shows discordance between the results of ctDNA assays and genotyping tumor specimens, and supports tumor tissue genotyping to confirm undetected results from ctDNA tests. There is no evidence of clinical utility and little evidence of clinical validity of ctDNA assays in early-stage cancer, treatment monitoring, or residual disease detection. There is no evidence of clinical validity or clinical utility to suggest that ctDNA assays are useful for cancer screening, outside of a clinical trial. Given the rapid pace of research, reevaluation of the literature will shortly be required, along with the development of tools and guidance for clinical practice.
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Affiliation(s)
- Jason D Merker
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Geoffrey R Oxnard
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Carolyn Compton
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Maximilian Diehn
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Patricia Hurley
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Alexander J Lazar
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Neal Lindeman
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Christina M Lockwood
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Alex J Rai
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Richard L Schilsky
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Apostolia M Tsimberidou
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Patricia Vasalos
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Brooke L Billman
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Thomas K Oliver
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Suanna S Bruinooge
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Daniel F Hayes
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Nicholas C Turner
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; hristina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
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113
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Merker JD, Oxnard GR, Compton C, Diehn M, Hurley P, Lazar AJ, Lindeman N, Lockwood CM, Rai AJ, Schilsky RL, Tsimberidou AM, Vasalos P, Billman BL, Oliver TK, Bruinooge SS, Hayes DF, Turner NC. Circulating Tumor DNA Analysis in Patients With Cancer: American Society of Clinical Oncology and College of American Pathologists Joint Review. J Clin Oncol 2018; 36:1631-1641. [PMID: 29504847 DOI: 10.1200/jco.2017.76.8671] [Citation(s) in RCA: 586] [Impact Index Per Article: 97.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Purpose Clinical use of analytical tests to assess genomic variants in circulating tumor DNA (ctDNA) is increasing. This joint review from ASCO and the College of American Pathologists summarizes current information about clinical ctDNA assays and provides a framework for future research. Methods An Expert Panel conducted a literature review on the use of ctDNA assays for solid tumors, including pre-analytical variables, analytical validity, interpretation and reporting, and clinical validity and utility. Results The literature search identified 1,338 references. Of those, 390, plus 31 references supplied by the Expert Panel, were selected for full-text review. There were 77 articles selected for inclusion. Conclusion The evidence indicates that testing for ctDNA is optimally performed on plasma collected in cell stabilization or EDTA tubes, with EDTA tubes processed within 6 hours of collection. Some ctDNA assays have demonstrated clinical validity and utility with certain types of advanced cancer; however, there is insufficient evidence of clinical validity and utility for the majority of ctDNA assays in advanced cancer. Evidence shows discordance between the results of ctDNA assays and genotyping tumor specimens and supports tumor tissue genotyping to confirm undetected results from ctDNA tests. There is no evidence of clinical utility and little evidence of clinical validity of ctDNA assays in early-stage cancer, treatment monitoring, or residual disease detection. There is no evidence of clinical validity and clinical utility to suggest that ctDNA assays are useful for cancer screening, outside of a clinical trial. Given the rapid pace of research, re-evaluation of the literature will shortly be required, along with the development of tools and guidance for clinical practice.
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Affiliation(s)
- Jason D Merker
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Geoffrey R Oxnard
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Carolyn Compton
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Maximilian Diehn
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Patricia Hurley
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Alexander J Lazar
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Neal Lindeman
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Christina M Lockwood
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Alex J Rai
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Richard L Schilsky
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Apostolia M Tsimberidou
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Patricia Vasalos
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Brooke L Billman
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Thomas K Oliver
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Suanna S Bruinooge
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Daniel F Hayes
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
| | - Nicholas C Turner
- Jason D. Merker and Maximilian Diehn, Stanford University School of Medicine; Stanford, CA; Geoffrey R. Oxnard, Dana Farber Cancer Institute and Harvard Medical School; Neal Lindeman, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Carolyn Compton, Arizona State University, Tempe, AZ; Patricia Hurley, Richard L. Schilsky, Thomas K. Oliver, and Suanna S. Bruinooge, American Society of Clinical Oncology, Alexandria, VA; Alexander J. Lazar and Apostolia M. Tsimberidou, The University of Texas MD Anderson Cancer Center, Houston, TX; Christina M. Lockwood, University of Washington, Seattle, WA; Alex J. Rai, Columbia University Medical Center, New York, NY; Patricia Vasalos and Brooke L. Billman, College of American Pathologists, Northfield, IL; Daniel F. Hayes, University of Michigan Comprehensive Cancer Center, Ann Arbor, MI; and Nicholas C. Turner, Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
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Mazzarella L. Are we ready for routine precision medicine? Highlights from the Milan Summit on Precision Medicine, Milan, Italy, 8-9 February 2018. Ecancermedicalscience 2018; 12:817. [PMID: 29662530 PMCID: PMC5880225 DOI: 10.3332/ecancer.2018.817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Indexed: 01/08/2023] Open
Abstract
On 8 and 9 February 2018, the IFOM-IEO campus in Milan hosted the Milan summit on Precision Medicine, which gathered clinical and translational research experts from academia, industry and regulatory bodies to discuss the state of the art of precision medicine in Europe. The meeting was pervaded by a generalised feeling of excitement for a field that is perceived to be technologically mature for the transition into clinical routine but still hampered by numerous obstacles of a methodological, ethical, regulatory and possibly cultural nature. Through lively discussions, the attendees tried to identify realistic ways to implement a technology-rich precision approach to cancer patients.
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Affiliation(s)
- Luca Mazzarella
- European Institute of Oncology, Via Ripamonti 435, Milan 20141, Italy
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Palmirotta R, Lovero D, Silvestris E, Felici C, Quaresmini D, Cafforio P, Silvestris F. Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA). Cancer Genomics Proteomics 2018; 14:173-179. [PMID: 28446532 DOI: 10.21873/cgp.20029] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Isolation and genotyping of circulating tumor cells (CTCs) is gaining an increasing interest by clinical researchers in oncology not only for investigative purposes, but also for concrete application in clinical practice in terms of diagnosis, prognosis and decision treatment with targeted therapies. For the mutational analysis of single CTCs, the most advanced biotechnology methodology currently available includes the combination of whole genome amplification (WGA) followed by next-generation sequencing (NGS). However, the sequence of these molecular techniques is time-consuming and may also favor operator-dependent errors, related to the procedures themselves that, as in the case of the WGA technique, might affect downstream molecular analyses. MATERIALS AND METHODS A preliminary approach of molecular analysis by NGS on a model of CTCs without previous WGA procedural step was performed. We set-up an artificial sample obtained by spiking the SK-MEL-28 melanoma cell line in normal donor peripheral whole blood. Melanoma cells were first enriched using an AutoMACS® (Miltenyi) cell separator and then isolated as single and pooled CTCs by DEPArray™ System (Silicon Biosystems). NGS analysis, using the Ion AmpliSeq™ Cancer Hotspot Panel v2 (Life Technologies) with the Ion Torrent PGM™ system (Life Technologies), was performed on the SK-MEL-28 cell pellet, a single CTC previously processed with WGA and on 1, 2, 4 and 8 recovered CTCs without WGA pre-amplification. RESULTS NGS directly carried out on CTCs without WGA showed the same mutations identified in SK-MEL-28 cell line pellet, with a considerable efficiency and avoiding the errors induced by the WGA procedure. CONCLUSION We identified a cost-effective, time-saving and reliable methodological approach that could improve the analytical accuracy of the liquid biopsy and appears promising in studying CTCs from cancer patients for both research and clinical purposes.
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Affiliation(s)
- Raffaele Palmirotta
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Domenica Lovero
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Erica Silvestris
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Claudia Felici
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Davide Quaresmini
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Paola Cafforio
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Franco Silvestris
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
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Poudineh M, Sargent EH, Pantel K, Kelley SO. Profiling circulating tumour cells and other biomarkers of invasive cancers. Nat Biomed Eng 2018; 2:72-84. [DOI: 10.1038/s41551-018-0190-5] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 01/09/2018] [Indexed: 02/07/2023]
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Yang M, Forbes ME, Bitting RL, O'Neill SS, Chou PC, Topaloglu U, Miller LD, Hawkins GA, Grant SC, DeYoung BR, Petty WJ, Chen K, Pasche BC, Zhang W. Incorporating blood-based liquid biopsy information into cancer staging: time for a TNMB system? Ann Oncol 2018; 29:311-323. [PMID: 29216340 PMCID: PMC5834142 DOI: 10.1093/annonc/mdx766] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tissue biopsy is the standard diagnostic procedure for cancer. Biopsy may also provide material for genotyping, which can assist in the diagnosis and selection of targeted therapies but may fall short in cases of inadequate sampling, particularly from highly heterogeneous tumors. Traditional tissue biopsy suffers greater limitations in its prognostic capability over the course of disease, most obviously as an invasive procedure with potential complications, but also with respect to probable tumor clonal evolution and metastasis over time from initial biopsy evaluation. Recent work highlights circulating tumor DNA (ctDNA) present in the blood as a supplemental, or perhaps an alternative, source of DNA to identify the clinically relevant cancer mutational landscape. Indeed, this noninvasive approach may facilitate repeated monitoring of disease progression and treatment response, serving as a means to guide targeted therapies based on detected actionable mutations in patients with advanced or metastatic solid tumors. Notably, ctDNA is heralding a revolution in the range of genomic profiling and molecular mechanisms to be utilized in the battle against cancer. This review will discuss the biology of ctDNA, current methods of detection and potential applications of this information in tumor diagnosis, treatment, and disease prognosis. Conventional classification of tumors to describe cancer stage follow the TNM notation system, heavily weighting local tumor extent (T), lymph node invasion (N), and detectable metastasis (M). With recent advancements in genomics and bioinformatics, it is conceivable that routine analysis of ctDNA from liquid biopsy (B) may make cancer diagnosis, treatment, and prognosis more accurate for individual patients. We put forward the futuristic concept of TNMB tumor classification, opening a new horizon for precision medicine with the hope of creating better outcomes for cancer patients.
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Affiliation(s)
- M Yang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA; Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - M E Forbes
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - R L Bitting
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - S S O'Neill
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Pathology, Wake Forest School of Medicine, Winston-Salem, USA
| | - P-C Chou
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - U Topaloglu
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - L D Miller
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA
| | - G A Hawkins
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, USA
| | - S C Grant
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - B R DeYoung
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Pathology, Wake Forest School of Medicine, Winston-Salem, USA
| | - W J Petty
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - K Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin, China; Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.
| | - B C Pasche
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA; Section of Hematology and Oncology, Department of Internal Medicine, Winston-Salem, USA
| | - W Zhang
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, USA.
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Affiliation(s)
- Joshua Donaldson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Ben Ho Park
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218
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Perdomo S, Anantharaman D, Foll M, Abedi-Ardekani B, Durand G, Reis Rosa LA, Holmila R, Le Calvez-Kelm F, Tajara EH, Wünsch-Filho V, Levi JE, Vilensky M, Polesel J, Holcatova I, Simonato L, Canova C, Lagiou P, McKay JD, Brennan P. Genomic analysis of head and neck cancer cases from two high incidence regions. PLoS One 2018; 13:e0191701. [PMID: 29377909 PMCID: PMC5788352 DOI: 10.1371/journal.pone.0191701] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/04/2017] [Indexed: 12/20/2022] Open
Abstract
We investigated how somatic changes in HNSCC interact with environmental and host risk factors and whether they influence the risk of HNSCC occurrence and outcome. 180-paired samples diagnosed as HNSCC in two high incidence regions of Europe and South America underwent targeted sequencing (14 genes) and evaluation of copy number alterations (SCNAs). TP53, PIK3CA, NOTCH1, TP63 and CDKN2A were the most frequently mutated genes. Cases were characterized by a low copy number burden with recurrent focal amplification in 11q13.3 and deletion in 15q22. Cases with low SCNAs showed an improved overall survival. We found significant correlations with decreased overall survival between focal amplified regions 4p16, 10q22 and 22q11, and losses in 12p12, 15q14 and 15q22. The mutational landscape in our cases showed an association to both environmental exposures and clinical characteristics. We confirmed that somatic copy number alterations are an important predictor of HNSCC overall survival.
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Affiliation(s)
- Sandra Perdomo
- International Agency for Research on Cancer (IARC), Lyon, France
- Institute of Nutrition, Genetics and Metabolism Research, Faculty of Medicine, Universidad El Bosque, Bogotá, Colombia
| | | | - Matthieu Foll
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Geoffroy Durand
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Reetta Holmila
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Eloiza H. Tajara
- School of Medicine of São José do Rio Preto, São José do Rio Preto, Brazil
| | | | - José Eduardo Levi
- Instituto de Medicina Tropical de SP Universidade de São Paulo- USP, São Paulo, Brazil
| | | | - Jerry Polesel
- Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | | | - Lorenzo Simonato
- Laboratory of Public Health and Population Studies, Padova, Italy
| | - Cristina Canova
- Laboratory of Public Health and Population Studies, Padova, Italy
| | | | - James D. McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
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120
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Derks JL, Leblay N, Thunnissen E, van Suylen RJ, den Bakker M, Groen HJM, Smit EF, Damhuis R, van den Broek EC, Charbrier A, Foll M, McKay JD, Fernandez-Cuesta L, Speel EJM, Dingemans AMC. Molecular Subtypes of Pulmonary Large-cell Neuroendocrine Carcinoma Predict Chemotherapy Treatment Outcome. Clin Cancer Res 2018; 24:33-42. [PMID: 29066508 DOI: 10.1158/1078-0432.ccr-17-1921] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/12/2017] [Accepted: 10/11/2017] [Indexed: 12/12/2022]
Abstract
Purpose: Previous genomic studies have identified two mutually exclusive molecular subtypes of large-cell neuroendocrine carcinoma (LCNEC): the RB1 mutated (mostly comutated with TP53) and the RB1 wild-type groups. We assessed whether these subtypes have a predictive value on chemotherapy outcome.Experimental Design: Clinical data and tumor specimens were retrospectively obtained from the Netherlands Cancer Registry and Pathology Registry. Panel-consensus pathology revision confirmed the diagnosis of LCNEC in 148 of 232 cases. Next-generation sequencing (NGS) for TP53, RB1, STK11, and KEAP1 genes, as well as IHC for RB1 and P16 was performed on 79 and 109 cases, respectively, and correlated with overall survival (OS) and progression-free survival (PFS), stratifying for non-small cell lung cancer type chemotherapy including platinum + gemcitabine or taxanes (NSCLC-GEM/TAX) and platinum-etoposide (SCLC-PE).Results:RB1 mutation and protein loss were detected in 47% (n = 37) and 72% (n = 78) of the cases, respectively. Patients with RB1 wild-type LCNEC treated with NSCLC-GEM/TAX had a significantly longer OS [9.6; 95% confidence interval (CI), 7.7-11.6 months] than those treated with SCLC-PE [5.8 (5.5-6.1); P = 0.026]. Similar results were obtained for patients expressing RB1 in their tumors (P = 0.001). RB1 staining or P16 loss showed similar results. The same outcome for chemotherapy treatment was observed in LCNEC tumors harboring an RB1 mutation or lost RB1 protein.Conclusions: Patients with LCNEC tumors that carry a wild-type RB1 gene or express the RB1 protein do better with NSCLC-GEM/TAX treatment than with SCLC-PE chemotherapy. However, no difference was observed for RB1 mutated or with lost protein expression. Clin Cancer Res; 24(1); 33-42. ©2017 AACR.
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Affiliation(s)
- Jules L Derks
- Department of Pulmonary Diseases, GROW School for Oncology & Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Noémie Leblay
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Erik Thunnissen
- Department of Pathology, VU University Medical Centre, Amsterdam, the Netherlands
| | | | | | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen and University Medical Centre, Groningen, the Netherlands
| | - Egbert F Smit
- Department of Pulmonary Diseases, VU medical centre, Amsterdam, the Netherlands
| | - Ronald Damhuis
- Department Research, Comprehensive Cancer Association, Utrecht, the Netherlands
| | | | - Amélie Charbrier
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Matthieu Foll
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | | | - Lynnette Fernandez-Cuesta
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC-WHO), Lyon, France.
| | - Ernst-Jan M Speel
- Department of Pathology, GROW school for Oncology & Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Anne-Marie C Dingemans
- Department of Pulmonary Diseases, GROW School for Oncology & Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands.
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Abstract
In the August 16th issue of Science Translational Medicine, Phallen et al propose a method for early cancer diagnosis by using circulating tumor DNA (1). One major advance of this paper includes optimized sequencing of cell-free/circulating tumor DNA (ctDNA) without knowledge of tumor mutations. Evaluation of 200 patients with colorectal, breast, lung and ovarian cancer revealed mutations in ctDNA in approx. 60-70% of all patients, including stage 1 and stage 2 disease. If this data can be reproduced in asymptomatic individuals, they will likely have a major impact on early cancer detection and patient outcomes. In this commentary, we examine the feasibility of this approach for detecting small, asymptomatic tumors, based on previously published empirical data.
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Affiliation(s)
- Eleftherios P Diamandis
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Clare Fiala
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
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Postel M, Roosen A, Laurent-Puig P, Taly V, Wang-Renault SF. Droplet-based digital PCR and next generation sequencing for monitoring circulating tumor DNA: a cancer diagnostic perspective. Expert Rev Mol Diagn 2017; 18:7-17. [PMID: 29115895 DOI: 10.1080/14737159.2018.1400384] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Early detection of cancers through the analysis of ctDNA could have a significant impact on morbidity and mortality of cancer patients. However, using ctDNA for early cancer diagnosis is challenging partly due to the low amount of tumor DNA released in the circulation and its dilution within DNA originating from non-tumor cells. Development of new technologies such as droplet-based digital PCR (ddPCR) or optimized next generation sequencing (NGS) has greatly improved the sensitivity, specificity and precision for the detection of rare sequences. Areas covered: This paper will focus on the potential application of ddPCR and optimized NGS to detect ctDNA for detection of cancer recurrence and minimal residual disease as well as early diagnosis of cancer patients. Expert commentary: Compared to tumor tissue biopsies, blood-based ctDNA analyses are minimally invasive and accessible for regular follow-up of cancer patients. They are also described as a better picture of patients' pathology allowing to highlight both tumor heterogeneity and multiple tumor sites. After a brief introduction on the application of the follow-up of ctDNA using genetic or epigenetic biomarkers for prognosis and surveillance of cancer patients, potential perspectives of using ctDNA for early diagnosis of cancers will be presented.
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Affiliation(s)
- Mathilde Postel
- a INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer , Paris , France
| | - Alice Roosen
- a INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer , Paris , France
| | - Pierre Laurent-Puig
- a INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer , Paris , France.,b Department of Biology , European Georges Pompidou Hospital, AP-HP , Paris , France
| | - Valerie Taly
- a INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer , Paris , France
| | - Shu-Fang Wang-Renault
- a INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe labellisée Ligue Nationale contre le cancer , Paris , France
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Li J, Zhou C, Wang G, Wang S, Ni S, Ye M, Zhang J. Promoter hypermethylation of SLIT2 is a risk factor and potential diagnostic biomarker for nasopharyngeal carcinoma. Gene 2017; 644:74-79. [PMID: 29107007 DOI: 10.1016/j.gene.2017.10.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 10/04/2017] [Accepted: 10/20/2017] [Indexed: 02/06/2023]
Abstract
SLIT2 is a candidate tumor suppressor gene and recent studies have shown that SLIT2 expression is suppressed or reduced by hypermethylation in the promoter region in various cancers. The aim of this study was to investigate the association between SLIT2 promoter methylation and nasopharyngeal carcinoma (NPC) and its relative diagnostic ability for NPC. Bisulfite pyrosequencing technology was performed to measure methylation levels of the SLIT2 promoter in tissue and plasma samples from 61 NPC patients and 38 normal volunteers. The receiver operating characteristic (ROC) curve and area under the curve (AUC) were used to evaluate the diagnostic ability of SLIT2 methylation for diagnosing NPC. Our results showed that methylation levels of the SLIT2 promoter were significantly higher in NPC patients compared with individuals, both in tissue samples (P=2.57E-10) and plasma samples (plasma: P=3.86E-13). In addition, the frequency of SLIT2 promoter methylation markedly increased in the advanced stage (tissue: P=3.50E-05; plasma: P=1.14E-04) and advanced T classified (tissue: P=9.00E-06; plasma: P=3.80E-05), as well as in lymph node metastasis patients (tissue: P=1.82E-03; plasma: P=2.22E-03). In addition, the AUCs according to tissue and plasma samples were 0.846 and 0.866, respectively. When these two sample-types were combined, the AUC increased slightly to 0.874. Our study revealed that elevated SLIT2 promoter methylation contributed to the risk of NPC, as well as being involved in its progression and metastasis. Therefore, the methylated SLIT2 promoter could serve as a potential biomarker for diagnosing NPC.
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Affiliation(s)
- Jinyun Li
- Department of Oncology and Hematology, Affiliated Hospital of Ningbo University, Ningbo 315000, Zhejiang, China
| | - Chongchang Zhou
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital of Ningbo University, Ningbo 315040, Zhejiang, China.
| | - Guoli Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital of Ningbo University, Ningbo 315040, Zhejiang, China
| | - Shaomin Wang
- Department of Oncology and Hematology, Affiliated Hospital of Ningbo University, Ningbo 315000, Zhejiang, China
| | - Shuming Ni
- Department of Oncology and Hematology, Affiliated Hospital of Ningbo University, Ningbo 315000, Zhejiang, China
| | - Meng Ye
- Department of Oncology and Hematology, Affiliated Hospital of Ningbo University, Ningbo 315000, Zhejiang, China.
| | - Jian Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Lihuili Hospital of Ningbo University, Ningbo 315040, Zhejiang, China.
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Cree IA, Uttley L, Buckley Woods H, Kikuchi H, Reiman A, Harnan S, Whiteman BL, Philips ST, Messenger M, Cox A, Teare D, Sheils O, Shaw J. The evidence base for circulating tumour DNA blood-based biomarkers for the early detection of cancer: a systematic mapping review. BMC Cancer 2017; 17:697. [PMID: 29061138 PMCID: PMC5654013 DOI: 10.1186/s12885-017-3693-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/18/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The presence of circulating cell-free DNA from tumours in blood (ctDNA) is of major importance to those interested in early cancer detection, as well as to those wishing to monitor tumour progression or diagnose the presence of activating mutations to guide treatment. In 2014, the UK Early Cancer Detection Consortium undertook a systematic mapping review of the literature to identify blood-based biomarkers with potential for the development of a non-invasive blood test for cancer screening, and which identified this as a major area of interest. This review builds on the mapping review to expand the ctDNA dataset to examine the best options for the detection of multiple cancer types. METHODS The original mapping review was based on comprehensive searches of the electronic databases Medline, Embase, CINAHL, the Cochrane library, and Biosis to obtain relevant literature on blood-based biomarkers for cancer detection in humans (PROSPERO no. CRD42014010827). The abstracts for each paper were reviewed to determine whether validation data were reported, and then examined in full. Publications concentrating on monitoring of disease burden or mutations were excluded. RESULTS The search identified 94 ctDNA studies meeting the criteria for review. All but 5 studies examined one cancer type, with breast, colorectal and lung cancers representing 60% of studies. The size and design of the studies varied widely. Controls were included in 77% of publications. The largest study included 640 patients, but the median study size was 65 cases and 35 controls, and the bulk of studies (71%) included less than 100 patients. Studies either estimated cfDNA levels non-specifically or tested for cancer-specific mutations or methylation changes (the majority using PCR-based methods). CONCLUSION We have systematically reviewed ctDNA blood biomarkers for the early detection of cancer. Pre-analytical, analytical, and post-analytical considerations were identified which need to be addressed before such biomarkers enter clinical practice. The value of small studies with no comparison between methods, or even the inclusion of controls is highly questionable, and larger validation studies will be required before such methods can be considered for early cancer detection.
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Affiliation(s)
- Ian A. Cree
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, CEDEX 08 France
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
- Institute of Ophthalmology, University College London, EC1V 9EL, London, UK
| | - Lesley Uttley
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Helen Buckley Woods
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Hugh Kikuchi
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX UK
| | - Anne Reiman
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
| | - Susan Harnan
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Becky L. Whiteman
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Road, Harrow, HA1 3UJ UK
| | | | - Michael Messenger
- Leeds Centre for Personalised Medicine and Health, University of Leeds and NIHR Diagnostic Evidence Co-Operative Leeds, Leeds Teaching Hospitals NHS Trust, Leeds, LS9 7TF UK
| | - Angela Cox
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield, S10 2RX UK
| | - Dawn Teare
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Orla Sheils
- Sir Patrick Dun Research Laboratory, Central Pathology Laboratory, St James’s Hospital & Trinity College Dublin, Dublin 8, Ireland
| | - Jacqui Shaw
- University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX UK
| | - For the UK Early Cancer Detection Consortium
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, CEDEX 08 France
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
- Institute of Ophthalmology, University College London, EC1V 9EL, London, UK
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX UK
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Road, Harrow, HA1 3UJ UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
- Leeds Centre for Personalised Medicine and Health, University of Leeds and NIHR Diagnostic Evidence Co-Operative Leeds, Leeds Teaching Hospitals NHS Trust, Leeds, LS9 7TF UK
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield, S10 2RX UK
- Sir Patrick Dun Research Laboratory, Central Pathology Laboratory, St James’s Hospital & Trinity College Dublin, Dublin 8, Ireland
- University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX UK
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The potential of liquid biopsies for the early detection of cancer. NPJ Precis Oncol 2017; 1:36. [PMID: 29872715 PMCID: PMC5871864 DOI: 10.1038/s41698-017-0039-5] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023] Open
Abstract
Precision medicine refers to the choosing of targeted therapies based on genetic data. Due to the increasing availability of data from large-scale tumor genome sequencing projects, genome-driven oncology may have enormous potential to change the clinical management of patients with cancer. To this end, components of tumors, which are shed into the circulation, i.e., circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), or extracellular vesicles, are increasingly being used for monitoring tumor genomes. A growing number of publications have documented that these “liquid biopsies” are informative regarding response to given therapies, are capable of detecting relapse with lead time compared to standard measures, and reveal mechanisms of resistance. However, the majority of published studies relate to advanced tumor stages and the use of liquid biopsies for detection of very early malignant disease stages is less well documented. In early disease stages, strategies for analysis are in principle relatively similar to advanced stages. However, at these early stages, several factors pose particular difficulties and challenges, including the lower frequency and volume of aberrations, potentially confounding phenomena such as clonal expansions of non-tumorous tissues or the accumulation of cancer-associated mutations with age, and the incomplete insight into driver alterations. Here we discuss biology, technical complexities and clinical significance for early cancer detection and their impact on precision oncology.
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Perdomo S, Avogbe PH, Foll M, Abedi-Ardekani B, Facciolla VL, Anantharaman D, Chopard P, Calvez-Kelm FL, Vilensky M, Polesel J, Holcatova I, Simonato L, Canova C, Lagiou P, McKay JD, Brennan P. Circulating tumor DNA detection in head and neck cancer: evaluation of two different detection approaches. Oncotarget 2017; 8:72621-72632. [PMID: 29069814 PMCID: PMC5641157 DOI: 10.18632/oncotarget.20004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/12/2017] [Indexed: 01/22/2023] Open
Abstract
The use of non-invasive biomarkers such as circulating tumor DNA (ctDNA) in head and neck tumors may be of relevance in early diagnosis and eventually improved outcome. We evaluated two different approaches from two case series in Europe and South America including (i) targeted screening of ctDNA mutations, and (ii) detection of TP53 mutations in plasma and oral rinses without previous knowledge of mutational status in tumor samples. Targeted sequencing in 5 genes identified ctDNA mutations in plasma among 42% of HNSCC cases, 67% of who were early stage cases. No association was found between ctDNA mutation detection and overall survival. Sequencing of the entire coding region of the TP53 gene resulted in identification of TP53 mutations in 76% of tumor cases. However, concordance of mutation detection was low between tumor, oral rinses (11%) and plasma (2,7%) samples. Identification of 5 pathogenic TP53 mutations in oral rinses from 3 non-cancer controls gives additional evidence of mutation occurrence in individuals without a diagnosed cancer and presents an additional challenge for the development of ctDNA diagnostic assays.
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Affiliation(s)
- Sandra Perdomo
- International Agency for Research on Cancer (IARC), Lyon 69372, France
- Institute of Nutrition, Genetics and Metabolism Research, Faculty of Medicine, Universidad El Bosque, Bogotá 110121, Colombia
| | - Patrice H. Avogbe
- International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC), Lyon 69372, France
| | | | - Violeta Lescher Facciolla
- Departamento de Saúde Coletiva, Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo CEP01221-020, Brazil
| | - Devasena Anantharaman
- International Agency for Research on Cancer (IARC), Lyon 69372, France
- Current present address: Rajiv Gandhi Centre for Biotechnology, Trivandrum 695010, India
| | - Priscilia Chopard
- International Agency for Research on Cancer (IARC), Lyon 69372, France
| | | | | | - Jerry Polesel
- CRO Aviano National Cancer Institute, Aviano 33081, Italy
| | - Ivana Holcatova
- Charles University, 1st Faculty of Medicine, Prague 116 36, Czech Republic
| | - Lorenzo Simonato
- Laboratory of Public Health and Population Studies, University of Padova, Padova 35122, Italy
| | - Cristina Canova
- Laboratory of Public Health and Population Studies, University of Padova, Padova 35122, Italy
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - James D. McKay
- International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon 69372, France
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127
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Youssef O, Knuuttila A, Piirilä P, Böhling T, Sarhadi V, Knuutila S. Presence of cancer-associated mutations in exhaled breath condensates of healthy individuals by next generation sequencing. Oncotarget 2017; 8:18166-18176. [PMID: 28199989 PMCID: PMC5392316 DOI: 10.18632/oncotarget.15233] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 01/16/2017] [Indexed: 01/29/2023] Open
Abstract
Exhaled breath condensate (EBC) is a non-invasive source that can be used for studying different genetic alterations occurring in lung tissue. However, the low yield of DNA available from EBC has hampered the more detailed mutation analysis by conventional methods. We applied the more sensitive amplicon-based next generation sequencing (NGS) to identify cancer related mutations in DNA isolated from EBC. In order to apply any method for the purpose of mutation screening in cancer patients, it is important to clarify the incidence of these mutations in healthy individuals. Therefore, we studied mutations in hotspot regions of 22 cancer genes of 20 healthy, mainly non-smoker individuals, using AmpliSeq colon and lung cancer panel and sequenced on Ion PGM. In 15 individuals, we detected 35 missense mutations in TP53, KRAS, NRAS, SMAD4, MET, CTNNB1, PTEN, BRAF, DDR2, EGFR, PIK3CA, NOTCH1, FBXW7, FGFR3, and ERBB2: these have been earlier reported in different tumor tissues. Additionally, 106 novel mutations not reported previously were also detected. One healthy non-smoker subject had a KRAS G12D mutation in EBC DNA. Our results demonstrate that DNA from EBC of healthy subjects can reveal mutations that could represent very early neoplastic changes or alternatively a normal process of apoptosis eliminating damaged cells with mutations or altered genetic material. Further assessment is needed to determine if NGS analysis of EBC could be a screening method for high risk individuals such as smokers, where it could be applied in the early diagnosis of lung cancer and monitoring treatment efficacy.
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Affiliation(s)
- Omar Youssef
- Faculty of Medicine, Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Aija Knuuttila
- Department of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Heart and Lung Center, Helsinki, Finland
| | - Päivi Piirilä
- Unit of Clinical Physiology, HUS-Medical Imaging Center, Helsinki University Hospital and Helsinki University, Helsinki, Finland
| | - Tom Böhling
- Department of Pathology, University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Virinder Sarhadi
- Faculty of Medicine, Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Sakari Knuutila
- Faculty of Medicine, Department of Pathology, University of Helsinki, Helsinki, Finland
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128
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Brennan P, Perola M, van Ommen GJ, Riboli E. Chronic disease research in Europe and the need for integrated population cohorts. Eur J Epidemiol 2017; 32:741-749. [PMID: 28986739 PMCID: PMC5662668 DOI: 10.1007/s10654-017-0315-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 09/11/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Paul Brennan
- Genetics Section, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372, Lyon Cedex 08, France.
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, Finland
| | - Gert-Jan van Ommen
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Biobanking and Biomolecular Research Resources Infrastructure (BBMRI-ERIC), Graz, Austria
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129
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Blandin Knight S, Crosbie PA, Balata H, Chudziak J, Hussell T, Dive C. Progress and prospects of early detection in lung cancer. Open Biol 2017; 7:170070. [PMID: 28878044 PMCID: PMC5627048 DOI: 10.1098/rsob.170070] [Citation(s) in RCA: 492] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/27/2017] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related death in the world. It is broadly divided into small cell (SCLC, approx. 15% cases) and non-small cell lung cancer (NSCLC, approx. 85% cases). The main histological subtypes of NSCLC are adenocarcinoma and squamous cell carcinoma, with the presence of specific DNA mutations allowing further molecular stratification. If identified at an early stage, surgical resection of NSCLC offers a favourable prognosis, with published case series reporting 5-year survival rates of up to 70% for small, localized tumours (stage I). However, most patients (approx. 75%) have advanced disease at the time of diagnosis (stage III/IV) and despite significant developments in the oncological management of late stage lung cancer over recent years, survival remains poor. In 2014, the UK Office for National Statistics reported that patients diagnosed with distant metastatic disease (stage IV) had a 1-year survival rate of just 15-19% compared with 81-85% for stage I.
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MESH Headings
- Adenocarcinoma/diagnostic imaging
- Adenocarcinoma/genetics
- Adenocarcinoma/mortality
- Adenocarcinoma/surgery
- Adenocarcinoma of Lung
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Bronchoscopy/methods
- Carcinoma, Non-Small-Cell Lung/diagnostic imaging
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/mortality
- Carcinoma, Non-Small-Cell Lung/surgery
- Carcinoma, Squamous Cell/diagnostic imaging
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/mortality
- Carcinoma, Squamous Cell/surgery
- Circulating Tumor DNA/blood
- Circulating Tumor DNA/genetics
- Early Detection of Cancer/methods
- Humans
- Liquid Biopsy/methods
- Lung Neoplasms/diagnostic imaging
- Lung Neoplasms/genetics
- Lung Neoplasms/mortality
- Lung Neoplasms/surgery
- Neoplasm Staging
- Neoplastic Cells, Circulating/metabolism
- Neoplastic Cells, Circulating/pathology
- Prognosis
- Radiography
- Small Cell Lung Carcinoma/diagnostic imaging
- Small Cell Lung Carcinoma/genetics
- Small Cell Lung Carcinoma/mortality
- Small Cell Lung Carcinoma/surgery
- Survival Analysis
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Affiliation(s)
- Sean Blandin Knight
- North West Lung Centre, University Hospital South Manchester, Manchester, UK
| | - Phil A Crosbie
- North West Lung Centre, University Hospital South Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence at Manchester and University College London, UK
| | - Haval Balata
- North West Lung Centre, University Hospital South Manchester, Manchester, UK
| | - Jakub Chudziak
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Tracy Hussell
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, UK
| | - Caroline Dive
- Cancer Research UK Lung Cancer Centre of Excellence at Manchester and University College London, UK
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
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130
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Ono Y, Sugitani A, Karasaki H, Ogata M, Nozaki R, Sasajima J, Yokochi T, Asahara S, Koizumi K, Ando K, Hironaka K, Daito T, Mizukami Y. An improved digital polymerase chain reaction protocol to capture low-copy KRAS mutations in plasma cell-free DNA by resolving 'subsampling' issues. Mol Oncol 2017; 11:1448-1458. [PMID: 28691390 PMCID: PMC5623814 DOI: 10.1002/1878-0261.12110] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 06/26/2017] [Accepted: 06/26/2017] [Indexed: 12/18/2022] Open
Abstract
Genetic alterations responsible for the initiation of cancer may serve as immediate biomarkers for early diagnosis. Plasma levels of cell‐free DNA (cfDNA) in patients with cancer are higher than those in healthy individuals; however, the major technical challenge for the widespread implementation of cfDNA genotyping as a diagnostic tool is the insufficient sensitivity and specificity of detecting early‐stage tumors that shed low amounts of cfDNA. To establish a protocol for ultrasensitive droplet digital polymerase chain reaction (ddPCR) for quantification of low‐frequency alleles within a limited cfDNA pool, two‐step multiplex ddPCR targeting eight clinically relevant mutant KRAS variants was examined. Plasma samples from patients with colorectal (n = 10) and pancreatic cancer (n = 9) were evaluated, and cfDNA from healthy volunteers (n = 50) was utilized to calculate reference intervals. Limited cfDNA yields in patients with resectable colorectal and pancreatic cancers did not meet the requirement for efficient capture and quantification of rate mutant alleles by ddPCR. Eight preamplification cycles followed by a second‐run ddPCR were sufficient to obtain approximately 5000–10 000 amplified copies per ng of cfDNA, resolving the subsampling issue. Furthermore, the signal‐to‐noise ratio for rare mutant alleles against the extensive background presented by the wild‐type allele was significantly enhanced. The cutoff limit of reference intervals for mutant KRAS was determined to be ~ 0.09% based on samples from healthy individuals. The modification introduced in the ddPCR protocol facilitated the quantification of low‐copy alleles carrying driver mutations, such as oncogenic KRAS, in localized and early‐stage cancers using small blood volumes, thus offering a minimally invasive modality for timely diagnosis.
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Affiliation(s)
- Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Hokkaido, Japan
| | - Ayumu Sugitani
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Hokkaido, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Hokkaido, Japan
| | - Munehiko Ogata
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Hokkaido, Japan
| | - Reo Nozaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Hokkaido, Japan
| | - Junpei Sasajima
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Hokkaido, Japan.,Department of Medicine, Asahikawa Medical University, Japan
| | - Tomoki Yokochi
- Department of Clinical Research, Chiba Tokushukai Hospital, Japan
| | - Shingo Asahara
- Department of Clinical Research, Chiba Tokushukai Hospital, Japan
| | - Kazuya Koizumi
- Center for Clinical and Translational Science, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Kiyohiro Ando
- Center for Clinical and Translational Science, Shonan Kamakura General Hospital, Kanagawa, Japan
| | | | | | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Hokkaido, Japan.,Department of Medicine, Asahikawa Medical University, Japan
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131
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Yohe S, Thyagarajan B. Review of Clinical Next-Generation Sequencing. Arch Pathol Lab Med 2017; 141:1544-1557. [PMID: 28782984 DOI: 10.5858/arpa.2016-0501-ra] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. OBJECTIVE - To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care. DATA SOURCES - The review is based on peer-reviewed literature and personal experience using NGS in a clinical setting at a major academic center. CONCLUSIONS - The clinical applications of NGS will increase as the technology, bioinformatics, and resources evolve to address the limitations and improve quality of results. The challenge for clinical laboratories is to ensure testing is clinically relevant, cost-effective, and can be integrated into clinical care.
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Affiliation(s)
- Sophia Yohe
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
| | - Bharat Thyagarajan
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
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132
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Beane J, Campbell JD, Lel J, Vick J, Spira A. Genomic approaches to accelerate cancer interception. Lancet Oncol 2017; 18:e494-e502. [PMID: 28759388 DOI: 10.1016/s1470-2045(17)30373-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022]
Abstract
Although major advances have been reported in the last decade in the treatment of late-stage cancer with targeted and immune-based therapies, there is a crucial unmet need to develop new approaches to improve the prevention and early detection of cancer. Advances in genomics and computational biology offer unprecedented opportunities to understand the earliest molecular events associated with carcinogenesis, enabling novel strategies to intercept the development of invasive cancers. This Series paper will highlight emerging big data genomic approaches with the potential to accelerate advances in cancer prevention, screening, and early detection across various tumour types, and the challenges inherent in the development of these tools for clinical use. Through coordinated multicentre consortia, these genomic approaches are likely to transform the landscape of cancer interception in the coming years.
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Affiliation(s)
- Jennifer Beane
- Department of Medicine and BU-BMC Cancer Center, Boston University, Boston, MA, USA
| | - Joshua D Campbell
- Department of Medicine and BU-BMC Cancer Center, Boston University, Boston, MA, USA
| | - Julian Lel
- Department of Medicine and BU-BMC Cancer Center, Boston University, Boston, MA, USA
| | - Jessica Vick
- Department of Medicine and BU-BMC Cancer Center, Boston University, Boston, MA, USA
| | - Avrum Spira
- Department of Medicine and BU-BMC Cancer Center, Boston University, Boston, MA, USA.
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133
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Manjili MH. Tumor Dormancy and Relapse: From a Natural Byproduct of Evolution to a Disease State. Cancer Res 2017; 77:2564-2569. [PMID: 28507050 PMCID: PMC5459601 DOI: 10.1158/0008-5472.can-17-0068] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/22/2017] [Accepted: 03/10/2017] [Indexed: 12/24/2022]
Abstract
Species evolve by mutations and epigenetic changes acting on individuals in a population; tumors evolve by similar mechanisms at a cellular level in a tissue. This article reviews growing evidence about tumor dormancy and suggests that (i) cellular malignancy is a natural byproduct of evolutionary mechanisms, such as gene mutations and epigenetic modifications, which is manifested in the form of tumor dormancy in healthy individuals as well as in cancer survivors; (ii) cancer metastasis could be an early dissemination event that could occur during malignant dormancy even before primary cancer is clinically detectable; and (iii) chronic inflammation is a key factor in awakening dormant malignant cells at the primary site, leading to primary cancer development, and at distant sites, leading to advanced stage diseases. On the basis of this evidence, it is reasonable to propose that we are all cancer survivors rather than cancer-free individuals because of harboring dormant malignant cells in our organs. A better understanding of local and metastatic tumor dormancy could lead to novel cancer therapeutics for the prevention of cancer. Cancer Res; 77(10); 2564-9. ©2017 AACR.
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Affiliation(s)
- Masoud H Manjili
- Department of Microbiology & Immunology, VCU School of Medicine, Massey Cancer Center, Richmond, Virginia.
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134
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MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. PLoS Comput Biol 2017; 13:e1005480. [PMID: 28475621 PMCID: PMC5419444 DOI: 10.1371/journal.pcbi.1005480] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/24/2017] [Indexed: 12/16/2022] Open
Abstract
Unique molecular identifiers (UMIs) show outstanding performance in targeted high-throughput resequencing, being the most promising approach for the accurate identification of rare variants in complex DNA samples. This approach has application in multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we introduce MAGERI, a computational pipeline that efficiently handles all caveats of UMI-based analysis to obtain high-fidelity mutation profiles and call ultra-rare variants. Using an extensive set of benchmark datasets including gold-standard biological samples with known variant frequencies, cell-free DNA from tumor patient blood samples and publicly available UMI-encoded datasets we demonstrate that our method is both robust and efficient in calling rare variants. The versatility of our software is supported by accurate results obtained for both tumor DNA and viral RNA samples in datasets prepared using three different UMI-based protocols.
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135
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Abstract
Characterizing and monitoring tumor genomes with blood samples could achieve significant improvements in precision medicine. As tumors shed parts of themselves into the circulation, analyses of circulating tumor cells, circulating tumor DNA, and tumor-derived exosomes, often referred to as "liquid biopsies", may enable tumor genome characterization by minimally invasive means. Indeed, multiple studies have described how molecular information about parent tumors can be extracted from these components. Here, we briefly summarize current technologies and then elaborate on emerging novel concepts that may further propel the field. We address normal and detectable mutation levels in the context of our current knowledge regarding the gradual accumulation of mutations during aging and in light of technological limitations. Finally, we discuss whether liquid biopsies are ready to be used in routine clinical practice.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010, Graz, Austria
| | - Michael R Speicher
- Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010, Graz, Austria. .,BioTechMed, Graz, Austria.
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136
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Spira A, Yurgelun MB, Alexandrov L, Rao A, Bejar R, Polyak K, Giannakis M, Shilatifard A, Finn OJ, Dhodapkar M, Kay NE, Braggio E, Vilar E, Mazzilli SA, Rebbeck TR, Garber JE, Velculescu VE, Disis ML, Wallace DC, Lippman SM. Precancer Atlas to Drive Precision Prevention Trials. Cancer Res 2017; 77:1510-1541. [PMID: 28373404 PMCID: PMC6681830 DOI: 10.1158/0008-5472.can-16-2346] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 02/07/2023]
Abstract
Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. In this Perspective, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity - basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape. Emerging genetic and pharmacologic (metformin) disruption of mitochondrial (mt) respiration increased autophagy to prevent cancer in a Li-Fraumeni mouse model (biology reproduced in clinical pilot) and revealed profound influences of subtle changes in mt DNA background variation on obesity, aging, and cancer risk. The elaborate communication between the immune system and neoplasia includes an increasingly complex cellular microenvironment and dynamic interactions between host genetics, environmental factors, and microbes in shaping the immune response. Cancer vaccines are in early murine and clinical precancer studies, building on the recent successes of immunotherapy and HPV vaccine immune prevention. Molecular monitoring in Barrett's esophagus to avoid overdiagnosis/treatment highlights an important PCA theme. Next generation sequencing (NGS) discovered age-related clonal hematopoiesis of indeterminate potential (CHIP). Ultra-deep NGS reports over the past year have redefined the premalignant landscape remarkably identifying tiny clones in the blood of up to 95% of women in their 50s, suggesting that potentially premalignant clones are ubiquitous. Similar data from eyelid skin and peritoneal and uterine lavage fluid provide unprecedented opportunities to dissect the earliest phases of stem/progenitor clonal (and microenvironment) evolution/diversity with new single-cell and liquid biopsy technologies. Cancer mutational signatures reflect exogenous or endogenous processes imprinted over time in precursors. Accelerating the prevention of cancer will require a large-scale, longitudinal effort, leveraging diverse disciplines (from genetics, biochemistry, and immunology to mathematics, computational biology, and engineering), initiatives, technologies, and models in developing an integrated multi-omics and immunity PCA - an immense national resource to interrogate, target, and intercept events that drive oncogenesis. Cancer Res; 77(7); 1510-41. ©2017 AACR.
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Affiliation(s)
- Avrum Spira
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Pathology and Bioinformatics, Boston University School of Medicine, Boston, Massachusetts
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ludmil Alexandrov
- Theoretical Division, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Rafael Bejar
- Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Olivera J Finn
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Madhav Dhodapkar
- Department of Hematology and Immunology, Yale Cancer Center, New Haven, Connecticut
| | - Neil E Kay
- Department of Hematology, Mayo Clinic Hospital, Rochester, Minnesota
| | - Esteban Braggio
- Department of Hematology, Mayo Clinic Hospital, Phoenix, Arizona
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah A Mazzilli
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Pathology and Bioinformatics, Boston University School of Medicine, Boston, Massachusetts
| | - Timothy R Rebbeck
- Division of Hematology and Oncology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Victor E Velculescu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
- Department of Pathology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Mary L Disis
- Department of Medicine, Center for Translational Medicine in Women's Health, University of Washington, Seattle, Washington
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Scott M Lippman
- Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California.
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137
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Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, Pacey S, Baird R, Rosenfeld N. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer 2017; 17:223-238. [PMID: 28233803 DOI: 10.1038/nrc.2017.7] [Citation(s) in RCA: 1576] [Impact Index Per Article: 225.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Improvements in genomic and molecular methods are expanding the range of potential applications for circulating tumour DNA (ctDNA), both in a research setting and as a 'liquid biopsy' for cancer management. Proof-of-principle studies have demonstrated the translational potential of ctDNA for prognostication, molecular profiling and monitoring. The field is now in an exciting transitional period in which ctDNA analysis is beginning to be applied clinically, although there is still much to learn about the biology of cell-free DNA. This is an opportune time to appraise potential approaches to ctDNA analysis, and to consider their applications in personalized oncology and in cancer research.
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Affiliation(s)
- Jonathan C M Wan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - Charles Massie
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - Javier Garcia-Corbacho
- Clinical Trials Unit, Clinic Institute of Haematological and Oncological Diseases, Hospital Clinic de Barcelona, IDIBAPs, Carrer de Villarroel, 170 Barcelona 08036, Spain
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Simon Pacey
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Richard Baird
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cancer Research UK Cambridge Centre, Cambridge CB2 0RE, UK
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138
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Bardelli A, Pantel K. Liquid Biopsies, What We Do Not Know (Yet). Cancer Cell 2017; 31:172-179. [PMID: 28196593 DOI: 10.1016/j.ccell.2017.01.002] [Citation(s) in RCA: 342] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 10/28/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022]
Abstract
The inherent molecular heterogeneity of metastatic tumors and the ability of cancer genomes to dynamically evolve are not properly captured by tissue specimens. Analysis of cell-free DNA and circulating tumor cells has the potential to change clinical practice by exploiting blood rather than tissue as a source of information. Liquid biopsies are already used to monitor disease response and track the emergence of drug resistance. The suitability of blood-based molecular profiles for early detection and monitoring minimal residual disease is being evaluated. In this review, we address open questions in this fast-evolving field of research.
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Affiliation(s)
- Alberto Bardelli
- University of Torino, Department of Oncology, SP 142, Km 3.95, 10060 Candiolo, Torino, Italy; Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy.
| | - Klaus Pantel
- Department of Tumor Biology, Center of Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistraβe 52, 20246 Hamburg, Germany.
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139
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Fumagalli C, Bianchi F, Raviele PR, Vacirca D, Bertalot G, Rampinelli C, Lazzeroni M, Bonanni B, Veronesi G, Fusco N, Barberis M, Guerini-Rocco E. Circulating and tissue biomarkers in early-stage non-small cell lung cancer. Ecancermedicalscience 2017; 11:717. [PMID: 28194229 PMCID: PMC5295844 DOI: 10.3332/ecancer.2017.717] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE We sought to characterise circulating and tissue tumour biomarkers of patients who developed early-stage non-small cell lung cancer (NSCLC) during long-term follow-up of a chemoprevention trial (NCT00321893). MATERIALS AND METHODS Blood and sputum samples were collected from 202 high-risk asymptomatic individuals with CT-detected stable lung nodules. Real-time PCR was performed on plasma to quantify free circulating DNA. Baseline serum was investigated with a previously validated test based on 13 circulating miRNAs (miR-Test). Promoter methylation status of p16, RASSF1a and RARβ2 and telomerase activity were assessed in sputum samples. DNA was extracted from each tumour developed during follow-up and subjected to a mutation survey using the LungCarta panel on the Sequenom MassARRAY platform. RESULTS During follow-up (9 years) six individuals underwent surgery for stage I NSCLC with a median time of disease onset of 20.5 months. MiR-Test scores were positive (range: 0.14-7.24) in four out of six baseline pre-disease onset sera. No association was identified between free circulating DNA or sputum biomarkers and disease onset. All tumours harboured at least one somatic mutation in well-known cancer genes, including KRAS (n = 4), BRAF (n = 1), and TP53 (n = 3). CONCLUSION Circulating miRNA tests may represent valuable tools to detect clinically-silent tumours. Early-stage lung adenocarcinomas harbour recurrent genetic events similar to those described in advanced-stage NSCLCs.
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Affiliation(s)
- Caterina Fumagalli
- Division of Pathology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Fabrizio Bianchi
- Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Paola Rafaniello Raviele
- Division of Pathology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Davide Vacirca
- Division of Pathology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Giovanni Bertalot
- Molecular Medicine Programme IEO, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Cristiano Rampinelli
- Department of Radiology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Matteo Lazzeroni
- Division of Cancer Prevention and Genetics, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Giulia Veronesi
- Division of Thoracic Surgery, Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano Milan, Italy
| | - Nicola Fusco
- Division of Pathology, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Massimo Barberis
- Division of Pathology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
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140
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Abstract
In a Perspective, Klaus Pantel discusses prospects for use of cell-free DNA and circulating tumor cells in cancer detection.
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141
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Le Calvez-Kelm F, Foll M, Wozniak MB, Delhomme TM, Durand G, Chopard P, Pertesi M, Fabianova E, Adamcakova Z, Holcatova I, Foretova L, Janout V, Vallee MP, Rinaldi S, Brennan P, McKay JD, Byrnes GB, Scelo G. KRAS mutations in blood circulating cell-free DNA: a pancreatic cancer case-control. Oncotarget 2016; 7:78827-78840. [PMID: 27705932 PMCID: PMC5346680 DOI: 10.18632/oncotarget.12386] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/19/2016] [Indexed: 12/30/2022] Open
Abstract
The utility of KRAS mutations in plasma circulating cell-free DNA (cfDNA) samples as non-invasive biomarkers for the detection of pancreatic cancer has never been evaluated in a large case-control series. We applied a KRAS amplicon-based deep sequencing strategy combined with analytical pipeline specifically designed for the detection of low-abundance mutations to screen plasma samples of 437 pancreatic cancer cases, 141 chronic pancreatitis subjects, and 394 healthy controls. We detected mutations in 21.1% (N=92) of cases, of whom 82 (89.1%) carried at least one mutation at hotspot codons 12, 13 or 61, with mutant allelic fractions from 0.08% to 79%. Advanced stages were associated with an increased proportion of detection, with KRAS cfDNA mutations detected in 10.3%, 17,5% and 33.3% of cases with local, regional and systemic stages, respectively. We also detected KRAS cfDNA mutations in 3.7% (N=14) of healthy controls and in 4.3% (N=6) of subjects with chronic pancreatitis, but at significantly lower allelic fractions than in cases. Combining cfDNA KRAS mutations and CA19-9 plasma levels on a limited set of case-control samples did not improve the overall performance of the biomarkers as compared to CA19-9 alone. Whether the limited sensitivity and specificity observed in our series of KRAS mutations in plasma cfDNA as biomarkers for pancreatic cancer detection are attributable to methodological limitations or to the biology of cfDNA should be further assessed in large case-control series.
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Affiliation(s)
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | | | - Geoffroy Durand
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Maroulio Pertesi
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Zora Adamcakova
- Regional Authority of Public Health, Banska Bystrica, Slovakia
| | - Ivana Holcatova
- Charles University of Prague, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Prague, Czech Republic
| | - Lenka Foretova
- Masaryk Memorial Cancer Institute and Medical Faculty of Masaryk University, Brno, Czech Republic
| | - Vladimir Janout
- Department of Preventive Medicine, Faculty of Medicine, Palacky University, Olomouc, Czech Republic
- Faculty of Medicine, University of Ostrava, Czech Republic
| | - Maxime P. Vallee
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Sabina Rinaldi
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - James D. McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Graham B. Byrnes
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
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142
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Wang S, Tsui ST, Liu C, Song Y, Liu D. EGFR C797S mutation mediates resistance to third-generation inhibitors in T790M-positive non-small cell lung cancer. J Hematol Oncol 2016; 9:59. [PMID: 27448564 PMCID: PMC4957905 DOI: 10.1186/s13045-016-0290-1] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/16/2016] [Indexed: 01/09/2023] Open
Abstract
T790M mutation is the most common mechanism for resistance to first- and second-generation tyrosine kinase inhibitors (TKI) for epidermal growth factor receptor (EGFR). Several third-generation EGFR mutant selective TKIs are being explored to conquer this resistance. AZD9291 (osimertinib, tagrisso) has been approved for treatment of the metastatic EGFR T790M mutation-positive non-small cell lung cancer. Resistance to AZD9291 has been described. C797S mutation was reported to be a major mechanism for resistance to T790M-targeting EGFR inhibitors. This review summarizes the latest development in identifying the C797S mutation and EAI045, the novel selective inhibitor overcoming the C797S mutant.
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Affiliation(s)
- Shuhang Wang
- The Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital, Beijing, China
| | - Stella T Tsui
- SUNY Stony Brook University, Stony Brook, NY, 11794, USA
| | - Christina Liu
- Weinberg College of Arts and Sciences, Northwestern University, Evanston, IL, 60208, USA
| | - Yongping Song
- Henan Cancer Hospital and the affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Delong Liu
- Henan Cancer Hospital and the affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China.
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143
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Pantel K. TP53 mutations on circulating cell-free DNA. EBioMedicine 2016; 10:15-6. [PMID: 27412263 PMCID: PMC5006662 DOI: 10.1016/j.ebiom.2016.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 07/06/2016] [Indexed: 01/05/2023] Open
Affiliation(s)
- Klaus Pantel
- University Medical Center Hamburg-Eppendorf, Institute of Tumor Biology, Martinistrasse 52, 20246 Hamburg, Germany.
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