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Werner R, Crosbie R, Dorney M, Connolly A, Collins D, Hand CK, Burke L. Implementation of an ISO 15189 accredited next generation sequencing service for cell-free total nucleic acid (cfTNA) analysis to facilitate driver mutation reporting in blood: the experience of a clinical diagnostic laboratory. J Clin Pathol 2024:jcp-2024-209514. [PMID: 38914446 DOI: 10.1136/jcp-2024-209514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/11/2024] [Indexed: 06/26/2024]
Abstract
AIMS Next generation sequencing (NGS) on tumour tissue is integral to the delivery of personalised medicine and targeted therapy. NGS on liquid biopsy, a much less invasive technology, is an emerging clinical tool that has rapidly expanded clinical utility. Gene mutations in cell-free total nucleic acids (cfTNA) circulating in the blood are representative of whole tumour biology and can reveal different mutations from different tumour sites, thus addressing tumour heterogeneity challenges. METHODS The novel Ion Torrent Genexus NGS system with automated sample preparation, onboard library preparation, templating, sequencing, data analysis and Oncomine Reporter software was used. cfTNA extracted from plasma was verified with the targeted pan-cancer (~50 genes) Oncomine Precision Assay (OPA). Assessment criteria included analytical sensitivity, specificity, limits of detection (LOD), accuracy, repeatability, reproducibility and the establishment of performance metrics. RESULTS An ISO 15189 accredited, minimally invasive cfTNA NGS diagnostic service has been implemented. High sensitivity (>83%) and specificity between plasma and tissue were observed. A sequencing LOD of 1.2% was achieved when the depth of coverage was >22 000×. A reduction (>68%) in turnaround time (TAT) of liquid biopsy results was achieved: 5 days TAT for in-house analysis from sample receipt to a final report issued to oncologists as compared with >15 days from reference laboratories. CONCLUSION Tumour-derived somatic variants can now be reliably assessed from plasma to provide minimally invasive tumour profiling. Successful implementation of this accredited service resulted in:Appropriate molecular profiling of patients where tumour tissue is unavailable or inaccessible.Rapid TAT of plasma NGS results.
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Affiliation(s)
- Reiltin Werner
- Pathology Department, Cork University Hospital, Cork, Ireland
- Department of Pathology, School of Medicine, University College Cork College of Medicine and Health, Cork, Ireland
| | - Ruth Crosbie
- Pathology Department, Cork University Hospital, Cork, Ireland
| | - Mairead Dorney
- Pathology Department, Cork University Hospital, Cork, Ireland
| | - Amy Connolly
- Pathology Department, Cork University Hospital, Cork, Ireland
| | | | - Collette K Hand
- Department of Pathology, School of Medicine, University College Cork College of Medicine and Health, Cork, Ireland
| | - Louise Burke
- Pathology Department, Cork University Hospital, Cork, Ireland
- Department of Pathology, School of Medicine, University College Cork College of Medicine and Health, Cork, Ireland
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Leenanitikul J, Chanchaem P, Mankhong S, Denariyakoon S, Fongchaiya V, Arayataweegool A, Angspatt P, Wongchanapai P, Prapanpoj V, Chatamra K, Pisitkun T, Sriswasdi S, Wongkongkathep P. Concordance between whole exome sequencing of circulating tumor DNA and tumor tissue. PLoS One 2023; 18:e0292879. [PMID: 37878600 PMCID: PMC10599540 DOI: 10.1371/journal.pone.0292879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/02/2023] [Indexed: 10/27/2023] Open
Abstract
Next generation sequencing of circulating tumor DNA (ctDNA) has been used as a noninvasive alternative for cancer diagnosis and characterization of tumor mutational landscape. However, low ctDNA fraction and other factors can limit the ability of ctDNA analysis to capture tumor-specific and actionable variants. In this study, whole-exome sequencings (WES) were performed on paired ctDNA and tumor biopsy in 15 cancer patients to assess the extent of concordance between mutational profiles derived from the two source materials. We found that up to 16.4% ctDNA fraction can still be insufficient for detecting tumor-specific variants and that good concordance with tumor biopsy is consistently achieved at higher ctDNA fractions. Most importantly, ctDNA analysis can consistently capture tumor heterogeneity and detect key cancer-related genes even in a patient with both primary and metastatic tumors.
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Affiliation(s)
- Julanee Leenanitikul
- Bioinformatics and Computational Biology Program, Chulalongkorn University, Bangkok, Thailand
| | - Prangwalai Chanchaem
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Suwanan Mankhong
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sikrit Denariyakoon
- The Queen Sirikit Center for Breast Cancer, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Valla Fongchaiya
- The Queen Sirikit Center for Breast Cancer, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Areeya Arayataweegool
- The Queen Sirikit Center for Breast Cancer, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Pattama Angspatt
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and the King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Ploytuangporn Wongchanapai
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and the King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | | | - Kris Chatamra
- The Queen Sirikit Center for Breast Cancer, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sira Sriswasdi
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Piriya Wongkongkathep
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Pesta M, Shetti D, Kulda V, Knizkova T, Houfkova K, Bagheri MS, Svaton M, Polivka J. Applications of Liquid Biopsies in Non-Small-Cell Lung Cancer. Diagnostics (Basel) 2022; 12:1799. [PMID: 35892510 PMCID: PMC9330570 DOI: 10.3390/diagnostics12081799] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022] Open
Abstract
The concept of liquid biopsy as an analysis tool for non-solid tissue carried out for the purpose of providing information about solid tumors was introduced approximately 20 years ago. Additional to the detection of circulating tumor cells (CTCs), the liquid biopsy approach quickly included the analysis of circulating tumor DNA (ctDNA) and other tumor-derived markers such as circulating cell-free RNA or extracellular vesicles. Liquid biopsy is a non-invasive technique for detecting multiple cancer-associated biomarkers that is easy to obtain and can reflect the characteristics of the entire tumor mass. Currently, ctDNA is the key component of the liquid biopsy approach from the point of view of the prognosis assessment, prediction, and monitoring of the treatment of non-small-cell lung cancer (NSCLC) patients. ctDNA in NSCLC patients carries variants or rearrangements that drive carcinogenesis, such as those in EGFR, KRAS, ALK, or ROS1. Due to advances in pharmacology, these variants are the subject of targeted therapy. Therefore, the detection of these variants has gained attention in clinical medicine. Recently, methods based on qPCR (ddPCR, BEAMing) and next-generation sequencing (NGS) are the most effective approaches for ctDNA analysis. This review addresses various aspects of the use of liquid biopsy with an emphasis on ctDNA as a biomarker in NSCLC patients.
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Affiliation(s)
- Martin Pesta
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Dattatrya Shetti
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Vlastimil Kulda
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic;
| | - Tereza Knizkova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Katerina Houfkova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Mahyar Sharif Bagheri
- Department of Histology, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic; (M.S.B.); (J.P.)
| | - Martin Svaton
- Department of Pneumology and Phthisiology, Faculty of Medicine in Pilsen, Charles University, University Hospital in Pilsen, E. Benese 13, 301 00 Plzen, Czech Republic;
| | - Jiri Polivka
- Department of Histology, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic; (M.S.B.); (J.P.)
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