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Zalis M, Viana Veloso GG, Aguiar Jr. PN, Gimenes N, Reis MX, Matsas S, Ferreira CG. Next-generation sequencing impact on cancer care: applications, challenges, and future directions. Front Genet 2024; 15:1420190. [PMID: 39045325 PMCID: PMC11263191 DOI: 10.3389/fgene.2024.1420190] [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: 04/19/2024] [Accepted: 06/13/2024] [Indexed: 07/25/2024] Open
Abstract
Fundamentally precision oncology illustrates the path in which molecular profiling of tumors can illuminate their biological behavior, diversity, and likely outcomes by identifying distinct genetic mutations, protein levels, and other biomarkers that underpin cancer progression. Next-generation sequencing became an indispensable diagnostic tool for diagnosis and treatment guidance in current clinical practice. Nowadays, tissue analysis benefits from further support through methods like comprehensive genomic profiling and liquid biopsies. However, precision medicine in the field of oncology presents specific hurdles, such as the cost-benefit balance and widespread accessibility, particularly in countries with low- and middle-income. A key issue is how to effectively extend next-generation sequencing to all cancer patients, thus empowering treatment decision-making. Concerns also extend to the quality and preservation of tissue samples, as well as the evaluation of health technologies. Moreover, as technology advances, novel next-generation sequencing assessments are being developed, including the study of Fragmentomics. Therefore, our objective was to delineate the primary uses of next-generation sequencing, discussing its' applications, limitations, and prospective paths forward in Oncology.
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Affiliation(s)
- Mariano Zalis
- Oncoclínicas&Co/MedSir, Rio de Janeiro, Brazil
- Medical School of the Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilson Gabriel Viana Veloso
- Oncoclínicas&Co/MedSir, Rio de Janeiro, Brazil
- Santa Casa de Misericórdia de Belo Horizonte, Belo Horizonte, Brazil
| | | | | | | | - Silvio Matsas
- Centro de Estudos e Pesquisas de Hematologia e Oncologia (CEPHO), Sao Paulo, Brazil
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Enko D, Schaflinger E, Müller DJ. [Clinical Application Examples of a Next-Generation Sequencing based Multi-Genepanel Analysis]. Dtsch Med Wochenschr 2023; 148:695-702. [PMID: 37216946 DOI: 10.1055/a-2033-5329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This review provides an overview of clinically useful applications of a next-generation sequencing (NGS)-based multi-gene panel testing strategy in the areas of oncology, hereditary tumor syndromes, and hematology. In the case of solid tumors (e.g. lung carcinoma, colon-rectal carcinoma), the detection of somatic mutations contributes not only to a better diagnostic but also therapeutic stratification of those affected. The increasing genetic complexity of hereditary tumor syndromes (e.g. breast and ovarian carcinoma, lynch syndrome/polyposis) requires a multi-gene panel analysis of germline mutations in affected families. Another useful indication for a multi-gene panel diagnostics and prognosis assessment are acute and chronic myeloid diseases. The criteria of the WHO-classification and the European LeukemiaNet-prognosis system for acute myeloid leukemia can only be met by a multi-gene panel test strategy.
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Affiliation(s)
- Dietmar Enko
- Medizinische Universität Graz Klinisches Institut für Medizinische und Chemische Labordiagnostik, Graz, Austria
| | - Erich Schaflinger
- Institut für Humangenetik, Medizinische Universität Graz, Neue Stiftingtalstraße 2, 8010 Graz, Austria
| | - Daniel J Müller
- Klinisches Institut für Pharmakogenetische Wissenschaft, Cambell Family Mental Health Research Institute, Zentrum für Suchtkrankheit und psychische Gesundheit, College Street 250, Toronto, ON M5T 1R8, Toronto, Kanada
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3
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Wadden J, Newell BS, Bugbee J, John V, Bruzek AK, Dickson RP, Koschmann C, Blaauw D, Narayanasamy S, Das R. Ultra-rapid somatic variant detection via real-time targeted amplicon sequencing. Commun Biol 2022; 5:708. [PMID: 35840782 PMCID: PMC9284968 DOI: 10.1038/s42003-022-03657-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 06/29/2022] [Indexed: 12/03/2022] Open
Abstract
Molecular markers are essential for cancer diagnosis, clinical trial enrollment, and some surgical decision making, motivating ultra-rapid, intraoperative variant detection. Sequencing-based detection is considered the gold standard approach, but typically takes hours to perform due to time-consuming DNA extraction, targeted amplification, and library preparation times. In this work, we present a proof-of-principle approach for sub-1 hour targeted variant detection using real-time DNA sequencers. By modifying existing protocols, optimizing for diagnostic time-to-result, we demonstrate confirmation of a hot-spot mutation from tumor tissue in ~52 minutes. To further reduce time, we explore rapid, targeted Loop-mediated Isothermal Amplification (LAMP) and design a bioinformatics tool-LAMPrey-to process sequenced LAMP product. LAMPrey's concatemer aware alignment algorithm is designed to maximize recovery of diagnostically relevant information leading to a more rapid detection versus standard read alignment approaches. Using LAMPrey, we demonstrate confirmation of a hot-spot mutation (250x support) from tumor tissue in less than 30 minutes.
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Affiliation(s)
- Jack Wadden
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA.
- Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA.
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA.
| | - Brandon S Newell
- Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joshua Bugbee
- Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Vishal John
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Amy K Bruzek
- Department of Neurosurgery, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Carl Koschmann
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - David Blaauw
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Satish Narayanasamy
- Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Reetuparna Das
- Division of Computer Science and Engineering, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA.
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Fatima S, Ma Y, Safrachi A, Haider S, Spring KJ, Vafaee F, Scott KF, Roberts TL, Becker TM, de Souza P. Harnessing Liquid Biopsies to Guide Immune Checkpoint Inhibitor Therapy. Cancers (Basel) 2022; 14:1669. [PMID: 35406441 PMCID: PMC8997025 DOI: 10.3390/cancers14071669] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 12/24/2022] Open
Abstract
Immunotherapy (IO), involving the use of immune checkpoint inhibition, achieves improved response-rates and significant disease-free survival for some cancer patients. Despite these beneficial effects, there is poor predictability of response and substantial rates of innate or acquired resistance, resulting in heterogeneous responses among patients. In addition, patients can develop life-threatening adverse events, and while these generally occur in patients that also show a tumor response, these outcomes are not always congruent. Therefore, predicting a response to IO is of paramount importance. Traditionally, tumor tissue analysis has been used for this purpose. However, minimally invasive liquid biopsies that monitor changes in blood or other bodily fluid markers are emerging as a promising cost-effective alternative. Traditional biomarkers have limitations mainly due to difficulty in repeatedly obtaining tumor tissue confounded also by the spatial and temporal heterogeneity of tumours. Liquid biopsy has the potential to circumvent tumor heterogeneity and to help identifying patients who may respond to IO, to monitor the treatment dynamically, as well as to unravel the mechanisms of relapse. We present here a review of the current status of molecular markers for the prediction and monitoring of IO response, focusing on the detection of these markers in liquid biopsies. With the emerging improvements in the field of liquid biopsy, this approach has the capacity to identify IO-eligible patients and provide clinically relevant information to assist with their ongoing disease management.
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Affiliation(s)
- Shadma Fatima
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia; (A.S.); (F.V.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Yafeng Ma
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- South Western Sydney Clinical School, UNSW, Sydney, NSW 2031, Australia
- Centre for Circulating Tumor Cell Diagnosis and Research, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Azadeh Safrachi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia; (A.S.); (F.V.)
| | - Sana Haider
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Kevin J. Spring
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia; (A.S.); (F.V.)
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW 2031, Australia
| | - Kieran F. Scott
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Tara L. Roberts
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
- South Western Sydney Clinical School, UNSW, Sydney, NSW 2031, Australia
| | - Therese M. Becker
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
- South Western Sydney Clinical School, UNSW, Sydney, NSW 2031, Australia
- Centre for Circulating Tumor Cell Diagnosis and Research, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Paul de Souza
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
- South Western Sydney Clinical School, UNSW, Sydney, NSW 2031, Australia
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Qin D. Molecular testing for acute myeloid leukemia. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0734. [PMID: 34347394 PMCID: PMC8763005 DOI: 10.20892/j.issn.2095-3941.2020.0734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/02/2021] [Indexed: 11/11/2022] Open
Abstract
In the era of personalized medicine, information on molecular change at the gene level is important for patient care. Such information has been used for disease classification, diagnosis, prognosis, risk stratification, and treatment, which is especially important in cancer patient care. Many molecular tests exist and can be used to detect the molecular changes at gene level. These tests include, but are not limited to, karyotyping, endpoint polymerase chain reaction (PCR), real-time PCR, Sanger sequencing, pyrosequencing, next-generation sequencing, and so forth. How to use the right tests for the right patients at the right time is essential for optimal patient outcome. This review puts together some information on molecular testing for acute myeloid leukemia.
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Affiliation(s)
- Dahui Qin
- Moffitt Cancer Center, Tampa, FL 33612-9416, USA
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