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Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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53
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Kato K, Uchida J, Kukita Y, Kumagai T, Nishino K, Inoue T, Kimura M, Imamura F. Transient appearance of circulating tumor DNA associated with de novo treatment. Sci Rep 2016; 6:38639. [PMID: 27934896 PMCID: PMC5146655 DOI: 10.1038/srep38639] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/11/2016] [Indexed: 12/18/2022] Open
Abstract
The limitation of circulating tumor DNA (ctDNA) is its inability to detect cancer cell subpopulations with few or no dying cells. Lung cancer patients subjected to the EGFR tyrosine kinase inhibitor (EGFR-TKI) treatment were prospectively collected, and ctDNA levels represented by the activating and T790M mutations were measured. The first data set (21 patients) consisting of samples collected in the period from before initiation of EGFR-TKI to at least 2 weeks after initiation: the ctDNA dynamics generally exhibited a rapid decrease and/or a transient increase. In 4 patients, we detected a transient increase of ctDNA bearing activating mutations not identified in biopsy samples. ctDNA with the same genotypical pattern was identified in 7 out of the 39 patients of the second data set intended to include samples until the onset of disease progression. In 6 of the 7 patients, this unique ctDNA appeared in the early period after treatment initiation, and did not reappear even after disease progression or chemotherapy. In another patient, similar ctDNA appeared upon radiation therapy. The identification of ctDNA with a unique genotype indicates the presence of cancer cell subpopulations that normally contain few or no dying cells, but generate dead cells because of the treatment.
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Affiliation(s)
- Kikuya Kato
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Junji Uchida
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Yoji Kukita
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Takako Inoue
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Madoka Kimura
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Fumio Imamura
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
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55
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Fawcett GL, Karina Eterovic A. Identification of Genomic Somatic Variants in Cancer: From Discovery to Actionability. Adv Clin Chem 2016; 78:123-162. [PMID: 28057186 DOI: 10.1016/bs.acc.2016.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The perfect method to discover and validate actionable somatic variants in cancer has not yet been developed, yet significant progress has been made toward this goal. There have been huge increases in the throughput and cost of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) sequencing technologies that have led to the burgeoning possibility of using sequencing data in clinical settings. Discovery of somatic mutations is relatively simple and has been improved recently due to laboratory methods optimization, bioinformatics algorithms development, and the expansion of various databases of population genomic information. Tiered systems of evidence evaluation are currently being used to classify genomic variants for clinicians to more rapidly and accurately determine actionability of these aberrations. These efforts are complicated by the intricacies of communicating sequencing results to physicians and supporting its biological relevance, emphasizing the need for increasing education of clinicians and administrators, and the ongoing development of ethical standards for dealing with incidental results. This chapter will focus on general aspects of DNA and RNA tumor sequencing technologies, data analysis and interpretation, assessment of biological and clinical relevance of genomic aberrations, ethical aspects of germline sequencing, and how these factors impact cancer personalized care.
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Affiliation(s)
- G L Fawcett
- Institute for Personalized Cancer Therapy (IPCT) at University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - A Karina Eterovic
- Institute for Personalized Cancer Therapy (IPCT) at University of Texas M.D. Anderson Cancer Center, Houston, TX, United States.
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56
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Alegre E, Fusco JP, Restituto P, Salas-Benito D, Rodríguez-Ruiz ME, Andueza MP, Pajares MJ, Patiño-García A, Pio R, Lozano MD, Gúrpide A, Lopez-Picazo JM, Gil-Bazo I, Perez-Gracia JL, Gonzalez A. Total and mutated EGFR quantification in cell-free DNA from non-small cell lung cancer patients detects tumor heterogeneity and presents prognostic value. Tumour Biol 2016; 37:13687-13694. [PMID: 27473086 DOI: 10.1007/s13277-016-5282-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/15/2016] [Indexed: 11/26/2022] Open
Abstract
Mutation analysis of epidermal growth factor receptor (EGFR) gene is essential for treatment selection in non-small cell lung cancer (NSCLC). Analysis is usually performed in tumor samples. We evaluated the clinical utility of EGFR analysis in plasma cell-free DNA (cfDNA) from patients under treatment with EGFR inhibitors. We selected 36 patients with NSCLC and EGFR-activating mutations. Blood samples were collected at baseline and during treatment with EGFR inhibitors. Wild-type EGFR, L858R, delE746-A750, and T790M mutations were quantified in cfDNA by droplet digital PCR. Stage IV patients had higher total circulating EGFR copy levels than stage I (3523 vs. 1003 copies/mL; p < 0.01). There was high agreement for activating mutations between baseline cfDNA and tumor samples, especially for L858R mutation (kappa index = 0.679; p = 0.001). In 34 % of advanced NSCLC patients, we detected mutations in cfDNA not previously detected in tumor samples and double mutations in 17 %. Patients with baseline total EGFR copy levels above the median presented decreased overall survival (OS) (341 vs. 870 days, p < 0.05) and progression-free survival (PFS) (238 vs. 783 days; p < 0.05) compared with those with total EGFR copy levels below the median. Patients with baseline concentrations of activating mutations above the median (94 copies/mL) had lower OS (317 vs. 805 days; p < 0.05) and PFS (195 vs. 724 days; p < 0.05). During follow-up, T790M resistance mutation was detected in 53 % of patients. Total and mutated EGFR analysis in cfDNA seems a relevant tool to characterize the molecular profile and prognosis of NSCLC patients harboring EGFR mutations.
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Affiliation(s)
- E Alegre
- Clinical Chemistry Department, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
- Department of Biochemistry and Genetics, Universidad de Navarra, Irunlarrea 1, 31008, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
| | - J P Fusco
- Department of Oncology, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
| | - P Restituto
- Clinical Chemistry Department, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
| | - D Salas-Benito
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
- Department of Oncology, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
| | - M E Rodríguez-Ruiz
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
- Department of Oncology, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
| | - M P Andueza
- Department of Oncology, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
| | - M J Pajares
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
- Program in Solid Tumors and Biomarkers|, Centro de Investigación Médica Aplicada (CIMA), Av Pio XII, 55 31008, Pamplona, Spain
- Department of Histology, Universidad de Navarra, Irunlarrea 1, 31008, Pamplona, Spain
| | - A Patiño-García
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
- Department of Pediatrics and CIMA LAB Diagnostics, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
| | - R Pio
- Department of Biochemistry and Genetics, Universidad de Navarra, Irunlarrea 1, 31008, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
- Program in Solid Tumors and Biomarkers|, Centro de Investigación Médica Aplicada (CIMA), Av Pio XII, 55 31008, Pamplona, Spain
| | - M D Lozano
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
- Department of Pathology, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
| | - A Gúrpide
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
- Department of Oncology, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
| | - J M Lopez-Picazo
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
- Department of Oncology, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
| | - I Gil-Bazo
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
- Department of Oncology, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
| | - J L Perez-Gracia
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain
- Department of Oncology, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain
| | - A Gonzalez
- Clinical Chemistry Department, Clínica Universidad de Navarra, Av Pio XII 36, 31008, Pamplona, Spain.
- Department of Biochemistry and Genetics, Universidad de Navarra, Irunlarrea 1, 31008, Pamplona, Spain.
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008, Pamplona, Spain.
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Trombetta D, Sparaneo A, Fabrizio FP, Muscarella LA. Liquid biopsy and NSCLC. Lung Cancer Manag 2016; 5:91-104. [PMID: 30643553 DOI: 10.2217/lmt-2016-0006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/20/2016] [Indexed: 12/18/2022] Open
Abstract
In the era of high-throughput molecular screening and personalized medicine, difficulty in determining whether cancer mutations are truly 'actionable' remains a gray zone in NSCLC. The most important prerequisite to perform such investigations is the tumor tissue retrieval via biopsy at diagnosis and after occurrence of resistance. Blood-based liquid biopsy as circulating tumor cells, circulating tumor DNA and exosomes can offer a fast and non-invasive method to elucidate the genetic heterogeneity of patients, the screening and patient stratification and give a dynamic surveillance for tumor progression and monitor treatments response. Here we prospectively discuss the three main approaches in the blood-biopsy field of lung cancer patients and its clinical applications in patient management. We also outline some of the analytical challenges that remain for liquid biopsy techniques in demonstrating that it could represent a true and actionable picture in lung cancer management for the implementation into clinical routine.
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Affiliation(s)
- Domenico Trombetta
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
| | - Angelo Sparaneo
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
| | - Federico Pio Fabrizio
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo (FG), Italy
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59
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Kato K, Uchida J, Kukita Y, Kumagai T, Nishino K, Inoue T, Kimura M, Oba S, Imamura F. Numerical indices based on circulating tumor DNA for the evaluation of therapeutic response and disease progression in lung cancer patients. Sci Rep 2016; 6:29093. [PMID: 27381430 PMCID: PMC4933907 DOI: 10.1038/srep29093] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/14/2016] [Indexed: 12/18/2022] Open
Abstract
Monitoring of disease/therapeutic conditions is an important application of circulating tumor DNA (ctDNA). We devised numerical indices, based on ctDNA dynamics, for therapeutic response and disease progression. 52 lung cancer patients subjected to the EGFR-TKI treatment were prospectively collected, and ctDNA levels represented by the activating and T790M mutations were measured using deep sequencing. Typically, ctDNA levels decreased sharply upon initiation of EGFR-TKI, however this did not occur in progressive disease (PD) cases. All 3 PD cases at initiation of EGFR-TKI were separated from other 27 cases in a two-dimensional space generated by the ratio of the ctDNA levels before and after therapy initiation (mutation allele ratio in therapy, MART) and the average ctDNA level. For responses to various agents after disease progression, PD/stable disease cases were separated from partial response cases using MART (accuracy, 94.7%; 95% CI, 73.5–100). For disease progression, the initiation of ctDNA elevation (initial positive point) was compared with the onset of objective disease progression. In 11 out of 28 eligible patients, both occurred within ±100 day range, suggesting a detection of the same change in disease condition. Our numerical indices have potential applicability in clinical practice, pending confirmation with designed prospective studies.
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Affiliation(s)
- Kikuya Kato
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Junji Uchida
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Yoji Kukita
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Takako Inoue
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Madoka Kimura
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Shigeyuki Oba
- Graduate School of Informatics, Kyoto University, Kyoto, Japan
| | - Fumio Imamura
- Department of Thoracic Oncology, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
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