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Ehman M, Punian J, Weymann D, Regier DA. Next-generation sequencing in oncology: challenges in economic evaluations. Expert Rev Pharmacoecon Outcomes Res 2024:1-18. [PMID: 39096135 DOI: 10.1080/14737167.2024.2388814] [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: 06/20/2024] [Revised: 07/19/2024] [Accepted: 08/01/2024] [Indexed: 08/04/2024]
Abstract
INTRODUCTION Next-generation sequencing (NGS) identifies genetic variants to inform personalized treatment plans. Insufficient evidence of cost-effectiveness impedes the integration of NGS into routine cancer care. The complexity of personalized treatment challenges conventional economic evaluation. Clearly delineating challenges informs future cost-effectiveness analyses to better value and contextualize health, preference-, and equity-based outcomes. AREAS COVERED We conducted a scoping review to characterize the applied methods and outcomes of economic evaluations of NGS in oncology and identify existing challenges. We included 27 articles published since 2016 from a search of PubMed, Embase, and Web of Science. Identified challenges included defining the evaluative scope, managing evidentiary limitations including lack of causal evidence, incorporating preference-based utility, and assessing distributional and equity-based impacts. These challenges reflect the difficulty of generating high-quality clinical effectiveness and real-world evidence (RWE) for NGS-guided interventions. EXPERT OPINION Adapting methodological approaches and developing life-cycle health technology assessment (HTA) guidance using RWE is crucial for implementing NGS in oncology. Healthcare systems, decision-makers, and HTA organizations are facing a pivotal opportunity to adapt to an evolving clinical paradigm and create innovative regulatory and reimbursement processes that will enable more sustainable, equitable, and patient-oriented healthcare.
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Affiliation(s)
- Morgan Ehman
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Jesman Punian
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Deirdre Weymann
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
- Faculty of Health Sciences, Simon Fraser University, Vancouver, BC, Canada
| | - Dean A Regier
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
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2
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Fernández Aceñero MJ, Díaz del Arco C. Hereditary Gastrointestinal Tumor Syndromes: When Risk Comes with Your Genes. Curr Issues Mol Biol 2024; 46:6440-6471. [PMID: 39057027 PMCID: PMC11275188 DOI: 10.3390/cimb46070385] [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: 05/27/2024] [Revised: 06/19/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Despite recent campaigns for screening and the latest advances in cancer therapy and molecular biology, gastrointestinal (GI) neoplasms remain among the most frequent and lethal human tumors. Most GI neoplasms are sporadic, but there are some well-known familial syndromes associated with a significant risk of developing both benign and malignant GI tumors. Although some of these entities were described more than a century ago based on clinical grounds, the increasing molecular information obtained with high-throughput techniques has shed light on the pathogenesis of several of them. The vast amount of information gained from next-generation sequencing has led to the identification of some high-risk genetic variants, although others remain to be discovered. The opportunity for genetic assessment and counseling in these families has dramatically changed the management of these syndromes, though it has also resulted in significant psychological distress for the affected patients, especially those with indeterminate variants. Herein, we aim to summarize the most relevant hereditary cancer syndromes involving the stomach and colon, with an emphasis on new molecular findings, novel entities, and recent changes in the management of these patients.
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Affiliation(s)
- María Jesús Fernández Aceñero
- Department of Legal Medicine, Psychiatry and Pathology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Pathology, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
| | - Cristina Díaz del Arco
- Department of Legal Medicine, Psychiatry and Pathology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Pathology, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
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3
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Takamizawa S, Koyama T, Sunami K, Sudo K, Hirata M, Kubo T, Tao K, Cho H, Narita Y, Kato K, Yamazaki N, Ohe Y, Okusaka T, Matsui Y, Ogawa C, Yonemori K, Yamamoto N. Identification of barriers to implementation of precision oncology in patients with rare cancers. Cancer Sci 2024; 115:2023-2035. [PMID: 38538548 PMCID: PMC11145155 DOI: 10.1111/cas.16165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 06/04/2024] Open
Abstract
Established treatment options for rare cancers are limited by the small number of patients. The current comprehensive genomic profiling (CGP) testing might not fully exploit opportunities for precision oncology in patients with rare cancers. Therefore, we aimed to explore the factors associated with CGP testing utility in rare cancers and identify barriers to implementing precision oncology. Patients who underwent CGP testing at our institution between September 2019 and June 2021 were enrolled in this retrospective study. Based on their results, the patients received molecularly targeted drugs or immune checkpoint inhibitors. Univariate and multivariate analyses evaluated the association between patient characteristics and the proportion of patients receiving molecularly targeted drugs. Overall, 790 patients underwent CGP testing. Among them, 333 patients with rare cancers were identified, of whom 278 (83.5%) had actionable genomic alterations, 127 (38.1%) had druggable genomic alterations, and 25 (7.5%) received genomically matched therapy. The proportion of patients receiving molecularly targeted drugs was significantly higher among those with treatment options with evidence levels A-D (8.7%) than those without treatment options with evidence levels A-D (2.9%). A potential barrier to CGP testing utility in rare cancers is the limited number of molecularly targeted drugs with clinical evidence. We propose that CGP testing be performed in patients with rare cancers who have treatment options with evidence levels A-D to maximize CGP testing utility in real-world practice.
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Affiliation(s)
- Shigemasa Takamizawa
- Department of Experimental TherapeuticsNational Cancer Center HospitalTokyoJapan
| | - Takafumi Koyama
- Department of Experimental TherapeuticsNational Cancer Center HospitalTokyoJapan
| | - Kuniko Sunami
- Department of Laboratory MedicineNational Cancer Center HospitalTokyoJapan
| | - Kazuki Sudo
- Department of Experimental TherapeuticsNational Cancer Center HospitalTokyoJapan
- Department of Medical OncologyNational Cancer Center HospitalTokyoJapan
| | - Makoto Hirata
- Department of Genetic Medicine and ServicesNational Cancer Center HospitalTokyoJapan
| | - Takashi Kubo
- Division of Translational GenomicsNational Cancer Center‐Exploratory Oncology Research and Clinical Trial CenterTokyoJapan
| | - Kayoko Tao
- Department of Pediatric OncologyNational Cancer Center HospitalTokyoJapan
| | - Hourin Cho
- Department of Genetic Medicine and ServicesNational Cancer Center HospitalTokyoJapan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro‐OncologyNational Cancer Center HospitalTokyoJapan
| | - Ken Kato
- Department of Gastrointestinal Medical OncologyNational Cancer Center HospitalTokyoJapan
- Department of Head and Neck, Esophageal Medical OncologyNational Cancer Center HospitalTokyoJapan
| | - Naoya Yamazaki
- Department of Dermatologic OncologyNational Cancer Center HospitalTokyoJapan
| | - Yuichiro Ohe
- Department of Thoracic OncologyNational Cancer Center HospitalTokyoJapan
| | - Takuji Okusaka
- Department of Hepatobiliary and Pancreatic OncologyNational Cancer Center HospitalTokyoJapan
| | | | - Chitose Ogawa
- Department of Pediatric OncologyNational Cancer Center HospitalTokyoJapan
| | - Kan Yonemori
- Department of Experimental TherapeuticsNational Cancer Center HospitalTokyoJapan
- Department of Medical OncologyNational Cancer Center HospitalTokyoJapan
| | - Noboru Yamamoto
- Department of Experimental TherapeuticsNational Cancer Center HospitalTokyoJapan
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Wang CW, Muzakky H, Firdi NP, Liu TC, Lai PJ, Wang YC, Yu MH, Chao TK. Deep learning to assess microsatellite instability directly from histopathological whole slide images in endometrial cancer. NPJ Digit Med 2024; 7:143. [PMID: 38811811 PMCID: PMC11137095 DOI: 10.1038/s41746-024-01131-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
Molecular classification, particularly microsatellite instability-high (MSI-H), has gained attention for immunotherapy in endometrial cancer (EC). MSI-H is associated with DNA mismatch repair defects and is a crucial treatment predictor. The NCCN guidelines recommend pembrolizumab and nivolumab for advanced or recurrent MSI-H/mismatch repair deficient (dMMR) EC. However, evaluating MSI in all cases is impractical due to time and cost constraints. To overcome this challenge, we present an effective and efficient deep learning-based model designed to accurately and rapidly assess MSI status of EC using H&E-stained whole slide images. Our framework was evaluated on a comprehensive dataset of gigapixel histopathology images of 529 patients from the Cancer Genome Atlas (TCGA). The experimental results have shown that the proposed method achieved excellent performances in assessing MSI status, obtaining remarkably high results with 96%, 94%, 93% and 100% for endometrioid carcinoma G1G2, respectively, and 87%, 84%, 81% and 94% for endometrioid carcinoma G3, in terms of F-measure, accuracy, precision and sensitivity, respectively. Furthermore, the proposed deep learning framework outperforms four state-of-the-art benchmarked methods by a significant margin (p < 0.001) in terms of accuracy, precision, sensitivity and F-measure, respectively. Additionally, a run time analysis demonstrates that the proposed method achieves excellent quantitative results with high efficiency in AI inference time (1.03 seconds per slide), making the proposed framework viable for practical clinical usage. These results highlight the efficacy and efficiency of the proposed model to assess MSI status of EC directly from histopathological slides.
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Affiliation(s)
- Ching-Wei Wang
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Hikam Muzakky
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Nabila Puspita Firdi
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Tzu-Chien Liu
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Po-Jen Lai
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Yu-Chi Wang
- Department of Gynecology and Obstetrics, Tri-Service General Hospital, Taipei, Taiwan
- Department of Gynecology and Obstetrics, National Defense Medical Center, Taipei, Taiwan
| | - Mu-Hsien Yu
- Department of Gynecology and Obstetrics, Tri-Service General Hospital, Taipei, Taiwan
- Department of Gynecology and Obstetrics, National Defense Medical Center, Taipei, Taiwan
| | - Tai-Kuang Chao
- Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan.
- Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan.
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Blanluet C, Kuo CJ, Bhattacharya A, Santiago JG. Design and Evaluation of a Robust CRISPR Kinetic Assay for Hot-Spot Genotyping. Anal Chem 2024; 96:7444-7451. [PMID: 38684052 DOI: 10.1021/acs.analchem.3c05657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Next-generation sequencing offers highly multiplexed and accurate detection of nucleic acid sequences but at the expense of complex workflows and high input requirements. The ease of use of CRISPR-Cas12 assays is attractive and may enable highly accurate detection of sequences implicated in, for example, cancer pathogenic variants. CRISPR assays often employ end-point measurements of Cas12 trans-cleavage activity after Cas12 activation by the target; however, end point-based methods can be limited in accuracy and robustness by arbitrary experimental choices. To overcome such limitations, we develop and demonstrate here an accurate assay targeting a mutation of the epidermal growth factor gene implicated in lung cancer (exon 19 deletion). The assay is based on characterizing the kinetics of Cas12 trans-cleavage to discriminate the mutant from wild-type targets. We performed extensive experiments (780 reactions) to calibrate key assay design parameters, including the guide RNA sequence, reporter sequence, reporter concentration, enzyme concentration, and DNA target type. Interestingly, we observed a competitive reaction between the target and reporter molecules that has important consequences for the design of CRISPR assays, which use preamplification to improve sensitivity. Finally, we demonstrate the assay on 18 tumor-extracted amplicons and 100 training iterations with 99% accuracy and discuss discrimination parameters and models to improve wild type versus mutant classification.
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Affiliation(s)
- Charles Blanluet
- CentraleSupelec─Universite Paris-Saclay, 91190 Gif-sur-Yvette, France
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Asmita Bhattacharya
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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Bou-Maroun LM, Hoff L, Joshi A, Bloom DA, Heider A, Geiger JD, Wu YM, Robinson D, Mody R, Rao RJ. Undifferentiated pleomorphic sarcoma of the pancreas with novel SARM1-NTRK1 gene fusion and associated pancreatitis, panniculitis, and polyarthritis syndrome. Pediatr Blood Cancer 2024; 71:e30819. [PMID: 38110803 DOI: 10.1002/pbc.30819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023]
Affiliation(s)
- Laura M Bou-Maroun
- Department of Pediatric Hematology/Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lauren Hoff
- University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Aparna Joshi
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
| | - David A Bloom
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Amer Heider
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - James D Geiger
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Yi-Mi Wu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Dan Robinson
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rajen Mody
- Department of Pediatric Hematology/Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rama Jasty Rao
- Department of Pediatric Hematology/Oncology, University of Michigan, Ann Arbor, Michigan, USA
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Zhao JY, He YX, Wu ML, Wang RQ. The application of high-throughput sequencing technology in corneal diseases. Int Ophthalmol 2024; 44:53. [PMID: 38340174 PMCID: PMC10858842 DOI: 10.1007/s10792-024-03049-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
High-throughput sequencing technology, also known as next-generation sequencing technology, can explore new biomarkers and specific gene mutations. It has a pivotal role in promoting the gene research, which can limit the detection area, lessen the time needed for sequencing. Also, it can quickly screen out the suspected pathogenic genes of patients, gain the necessary genetic data, and provide the basis for clinical diagnosis and genetic counseling. In the research of corneal diseases, through the DNA sequencing of patients' diseased cells, it can provide a deeper understanding of corneal diseases and improve the diagnosis, classification and treatment alternatives of various corneal diseases. This article will introduce the application progress of high-throughput sequencing technology in corneal diseases, which will help to understand the application of this technology in various corneal diseases.
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Affiliation(s)
- Jing Yi Zhao
- The Second Clinical Medical College of Jilin University, Changchun, 130012, Jilin, China
| | - Yu Xi He
- The Eye Center, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Mei Liang Wu
- The Eye Center, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Rui Qing Wang
- The Eye Center, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China.
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Zazo S, Pérez‐Buira S, Carvajal N, Plaza‐Sánchez J, Manso R, Pérez‐González N, Dominguez C, Prieto‐Potin I, Rubio J, Dómine M, Lozano V, Mohedano P, Carcedo D, Carias R, Rojo F. Actionable mutational profiling in solid tumors using hybrid-capture-based next-generation sequencing in a real-world setting in Spain. Cancer Med 2024; 13:e6827. [PMID: 38213074 PMCID: PMC10905216 DOI: 10.1002/cam4.6827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/09/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024] Open
Abstract
OBJECTIVE This study aimed to describe the performance of a next-generation sequencing (NGS) panel for the detection of precise genomic alterations in cancer in Spanish clinical practice. The impact of tumor characteristics was evaluated on informative NGS and actionable mutation rates. MATERIALS AND METHODS A cross-sectional study was conducted at the Fundación Jiménez Díaz University Hospital (May 2021-March 2022) where molecular diagnostic of 537 Formalin-Fixed Paraffin-Embedded (FFPE) tissue samples of diverse solid tumors (lung, colorectal, melanoma, gastrointestinal stromal, among others) was performed using AVENIO Tumor Tissue Targeted Kit. A descriptive analysis of the features of all samples was carried out. Multivariable logistic analysis was conducted to assess the impact of sample characteristics on NGS performance defined by informative results rate (for all tumors and for lung tumors), and on actionable mutations rate (for lung tumors only). RESULTS AVENIO performance rate was 75.2% in all tumor samples and 75.3% in lung cancer samples, and the multivariable analysis showed that surgical specimens are most likely to provide informative results than diagnostic biopsies. Regarding the mutational findings, 727 pathogenic, likely pathogenic, or variant of unknown significance mutations were found in all tumor samples. Single nucleotide variant was the most common genomic alteration, both for all tumor samples (85.3% and 81.9% for all solid tumors and lung samples, respectively). In lung tumors, multivariable analysis showed that it is more likely to find actionable mutations from non-smokers and patients with adenocarcinoma, large cell, or undifferentiated histologies. CONCLUSION This is the largest cohort-level study in Spain to profile the analyses of biopsy samples of different tumors using NGS in routine clinical practice. Our findings showed that the use of NGS routinely provides good rates of informative results and can improve tumor characterization and identify a greater number of actionable mutations.
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Affiliation(s)
- Sandra Zazo
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
- IIS‐Fundación Jimenez DiazCenter for Biomedical Network Research on Cancer (CIBERONC)MadridSpain
| | - Sandra Pérez‐Buira
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
| | - Nerea Carvajal
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
| | | | - Rebeca Manso
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
| | | | - Carolina Dominguez
- IIS‐Fundación Jimenez DiazCenter for Biomedical Network Research on Cancer (CIBERONC)MadridSpain
| | - Iván Prieto‐Potin
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
| | - Jaime Rubio
- Medical Oncology DepartmentFundación Jiménez Díaz University HospitalMadridSpain
| | - Manuel Dómine
- IIS‐Fundación Jimenez DiazCenter for Biomedical Network Research on Cancer (CIBERONC)MadridSpain
- Medical Oncology DepartmentFundación Jiménez Díaz University HospitalMadridSpain
| | | | | | | | - Rafael Carias
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
| | - Federico Rojo
- Department of PathologyFundación Jiménez Díaz University HospitalMadridSpain
- IIS‐Fundación Jimenez DiazCenter for Biomedical Network Research on Cancer (CIBERONC)MadridSpain
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Philips AO, Panda SS, Cyriac S, Moharana L, Kilaru S, Kolluri S, Rathnam K, Saju S, Raju HS, Kayal S, Biswajit D, Sehrawat A, Sundriyal D, Jose AT, Raju S, Paul P, Ganesan P. Real-World Experiences of Next-Generation Sequencing in Oncology: From an Indian Multicenter Registry and Collaborative Centers. Indian J Med Paediatr Oncol 2024. [DOI: 10.1055/s-0044-1779275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Abstract
Background The integration of next-generation sequencing (NGS) in guiding personalized therapy for oncology faces the challenges, primarily, of cost and drug accessibility. Limited data from Indian academic centers accentuate the need for comprehensive insights into the real-world applications of NGS in oncology.
Methods The Network of Oncology Clinical Trials in India (NOCI), accessible at www.noci-india.com, compiled data on patients who underwent NGS for solid organ cancers from January 1, 2018, to December 31, 2021. This study aimed to elucidate the testing indications, sample types analyzed, and the resultant impact on patient care.
Results Analysis of data from six centers included 278 subjects, with 24 specimens (9%) excluded due to quality test failure. Tissue constituted 59.7% of specimens, blood 38.5%, and both 1.8%. Predominantly, NGS was employed for identifying BRCA1/2 mutations (56%) and for targeted therapy in non-small-cell lung cancer (NSCLC; 28%). Only 41 (16%) patients with other cancers underwent multigene NGS panels in pursuit of targetable mutations. Among them, 13 exhibited targetable mutations, and 3 received treatment based on NGS findings.
Conclusion This study underscores that the majority of NGS applications focused on screening for BRCA1/2 mutations and identifying targetable mutations in NSCLC. However, among those undergoing NGS for advanced cancers, only a limited number received personalized therapy. The findings underscore the challenges of utilizing NGS in off-label indications within resource-constrained settings.
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Affiliation(s)
| | - Soumya Surath Panda
- Department of Medical Oncology, Institute of Medical Sciences and Sum Hospital, Odhisha, India
| | - Sunu Cyriac
- Department of Medical Oncology, Amala Institute of Medical Sciences, Kerala, India
| | - Lalatendu Moharana
- Department of Medical Oncology, Institute of Medical Sciences and Sum Hospital, Odhisha, India
| | - Sindhu Kilaru
- Department of Medical Oncology, Institute of Medical Sciences and Sum Hospital, Odhisha, India
| | - Spoorty Kolluri
- Department of Medical Oncology, Institute of Medical Sciences and Sum Hospital, Odhisha, India
| | - Krishnakumar Rathnam
- Department of Medical Oncology, Meenakshi Mission Medical College and Research Center, Madurai, India
| | - S.V. Saju
- Department of Medical Oncology, Meenakshi Mission Medical College and Research Center, Madurai, India
| | - Honey Susan Raju
- Department of Medical Oncology, Meenakshi Mission Medical College and Research Center, Madurai, India
| | - Smita Kayal
- Department of Medical Oncology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Dubashi Biswajit
- Department of Medical Oncology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Amit Sehrawat
- Department of Medical Oncology, All India Institute of Medical Sciences Rishikesh, India
| | - Deepak Sundriyal
- Department of Medical Oncology, All India Institute of Medical Sciences Rishikesh, India
| | - Anil T. Jose
- Department of Medical Oncology, Amala Institute of Medical Sciences, Kerala, India
| | - Sreeja Raju
- Department of Pathology, Amala Institute of Medical Sciences, Kerala, India
| | - Preethi Paul
- Department of Pathology, Christian Medical College, Ludhiana, Punjab, India
| | - Prasanth Ganesan
- Department of Medical Oncology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
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Hanafi AR, Hanif MA, Pangaribuan MTG, Ariawan WP, Sutandyo N, Kurniawati SA, Setiawan L, Cahyanti D, Rayhani F, Imelda P. Genomic features of lung cancer patients in Indonesia's national cancer center. BMC Pulm Med 2024; 24:43. [PMID: 38245692 PMCID: PMC10799463 DOI: 10.1186/s12890-024-02851-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
INTRODUCTION Advances in molecular biology bring advantages to lung cancer management. Moreover, high-throughput molecular tests are currently useful for revealing genetic variations among lung cancer patients. We investigated the genomics profile of the lung cancer patients at the National Cancer Centre of Indonesia. METHODS A retrospective study enrolled 627 tissue biopsy samples using real time polymerase chain reaction (RT-PCR) and 80 circulating tumour DNA (ctDNA) liquid biopsy samples using next-generation sequencing (NGS) from lung cancer patients admitted to the Dharmais Cancer Hospital from January 2018 to December 2022. Data were obtained from medical records. Data statistically analysed with p < 0.05 is considered significant. RESULT The EGFR test results revealed by RT-PCR were wild type (51.5%), single variant (38.8%), double variant (8.3%), and triple variant (1.4%), with 18.66% L85R, 18.22% Ex19del, and 11.08% L861Q variant. Liquid biopsy ctDNA using NGS showed only 2.5% EGFR wild type, 62.5% single variant and 35% co-variant, with EGFR/TP53 and EGFR/PIK3CA as the highest. CONCLUSION EGFR variants are the most found in our centre. Liquid biopsy with ctDNA using NGS examination could detect broad variants and co-variants that will influence the treatment planning.
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Affiliation(s)
- Arif Riswahyudi Hanafi
- Department of Pulmonology, Dharmais Cancer Hospital, National Cancer Center, Letjen S. Parman Street Kav. 84-86 Slipi Jakarta Barat, DKI Jakarta, West Jakarta, 11420, Indonesia.
| | - Muhammad Alfin Hanif
- Department of Pulmonology, Dharmais Cancer Hospital, National Cancer Center, Letjen S. Parman Street Kav. 84-86 Slipi Jakarta Barat, DKI Jakarta, West Jakarta, 11420, Indonesia
| | - Mariska T G Pangaribuan
- Department of Pulmonology, Dharmais Cancer Hospital, National Cancer Center, Letjen S. Parman Street Kav. 84-86 Slipi Jakarta Barat, DKI Jakarta, West Jakarta, 11420, Indonesia
| | - Wily Pandu Ariawan
- Department of Pulmonology, Dharmais Cancer Hospital, National Cancer Center, Letjen S. Parman Street Kav. 84-86 Slipi Jakarta Barat, DKI Jakarta, West Jakarta, 11420, Indonesia
| | - Noorwati Sutandyo
- Department of Internal Medicine, Division of Hematology and Medical Oncology, Dharmais Cancer Hospital, National Cancer Center, West Jakarta, Indonesia
| | - Sri Agustini Kurniawati
- Department of Internal Medicine, Division of Hematology and Medical Oncology, Dharmais Cancer Hospital, National Cancer Center, West Jakarta, Indonesia
| | - Lyana Setiawan
- Department of Clinical Pathology, Dharmais Cancer Hospital, National Cancer Center, West Jakarta, Indonesia
| | - Dian Cahyanti
- Department of Anatomical Pathology, Dharmais Cancer Hospital, National Cancer Center, West Jakarta, Indonesia
| | - Farilaila Rayhani
- Department of Anatomical Pathology, Dharmais Cancer Hospital, National Cancer Center, West Jakarta, Indonesia
| | - Priscillia Imelda
- Cancer Research Team, Dharmais Cancer Hospital, National Cancer Center, West Jakarta, Indonesia
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Kathiresan N, Ramachandran S, Kulanthaivel L. Next-Generation Sequencing to Study the DNA Interaction. Methods Mol Biol 2024; 2719:249-264. [PMID: 37803122 DOI: 10.1007/978-1-0716-3461-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
Next-generation sequencing (NGS) has transformed genomics by allowing researchers to sequence DNA and RNA at highest speed, accuracy, and cost-effectiveness. Researchers investigate DNA interactions with the help next-generation sequencing with a great deal of information. Over the last decade, NGS technologies have advanced significantly, with the development of several platforms, including Illumina, PacBio, and Oxford Nanopore, each offering distinct advantages and uses. The use of next-generation sequencing (NGS) has aided in the discovery of genetic variations, gene expression patterns, and epigenetic modifications connected with a variety of diseases, including cancer, neurological disorders, and infectious diseases. By identifying these regions, we can control the expression of genes, cellular signaling pathways, and other key biological processes. NGS is an effective method for researching DNA interactions that has completely transformed the area of genomics. NGS has also played an important part in personalized medicine, enabling the discovery of disease-causing mutations and the creation of targeted medicines. Finally, NGS has transformed the field of genomics, resulting in new discoveries and applications in medicine, environmental sciences, and other fields.
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Affiliation(s)
| | | | - Langeswaran Kulanthaivel
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
- Molecular Cancer Biology Laboratory, Department of Biomedical Science, Alagappa University, Karaikudi, Tamil Nadu, India
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12
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Afonso S, Vieira ACL, Pereira C, Oliveira MD. Advancing hospital-based health technology assessment: evaluating genomic panel contracting strategies for blood tumors through a multimethodology. Int J Technol Assess Health Care 2023; 39:e76. [PMID: 38130159 DOI: 10.1017/s0266462323002751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
INTRODUCTION The adoption of genomic technologies in the context of hospital-based health technology assessment presents multiple practical and organizational challenges. OBJECTIVE This study aimed to assist the Instituto Português de Oncologia de Lisboa Francisco Gentil (IPO Lisboa) decision makers in analyzing which acute myeloid leukemia (AML) genomic panel contracting strategies had the highest value-for-money. METHODS A tailored, three-step approach was developed, which included: mapping clinical pathways of AML patients, building a multicriteria value model using the MACBETH approach to evaluate each genomic testing contracting strategy, and estimating the cost of each strategy through Monte Carlo simulation modeling. The value-for-money of three contracting strategies - "Standard of care (S1)," "FoundationOne Heme test (S2)," and "New diagnostic test infrastructure (S3)" - was then analyzed through strategy landscape and value-for-money graphs. RESULTS Implementing a larger gene panel (S2) and investing in a new diagnostic test infrastructure (S3) were shown to generate extra value, but also to entail extra costs in comparison with the standard of care, with the extra value being explained by making available additional genetic information that enables more personalized treatment and patient monitoring (S2 and S3), access to a broader range of clinical trials (S2), and more complete databases to potentiate research (S3). CONCLUSION The proposed multimethodology provided IPO Lisboa decision makers with comprehensive and insightful information regarding each strategy's value-for-money, enabling an informed discussion on whether to move from the current Strategy S1 to other competing strategies.
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Affiliation(s)
- Susana Afonso
- CEGIST, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Ana C L Vieira
- CEGIST, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Carla Pereira
- Instituto Português de Oncologia de Lisboa Francisco Gentil (IPO Lisboa), Lisbon, Portugal
| | - Mónica D Oliveira
- CEGIST, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- iBB - Institute for Bioengineering and Biosciences and i4HB - Associate Laboratory Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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13
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Puddester R, Limoges J, Dewell S, Maddigan J, Carlsson L, Pike A. The Canadian Landscape of Genetics and Genomics in Nursing: A Policy Document Analysis. Can J Nurs Res 2023; 55:494-509. [PMID: 36850071 PMCID: PMC10619171 DOI: 10.1177/08445621231159164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Genetics and genomics (GG) are transforming approaches to healthcare in Canada and around the globe. Canadian nurses must be prepared to integrate GG in their practice, but modest research in this area suggests that Canadian nurses have limited GG competency. Countries that have integrated GG across nursing provided guidance to nurses about the practice implications of GG through regional nursing policy documents. These documents propelled action to integrate GG across nursing. Little is known about the GG content in the nursing policy document infrastructure in Canada. PURPOSE This study aimed to examine the guidance for GG-informed nursing practice as provided by Canadian nursing organizations in official professional documents. METHODS Qualitative document analysis was used. A hybrid inductive/deductive analysis approach was used to analyze findings within the diffusion of innovation theory framework. RESULTS There is an overall lack of depth and breadth of Canadian nursing documents that include content related to GG. Of the (n = 37) documents analyzed, four themes were generated including (a) GG guidance in nursing education; (b) regulators' requirements for foundational GG knowledge, (c) Canadian Nurses Association (CNA) as an early catalyst to GG integration; and (d) early adopters in speciality practice. CONCLUSION There are opportunities to enhance the guidance available to Canadian nurses for the application of GG, through documents of nursing professional associations, nursing education accreditation organizations, and regulatory bodies. Findings suggest oncology and perinatal nurses are the early adopters which is an important consideration in future strategies to implement GG into Canadian nursing.
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Affiliation(s)
- Rebecca Puddester
- Faculty of Nursing, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Jacqueline Limoges
- Faculty of Health Disciplines, Athabasca University, Athabasca, AB, Canada
| | - Sarah Dewell
- School of Nursing, University of Northern British Columbia, Prince George, BC, Canada
| | - Joy Maddigan
- Faculty of Nursing, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Lindsay Carlsson
- Drug Development Program, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - April Pike
- Faculty of Nursing, Memorial University of Newfoundland, St. John's, NL, Canada
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14
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Li C, Fan S, Zhao H, Liu X. CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data. J Bioinform Comput Biol 2023; 21:2350026. [PMID: 38212874 DOI: 10.1142/s0219720023500269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Copy number variation (CNV), as a type of genomic structural variation, accounts for a large proportion of structural variation and is related to the pathogenesis and susceptibility to some human diseases, playing an important role in the development and change of human diseases. The development of next-generation sequencing technology (NGS) provides strong support for the design of CNV detection algorithms. Although a large number of methods have been developed to detect CNVs using NGS data, it is still considered a difficult problem to detect CNVs with low purity and coverage. In this paper, a new calculation method CNV-FB is proposed to detect CNVs from NGS data. The core idea of CNV-FB is to randomly sample the read depth values of the genome fragment, and then each sample is individually detected for outliers, and finally combined into a final outlier score. The CNV-FB method was applied to simulation data and real data experiments and compared with the other five methods of the same type. The results show that the CNV-FB method has a better detection effect than other methods. Therefore, the CNV-FB method may be an effective algorithm for detecting genomic mutations.
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Affiliation(s)
- Chengyou Li
- School of Computer Science, Liaocheng University, Liaocheng 252000, P. R. China
| | - Shiqiang Fan
- School of Computer Science, Liaocheng University, Liaocheng 252000, P. R. China
| | - Haiyong Zhao
- School of Computer Science, Liaocheng University, Liaocheng 252000, P. R. China
| | - Xiaotong Liu
- School of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng 252000, P. R. China
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15
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Sang J, Ye X. Potential biomarkers for predicting immune response and outcomes in lung cancer patients undergoing thermal ablation. Front Immunol 2023; 14:1268331. [PMID: 38022658 PMCID: PMC10646301 DOI: 10.3389/fimmu.2023.1268331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Thermal ablation is a promising alternative treatment for lung cancer. It disintegrates cancer cells and releases antigens, followed by the remodeling of local tumor immune microenvironment and the activation of anti-tumor immune responses, enhancing the overall effectiveness of the treatment. Biomarkers can offer insights into the patient's immune response and outcomes, such as local tumor control, recurrence, overall survival, and progression-free survival. Identifying and validating such biomarkers can significantly impact clinical decision-making, leading to personalized treatment strategies and improved patient outcomes. This review provides a comprehensive overview of the current state of research on potential biomarkers for predicting immune response and outcomes in lung cancer patients undergoing thermal ablation, including their potential role in lung cancer management, and the challenges and future directions.
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Affiliation(s)
| | - Xin Ye
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Lung Cancer Institute, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, China
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16
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Chen H, Wang B, Zhang Y, Shu Y, Dong H, Zhao Q, Yang C, Li J, Duan X, Zhou Q. A unified DNA- and RNA-based NGS strategy for the analysis of multiple types of variants at the dual nucleic acid level in solid tumors. J Clin Lab Anal 2023; 37:e24977. [PMID: 37877443 PMCID: PMC10681543 DOI: 10.1002/jcla.24977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/27/2023] [Accepted: 10/15/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) is a powerful and suitable approach to comprehensively identify multiple types of variants in tumors. RNA-based NGS is increasingly playing an important role in precision oncology. Both parallel and sequential DNA- and RNA-based approaches are expensive, burdensome, and have long turnaround times, which can be impractical in clinical practice. A streamlined, unified DNA- and RNA-based NGS approach is urgently needed in clinical practice. METHODS A DNA/RNA co-hybrid capture sequencing (DRCC-Seq) approach was designed to capture pre-capture DNA and RNA libraries in a single tube and convert them into one NGS library. The performance of the DRCC-Seq approach was evaluated by a panel of reference standards and clinical samples. RESULTS The average depth, DNA data ratio, capture ratio, and target coverage 250 (×) of the DNA panel data had a negative correlation with an increase in the proportion of RNA probes. The SNVs, indels, fusions, and MSI status were not affected by the proportion of RNA probes, but the copy numbers of the target genes were higher than expected in the standard materials, and many unexpected gene amplifications were found using D:R (1:2) and D:R (1:4) probe panels. The optimal ratio of DNA and RNA probes in the combined probe panel was 1:1 using the DRCC-Seq approach. The DRCC-Seq approach was feasible and reliable for detecting multiple types of variants in reference standards and real-world clinical samples. CONCLUSIONS The DRCC-Seq approach is more cost-effective, with a shorter turnaround time and lower labor requirements than either parallel or sequential targeted DNA NGS and RNA NGS. It is feasible to identify multiple genetic variations at the DNA and RNA levels simultaneously in clinical practice.
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Affiliation(s)
- Huijuan Chen
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
- Computer Network Information Center, Chinese Academy of SciencesBeijingChina
- WillingMed Technology Beijing Co., Ltd.BeijingChina
| | - Bing Wang
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Yiran Zhang
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Yingshuang Shu
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Henan Dong
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Qian Zhao
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Chunyan Yang
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Jianji Li
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Xiaohong Duan
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
- ChosenMed Technology (Zhejiang) Co. Ltd.ZhejiangChina
- Institute of Disaster and Emergency Medicine, Medical CollegeTianjin UniversityTianJinChina
| | - Qiming Zhou
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
- ChosenMed Technology (Zhejiang) Co. Ltd.ZhejiangChina
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17
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Liu C, Li K, Sui Y, Liu H, Zhang Y, Lu Y, Lu W, Chen Y, Wang G, Xu S, Xiang T, Cai Y, Huang K. Different gene alterations in patients with non-small-cell lung cancer between the eastern and southern China. Heliyon 2023; 9:e20171. [PMID: 37767514 PMCID: PMC10520317 DOI: 10.1016/j.heliyon.2023.e20171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Geographical differences are conspicuous in lung cancer, and the distinct molecular features of lung tumor between Western patients and Asian patients have been demonstrated. However, the etiology of non-small-cell lung cancer (NSCLC) and the distribution of associated molecular aberrations in China have not been fully elucidated. The mutational profiles of 12 lung cancer-related genes were investigated in 85 patients from eastern China and 88 patients from southern China who had been histologically confirmed NSCLC. Overall, 93.6% (162/173) of tumor samples harbored at least one somatic alteration. The most frequently mutated genes were TP53 (56.1%), EGFR (50.3%), and KRAS (14.5%). We found that EGFR mutated much more frequently (60.0% vs 40.9%, P = 0.012) and TP53 mutations had significantly lower incidence (47.1% vs 64.8%, P = 0.019) in eastern cohort than that in southern cohort. Mutational signature analysis revealed a region-related mutagenesis mechanism characterized by a high prevalence of C to T transitions mainly occurring at CpG dinucleotides in southern patients. This study reveals the difference in the mutational features between NSCLC patients in eastern and southern China. The distinct patterns of gene mutation could provide clues for the mechanism of carcinogenesis of lung cancer, offering opportunities to stratify patients into optimal treatment plans based on genomic profiles.
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Affiliation(s)
- Chengdong Liu
- Department of thoracic surgery, Naval Medical Center of PLA, 338 Huaihai Road, Changning District, Shanghai 200052, China
| | - Kangbao Li
- Department of Geriatrics, Gastroenterology Ward, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Yi Sui
- Singlera Genomics Inc., Shanghai 201318, China
| | - Hongmei Liu
- Singlera Genomics Inc., Shanghai 201318, China
| | | | - Yuan Lu
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Wei Lu
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Yongfeng Chen
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Gehui Wang
- Singlera Genomics Inc., Shanghai 201318, China
| | - Suqian Xu
- Singlera Genomics Inc., Shanghai 201318, China
| | | | - Yongguang Cai
- Medical Oncology Department V, Central Hospital of Guangdong Nongken 524002, China
| | - Kenan Huang
- Department of Thoracic Surgery, Shanghai Changzheng Hospital, Navy Military Medical University, 415 Fengyang Road, Huangpu District, Shanghai 200003, China
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
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18
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Yang Y, Liu C, Zhuo ZL, Xie F, Wang K, Wang S, Zhao XT. Germline Mutations in 32 Cancer Susceptibility Genes by Next-Generation Sequencing among Breast Cancer Patients. Oncology 2023; 102:206-216. [PMID: 37517399 DOI: 10.1159/000532095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
INTRODUCTION BRCA1/2 germline mutations are the most well-known genetic determinants for breast cancer. However, the distribution of germline mutations in non-BRCA1/2 cancer susceptibility genes in Chinese breast cancer patients is unclear. The association between clinical characteristics and germline mutations remains to be explored. METHODS Consecutive breast cancer patients from Peking University People's Hospital were enrolled. Clinical characteristics were collected, and next-generation sequencing was performed using blood samples of participants to identify pathogenic/likely pathogenic (P/LP) germline mutations in 32 cancer susceptibility genes including homologous recombination repair (HRR) genes. RESULTS A total of 885 breast cancer patients underwent the detection of germline mutations. 107 P/LP germline mutations of 17 genes were identified in 116 breast cancer patients including 79 (8.9%) in BRCA1/2 and 40 (4.5%) in 15 non-BRCA1/2 genes. PALB2 was the most frequently mutated gene other than BRCA1/2 but still relatively rare (1.1%). There were 38 novel P/LP germline variants detected. P/LP germline mutations in BRCA1/2 were significantly associated with onset age (p < 0.001), the family history of breast/ovarian cancer (p = 0.010), and molecular subtype (p < 0.001), while being correlated with onset age (p < 0.001), site of breast tumor (p = 0.028), and molecular subtype (p < 0.001) in HRR genes. CONCLUSIONS The multiple-gene panel prominently increased the detection rate of P/LP germline mutations in 32 cancer susceptibility genes compared to BRCA1/2 alone. Onset younger than or equal to 45 years of age, bilateral and triple-negative breast cancer patients may be more likely to be recommended for detecting P/LP germline mutations in HRR genes.
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Affiliation(s)
- Yu Yang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Chang Liu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Zhong-Ling Zhuo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Fei Xie
- Breast Center, Peking University People's Hospital, Beijing, China
| | - Ke Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shu Wang
- Breast Center, Peking University People's Hospital, Beijing, China
| | - Xiao-Tao Zhao
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
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Bray J, Eward W, Breen M. Evaluating the relevance of surgical margins. Part one: The problems with current methodology. Vet Comp Oncol 2023; 21:1-11. [PMID: 36308442 DOI: 10.1111/vco.12865] [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: 05/10/2022] [Revised: 10/11/2022] [Accepted: 10/24/2022] [Indexed: 11/28/2022]
Abstract
The goal of cancer surgery is to achieve a "clean" microscopic resection, with no residual tumour remaining in the wound. To achieve that goal, the surgeon typically incorporates a measured buffer of grossly normal tissue about the entire circumference of the tumour. Microscopic analysis of the resection boundaries is then performed to determine if all traces of the tumour have been completely removed. This analysis is thought to provide a surrogate indication as to the likelihood for that tumour to recur after surgery. However, it is recognised that tumour recurrence may not occur even when microscopic evidence of tumour has been identified at the resection margins, and recurrence can also occur when conventional histology has considered the tumour to have been completely removed. The explanations for this dichotomy are numerous and include technical and practical limitations of the processing methodology, and also several surgeon-related and tumour-related reasons. Ultimately, the inability to confidently determine when a tumour has been removed sufficiently to prevent recurrence can impact on the ability to provide owners with confident treatment advice. In this article, the authors describe the challenges with defining the true extent of the tumour margin from the perspective of the surgeon, the pathologist and the tumour. The authors also provide an analysis of why our current efforts to ensure that all traces of the local tumour have been successfully removed may provide an imperfect assessment of the risk of recurrence.
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Affiliation(s)
| | - Will Eward
- Duke Cancer Center, Durham, North Carolina, USA
| | - Matthew Breen
- College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Jiang L, Wang M, Li Y, Zhang S, Zhu X, Zhong J, Sun J, Tinoco M, Chen X. Enzyme-Free Colorimetric Method for Fast Detection of PIK3CA Gene Mutation by Praseodymia Nanorods. Anal Chem 2023; 95:2884-2892. [PMID: 36701639 DOI: 10.1021/acs.analchem.2c04419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The frequently mutated phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) gene is associated with multiple tumors and endocytosis of viruses. Identification of muted nucleotides at the hotspot can help in finding the susceptible people who are vulnerable to cancers and viruses. Herein, a simple enzyme-free colorimetric method is developed for the quick detection of PIK3CA gene mutations. The main mechanism lies in the dissimilar interactions between praseodymia nanorods and different nucleotides, as well as the underlying oxidase-mimicking characteristics of praseodymia. With rational designs of probes and processes, this method has great potential for expanded applications in the screening of mutations in other genes of interest.
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Affiliation(s)
- Lei Jiang
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Meng Wang
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Youxun Li
- Marine Science Research Institute of Shandong Province & National Oceanographic Center, 7 Youyun Road, Qingdao 266104, China
| | - Shuyuan Zhang
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiudong Zhu
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Junjie Zhong
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Jingtao Sun
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Miguel Tinoco
- Departamento de Ciencia de los Materiales, Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias and Instituto Universitario de Investigación en Microscopía Electrónica y Materiales (IMEYMAT), Universidad de Cádiz, Puerto Real, Cádiz E-11510, Spain
| | - Xiaowei Chen
- Departamento de Ciencia de los Materiales, Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias and Instituto Universitario de Investigación en Microscopía Electrónica y Materiales (IMEYMAT), Universidad de Cádiz, Puerto Real, Cádiz E-11510, Spain
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Bray J, Eward W, Breen M. Defining the relevance of surgical margins. Part two: Strategies to improve prediction of recurrence risk. Vet Comp Oncol 2023; 21:145-158. [PMID: 36745110 DOI: 10.1111/vco.12881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 12/03/2022] [Accepted: 02/03/2023] [Indexed: 02/07/2023]
Abstract
Due to the complex nature of tumour biology and the integration between host tissues and molecular processes of the tumour cells, a continued reliance on the status of the microscopic cellular margin should not remain our only determinant of the success of a curative-intent surgery for patients with cancer. Based on current evidence, relying on a purely cellular focus to provide a binary indication of treatment success can provide an incomplete interpretation of potential outcome. A more holistic analysis of the cancer margin may be required. If we are to move ahead from our current situation - and allow treatment plans to be more intelligently tailored to meet the requirements of each individual tumour - we need to improve our utilisation of techniques that either improve recognition of residual tumour cells within the surgical field or enable a more comprehensive interrogation of tumour biology that identifies a risk of recurrence. In the second article in this series on defining the relevance of surgical margins, the authors discuss possible alternative strategies for margin assessment and evaluation in the canine and feline cancer patient. These strategies include considering adoption of the residual tumour classification scheme; intra-operative imaging systems including fluorescence-guided surgery, optical coherence tomography and Raman spectroscopy; molecular analysis and whole transcriptome analysis of tissues; and the development of a biologic index (nomogram). These techniques may allow evaluation of individual tumour biology and the status of the resection margin in ways that are different to our current techniques. Ultimately, these techniques seek to better define the risk of tumour recurrence following surgery and provide the surgeon and patient with more confidence in margin assessment.
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Affiliation(s)
| | - Will Eward
- Orthopedic Surgical Oncologist, Duke Cancer Center, Durham, North Carolina, USA
| | - Matthew Breen
- Oscar J. Fletcher Distinguished Professor of Comparative Oncology Genetics, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Keraite I, Alvarez-Garcia V, Leslie NR. Nuclease Enrichment and qPCR Detection of Rare Nucleotide Variants. Methods Mol Biol 2023; 2621:41-56. [PMID: 37041439 DOI: 10.1007/978-1-0716-2950-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
The emergence of circulating DNA analysis in blood during the past decade has responded to the need for noninvasive alternatives to classical tissue biopsies. This has coincided with the development of techniques that allow the detection of low-frequency allele variants in clinical samples that typically carry very low amounts of fragmented DNA, such as plasma or FFPE samples. Enrichment of rare variants by nuclease-assisted mutant allele enrichment with overlapping probes (NaME-PrO) enables a more sensitive detection of mutations in tissue biopsy samples alongside standard qPCR detection assays. Such sensitivity is normally achieved by other more complex PCR methods, such as TaqMan qPCR and digital droplet PCR (ddPCR). Here we describe a workflow of mutation-specific nuclease-based enrichment combined with a SYBR Green real-time quantitative PCR detection method that provides comparable results to ddPCR. Using a PIK3CA mutation as an example, this combined workflow enables detection and accurate prediction of initial variant allele fraction in samples with a low mutant allele frequency (<1%) and could be applied flexibly to detect other mutations of interest.
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Affiliation(s)
- Ieva Keraite
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, UK
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona, Institute of Science and Technology (BIST), Barcelona, Spain
| | - Virginia Alvarez-Garcia
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Nicholas R Leslie
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, UK.
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Barr MP, Baird AM, Halliday S, Martin P, Allott EH, Phelan J, Korpanty G, Coate L, O’Brien C, Gray SG, Sui JSY, Hayes B, Cuffe S, Finn SP. Liquid Biopsy: A Multi-Parametric Analysis of Mutation Status, Circulating Tumor Cells and Inflammatory Markers in EGFR-Mutated NSCLC. Diagnostics (Basel) 2022; 12:diagnostics12102360. [PMID: 36292049 PMCID: PMC9600124 DOI: 10.3390/diagnostics12102360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/07/2022] [Accepted: 09/17/2022] [Indexed: 11/22/2022] Open
Abstract
The liquid biopsy has the potential to improve patient care in the diagnostic and therapeutic setting in non-small cell lung cancer (NSCLC). Consented patients with epidermal growth factor receptor (EGFR) positive disease (n = 21) were stratified into two cohorts: those currently receiving EGFR tyrosine kinase inhibitor (TKI) therapy (n = 9) and newly diagnosed EGFR TKI treatment-naïve patients (n = 12). Plasma genotyping of cell-free DNA was carried out using the FDA-approved cobas® EGFR mutation test v2 and compared to next generation sequencing (NGS) cfDNA panels. Circulating tumor cell (CTC) numbers were correlated with treatment response and EGFR exon 20 p.T790M. The prognostic significance of the neutrophil to lymphocyte ratio (NLR) and lactate dehydrogenase (LDH) was also investigated. Patients in cohort 1 with an EGFR exon 20 p.T790M mutation progressed more rapidly than those with an EGFR sensitizing mutation, while patients in cohort 2 had a significantly longer progression-free survival (p = 0.04). EGFR exon 20 p.T790M was detected by liquid biopsy prior to disease progression indicated by computed tomography (CT) imaging. The cobas® EGFR mutation test detected a significantly greater number of exon 20 p.T790M mutations (p = 0.05). High NLR and derived neutrophil to lymphocyte ratio (dNLR) were associated with shorter time to progression and worse survival outcomes (p < 0.05). High LDH levels were significantly associated with shorter time to disease progression (p = 0.03). These data support the use of liquid biopsy for monitoring EGFR mutations and inflammatory markers as prognostic indicators in NSCLC.
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Affiliation(s)
- Martin P. Barr
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Correspondence: ; Tel.: +353-1-8963620
| | - Anne-Marie Baird
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Sophia Halliday
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
| | - Petra Martin
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- Department of Medical Oncology, Midlands Regional Hospital, R35 NY51 Tullamore, Ireland
| | - Emma H. Allott
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
| | - James Phelan
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Greg Korpanty
- Department of Medical Oncology, University Hospital Limerick, V94 F858 Limerick, Ireland
| | - Linda Coate
- Department of Medical Oncology, University Hospital Limerick, V94 F858 Limerick, Ireland
| | - Cathal O’Brien
- Cancer Molecular Diagnostics Laboratory, St James’s Hospital, D08 W9RT Dublin, Ireland
| | - Steven G. Gray
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Jane S. Y. Sui
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
| | - Brian Hayes
- Department of Histopathology, Cork University Hospital, T12 XF62 Cork, Ireland
- Department of Pathology, University College Cork, T12 DC4A Cork, Ireland
| | - Sinead Cuffe
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- Department of Medical Oncology, St James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Stephen P. Finn
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- Department of Histopathology, St James’s Hospital, D08 RX0X Dublin, Ireland
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Zhang J, Xiao J, Wang Y, Zheng X, Cui J, Wang C. A universal co-expression gene network and prognostic model for hepatic-biliary-pancreatic cancers identified by integrative analyses. FEBS Open Bio 2022; 12:2006-2024. [PMID: 36054420 PMCID: PMC9623511 DOI: 10.1002/2211-5463.13478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/12/2022] [Accepted: 08/25/2022] [Indexed: 01/25/2023] Open
Abstract
Hepatic, biliary and pancreatic cancers are a diverse set of malignancies with poor prognoses. It is possible that common molecular mechanisms are involved in the carcinogenesis of these cancers. Here, we identified LINC01537 and seven protein-coding genes by integrative analysis of transcriptomes of mRNAs, microRNAs and long non-coding RNAs from cholangiocarcinoma, hepatocellular carcinoma and pancreatic adenocarcinoma cohorts in TCGA. A predictive model constructed from seven biomarkers was established to successfully predict the survival rate of patients, which was then further verified in external cohorts. Additionally, patients with high-risk scores in our model were prone to epithelial-mesenchymal transition. Finally, activation of the biomarker PDE2A significantly attenuated migration and epithelial-mesenchymal transition in the HepG2 liver cancer cell line.
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Affiliation(s)
- Jing Zhang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Juan Xiao
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and RepairAffiliated Hospital of Guilin Medical UniversityChina
| | - Yixuan Wang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Xiao Zheng
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Jiajun Cui
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Chaochen Wang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
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25
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Schubert J, Wu J, Li MM, Cao K. Best Practice for Clinical Somatic Variant Interpretation and Reporting. Clin Lab Med 2022; 42:423-434. [DOI: 10.1016/j.cll.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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26
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Wang X, Stelzer-Braid S, Scotch M, Rawlinson WD. Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use. Rev Med Virol 2022; 32:e2375. [PMID: 35775736 PMCID: PMC9539958 DOI: 10.1002/rmv.2375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/15/2022]
Abstract
Acute respiratory infection is the third most frequent cause of mortality worldwide, causing over 4.25 million deaths annually. Although most diagnosed acute respiratory infections are thought to be of viral origin, the aetiology often remains unclear. The advent of next‐generation sequencing (NGS) has revolutionised the field of virus discovery and identification, particularly in the detection of unknown respiratory viruses. We systematically reviewed the application of NGS technologies for detecting respiratory viruses from clinical samples and outline potential barriers to the routine clinical introduction of NGS. The five databases searched for studies published in English from 01 January 2010 to 01 February 2021, which led to the inclusion of 52 studies. A total of 14 different models of NGS platforms were summarised from included studies. Among these models, second‐generation sequencing platforms (e.g., Illumina sequencers) were used in the majority of studies (41/52, 79%). Moreover, NGS platforms have proven successful in detecting a variety of respiratory viruses, including influenza A/B viruses (9/52, 17%), SARS‐CoV‐2 (21/52, 40%), parainfluenza virus (3/52, 6%), respiratory syncytial virus (1/52, 2%), human metapneumovirus (2/52, 4%), or a viral panel including other respiratory viruses (16/52, 31%). The review of NGS technologies used in previous studies indicates the advantages of NGS technologies in novel virus detection, virus typing, mutation identification, and infection cluster assessment. Although there remain some technical and ethical challenges associated with NGS use in clinical laboratories, NGS is a promising future tool to improve understanding of respiratory viruses and provide a more accurate diagnosis with simultaneous virus characterisation.
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Affiliation(s)
- Xinye Wang
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Scotch
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.,Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
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Shen Y, Lian D, Shi K, Gao Y, Hu X, Yu K, Zhao Q, Feng C. Cancer Risk and Mutational Patterns Following Organ Transplantation. Front Cell Dev Biol 2022; 10:956334. [PMID: 35837331 PMCID: PMC9274140 DOI: 10.3389/fcell.2022.956334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/13/2022] [Indexed: 12/24/2022] Open
Abstract
The rapid development of medical technology and widespread application of immunosuppressive drugs have improved the success rate of organ transplantation significantly. However, the use of immunosuppressive agents increases the frequency of malignancy greatly. With the prospect of “precision medicine” for tumors and development of next-generation sequencing technology, more attention has been paid to the application of high-throughput sequencing technology in clinical oncology research, which is mainly applied to the early diagnosis of tumors and analysis of tumor-related genes. All generations of cancers carry somatic mutations, meanwhile, significant differences were observed in mutational signatures across tumors. Systematic sequencing of cancer genomes from patients after organ transplantation can reveal DNA damage and repair processes in exposed cancer cells and their precursors. In this review, we summarize the application of high-throughput sequencing and organoids in the field of organ transplantation, the mutational patterns of cancer genomes, and propose a new research strategy for understanding the mechanism of cancer following organ transplantation.
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Affiliation(s)
- Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Di Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuefeng Gao
- College of Applied Engineering, Henan University of Science and Technology, Sanmenxia, China
- Sanmenxia Polytechnic, Sanmenxia, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kun Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
| | - Qian Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Yu, ; Qian Zhao, ; Chungang Feng,
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Identification and Verification of Key Tumor Genes Associated with Diagnosis and Prognosis of Breast Cancer Based on Bioinformatics Analysis. DISEASE MARKERS 2022; 2022:9041466. [PMID: 35686034 PMCID: PMC9173900 DOI: 10.1155/2022/9041466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
Breast cancer (BC) is the most common cancer and the most frequent cause of cancer death among women worldwide. The aim of the present study was to identify the critical genes for the diagnosis and prognosis of BC. Two mRNA expression data (GSE29431 and GSE42568) were acquired from the GEO database. The determination of differently expressed genes (DEGs) between BC specimens and nontumor specimens was completed via the LIMMA package of R. GO annotation and KEGG pathway enrichment analyses were applied to explore the function of DEGs. Kaplan-Meier methods were used to determine the prognostic value of DEGs in BC using TCGA datasets. The diagnostic value of the survival-related DGEs were confirmed using ROC assays in two GEO datasets. RT-PCR was used to examine the expression of the critical genes in BC cells and normal breast cells. CCK-8 experiments were applied to explore the function of the critical genes in BC cells. In this study, we identified 31 DEGs between BC specimens and nontumor specimens. KEGG analysis revealed 31 DEGs were involved in PPAR signal path, AMPK signal path, glycerolipid metabolism, adipocytokine signaling pathway, phenylalanine metabolism, tyrosine metabolic process, and glycine, serine, and threonine metabolic process. Four DEGs including CRYAB, DEFB132, MAOA, and RBP4 were observed to be associated with clinical outcome of BC patients. Their diagnostic values were also confirmed in both GSE29431 and GSE42568 datasets. In addition, we analyzed TCGA datasets and confirmed that the results were consistent with GEO datasets. Finally, the results of RT-PCR confirmed that the expression of CRYAB and RBP4 was distinctly downregulated in BC cells. CCK-8 analysis revealed that overexpression of CRYAB and RBP4 distinctly suppressed the proliferation of BC cells. Overall, our findings suggested CRYAB and RBP4 as critical genes for the diagnosis and prognosis of BC patients. They may be used as novel biomarkers for BC patients.
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BRCA1 and BRCA2 screening of nine Chilean founder mutations through allelic-discrimination and real-time PCR in breast/ovarian cancer patients. Mol Biol Rep 2022; 49:7531-7539. [PMID: 35596815 PMCID: PMC9123627 DOI: 10.1007/s11033-022-07561-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/04/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND In a previous work, we identified nine founder mutations present in close to 80% of BRCA1 and BRCA2 mutation carriers, and distributed across the country. The presence of founder mutations constitutes a valuable opportunity to develop new strategies for genetic screening. Genetic tests are primarily performed by NGS sequencing, which requires sophisticated and expensive equipment, and it takes 2-3 weeks for the results to be informed to the patient. In addition, genetic tests are not covered by insurance companies in Latin American countries. In this work, we present the standardization and technical validation of a real-time PCR based methodology for allelic discrimination in order to identify the nine Chilean founder mutations in BRCA1 and BRCA2 genes. METHODS AND RESULTS We designed nine pairs of probes and nine pairs of primers to amplify synchronically nine regions of the BRCA1/BRCA2 genes by real-time PCR, in order to identify the nine founder mutations through allelic discrimination analyses. Technical validation was performed using 90 positive and 90 negative samples for each mutation. The methodology was tested in a second group of 60 patients. Our method correctly classified carriers and non-carriers of one of the nine Chilean founder mutations with a 100% specificity and 100% sensitivity, compared with Sanger sequencing performance. CONCLUSIONS We develop an inexpensive, simple, and fast mutation detection method that could be implemented locally in Hospitals from the Private to Public health system. This methodology may be useful for the screening of BRCA1 and BRCA2 mutations in other populations.
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Genomics and Immunomics in the Treatment of Urothelial Carcinoma. Curr Oncol 2022; 29:3499-3518. [PMID: 35621673 PMCID: PMC9139747 DOI: 10.3390/curroncol29050283] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 12/21/2022] Open
Abstract
Urothelial carcinoma is a complex cancer with genomic immunomic drivers that have prognostic and predictive treatment implications. Identifying potential targetable alterations via next-generation sequencing and RNA sequencing may allow for elucidation of such targets and exploitation with targeted therapeutics. The role of immunotherapy in treating urothelial carcinoma has shown benefit, but it is unclear in which patients immunotherapeutics have the highest yield. Continuing efforts into better identifying which patients may benefit most from targeted therapies, immunotherapies, and combination therapies may ultimately lead to improved outcomes for patients with this disease.
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Akabari R, Qin D, Hussaini M. Technological Advances: CEBPA and FLT3 Internal Tandem Duplication Mutations Can be Reliably Detected by Next Generation Sequencing. Genes (Basel) 2022; 13:genes13040630. [PMID: 35456436 PMCID: PMC9028339 DOI: 10.3390/genes13040630] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/21/2022] [Accepted: 03/30/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The detection of CEBPA and FLT3 mutations by next generation sequencing (NGS) is challenging due to high GC content and Internal Tandem Duplications (ITDs). Recent advances have been made to surmount these challenges. In this study, we compare three commercial kits and evaluate the performance of these more advanced hybrid-capture and AMP-chemistry based methods. METHODS Amplicon-based TSM 54-Gene Panel (Illumina) was evaluated against hybridization-capture SOPHiA Genetics MSP, OGT SureSeq, and AMP chemistry-based VariantPlex (Archer) for wet-lab workflow and data-analysis pipelines. Standard kit directions and commercial analysis pipelines were followed. Seven CEBPA and 10 FLT3-positive cases were identified that previously were missed on an amplicon NGS assay. The average reads, coverage uniformity, and the detection of CEBPA or FLT3 mutations were compared. RESULTS All three panels detected all 10 CEBPA mutations and all 10 FLT3 ITDs with 100% sensitivity. In addition, there was high concordance (100%) between all three panels detecting 47/47 confirmed variants in a set of core myeloid genes. CONCLUSIONS The results show that the NGS assays are now able to reliably detect CEBPA mutations and FLT3 ITDs. These assays may allow foregoing additional orthogonal testing for CEBPA and FLT3.
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Affiliation(s)
- Ratilal Akabari
- Department of Pathology, Molecular Oncology and Genetics Diagnostics, SUNY Upstate Medical University, Syracuse, NY 13210, USA;
| | - Dahui Qin
- Department of Pathology, Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Mohammad Hussaini
- Department of Pathology, Moffitt Cancer Center, Tampa, FL 33612, USA;
- Correspondence: ; Tel.: +1-813-745-6118
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Public interest in unexpected genomic findings: a survey study identifying aspects of sequencing attitudes that influence preferences. J Community Genet 2022; 13:235-245. [DOI: 10.1007/s12687-022-00577-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/14/2022] [Indexed: 10/19/2022] Open
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Chen C, Zhang W, Zhou D, Zhang Y. Sintilimab and Chidamide for Refractory Transformed Diffuse Large B Cell Lymphoma: A Case Report and A Literature Review. Front Oncol 2021; 11:757403. [PMID: 34820328 PMCID: PMC8606549 DOI: 10.3389/fonc.2021.757403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/18/2021] [Indexed: 01/22/2023] Open
Abstract
Patients with relapsed/refractory (R/R) transformed diffused large B cell lymphoma (tDLBCL) have a poor prognosis and a low survival rate. In addition, no standard therapy has yet been established for R/R tDLBCL. Herein we presented a single case of a patient with R/R tDLBCL who was successfully treated with sintilimab and chidamide. The patient was a 71-year-old man with pulmonary mucosa-associated lymphoid tissue lymphoma. He did not receive any treatment until tDLBCL was confirmed 2 years later. The tDLBCL was primary refractory to R2-CHOP, R2-MTX, and Gemox regimens. However, the patient achieved sustained complete remission after the combination therapy of sintilimab and chidamide. To the best of our knowledge, this is the first report of sintilimab combined with chidamide for the treatment of R/R tDLBCL, which opens up new therapeutic possibilities for this new combination therapy in future prospective clinical trials.
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Affiliation(s)
- Chao Chen
- Department of Hematology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Wei Zhang
- Department of Hematology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Daobin Zhou
- Department of Hematology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences (CAMS), Beijing, China
| | - Yan Zhang
- Department of Hematology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences (CAMS), Beijing, China
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Next Generation Sequencing Technology in Lung Cancer Diagnosis. BIOLOGY 2021; 10:biology10090864. [PMID: 34571741 PMCID: PMC8467994 DOI: 10.3390/biology10090864] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022]
Abstract
Simple Summary Lung cancer is still one of the most commonly diagnosed and deadliest cancers in the world. Its diagnosis at an early stage is highly necessary and will improve the standard of care of this disease. The aim of this article is to review the importance and applications of next generation sequencing in lung cancer diagnosis. As observed in many studies, next generation sequencing has been proven as a very helpful tool in the early detection of different types of cancers, including lung cancer, and has been used in the clinic, mainly due to its many advantages, such as low cost, speed, efficacy, low quantity usage of biological samples, and diversity. Abstract Lung cancer is still one of the most commonly diagnosed cancers, and one of the deadliest. The high death rate is mainly due to the late stage of diagnosis and low response rate to therapy. Previous and ongoing research studies have tried to discover new reliable and useful cbiomarkers for the diagnosis and prognosis of lung cancer. Next generation sequencing has become an essential tool in cancer diagnosis, prognosis, and evaluation of the treatment response. This article aims to review the leading research and clinical applications in lung cancer diagnosis using next generation sequencing. In this scope, we identified the most relevant articles that present the successful use of next generation sequencing in identifying biomarkers for early diagnosis correlated to lung cancer diagnosis and treatment. This technique can be used to evaluate a high number of biomarkers in a short period of time and from small biological samples, which makes NGS the preferred technique to develop clinical tests for personalized medicine using liquid biopsy, the new trend in oncology.
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Príncipe C, Dionísio de Sousa IJ, Prazeres H, Soares P, Lima RT. LRP1B: A Giant Lost in Cancer Translation. Pharmaceuticals (Basel) 2021; 14:836. [PMID: 34577535 PMCID: PMC8469001 DOI: 10.3390/ph14090836] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 12/23/2022] Open
Abstract
Low-density lipoprotein receptor-related protein 1B (LRP1B) is a giant member of the LDLR protein family, which includes several structurally homologous cell surface receptors with a wide range of biological functions from cargo transport to cell signaling. LRP1B is among the most altered genes in human cancer overall. Found frequently inactivated by several genetic and epigenetic mechanisms, it has mostly been regarded as a putative tumor suppressor. Still, limitations in LRP1B studies exist, in particular associated with its huge size. Therefore, LRP1B expression and function in cancer remains to be fully unveiled. This review addresses the current understanding of LRP1B and the studies that shed a light on the LRP1B structure and ligands. It goes further in presenting increasing knowledge brought by technical and methodological advances that allow to better manipulate LRP1B expression in cells and to more thoroughly explore its expression and mutation status. New evidence is pushing towards the increased relevance of LRP1B in cancer as a potential target or translational prognosis and response to therapy biomarker.
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Affiliation(s)
- Catarina Príncipe
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- Cancer Signalling and Metabolism Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Isabel J. Dionísio de Sousa
- Department of Oncology, Centro Hospitalar Universitário de São João, 4200-450 Porto, Portugal;
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Hugo Prazeres
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- IPO-Coimbra, Portuguese Oncology Institute of Coimbra, 3000-075 Coimbra, Portugal
| | - Paula Soares
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- Cancer Signalling and Metabolism Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Raquel T. Lima
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (C.P.); (H.P.); (P.S.)
- Cancer Signalling and Metabolism Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
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Jones TE, Zou J, Tseng GC, Roy S, Bhargava R. The Utility of Next-Generation Sequencing in Advanced Breast and Gynecologic Cancers. Am J Clin Pathol 2021; 156:455-460. [PMID: 33728425 DOI: 10.1093/ajcp/aqaa256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Next-generation sequencing (NGS) has the potential to identify genetic alterations that are actionable with targeted therapy. Our objective was to identify the impact of NGS testing on advanced breast and gynecologic malignancies. METHODS A retrospective review of 108 patients who underwent NGS testing between 2015 and 2019 was performed. The NGS clinical action rate was calculated based on documentation of positive clinical action taken in cases with an actionable NGS result. RESULTS The 108 specimens tested included 35 breast cancers and 73 gynecologic malignancies, with most of the testing performed at Foundation Medicine (90%). Actionable mutation(s) were identified in 79 (73%) of 108 cases. The overall clinical action rate of NGS testing was 38% (30 of 79 cases). Overall, 47 (44%) of 108 patients died, all succumbing to disease. The average survival was 10.9 months. The survival difference between patients with actionable NGS result and targeted treatment, actionable NGS result but no targeted treatment, and patients with nonactionable NGS result was not significant (log-rank test, P = .5160). CONCLUSIONS NGS testing for advanced breast and gynecologic cancers at our institution has a 38% clinical action rate. However, the increased clinical action rate over the years did not translate into improved survival.
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Affiliation(s)
- Terrell E Jones
- Department of Pathology, Presbyterian University Hospital, Pittsburgh, PA, USA
| | - Jian Zou
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Somak Roy
- Department of Pathology, Presbyterian University Hospital, Pittsburgh, PA, USA
| | - Rohit Bhargava
- Department of Pathology, Magee-Womens Hospital, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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Abstract
ELSI (Ethical, Legal, and Social Issues) is a widely used acronym in the bioethics literature that encompasses a broad range of research examining the various impacts of science and technology on society. In Canada, GE3LS (Genetics, Ethical, Economic, Environmental, Legal, Social issues) is the term used to describe ELSI studies in the context of genetics and genomics research. It is intentionally more expansive in that GE3LS explicitly brings economic and environmental issues under its purview. ELSI/GE3LS research is increasingly relevant in recent years as there has been a greater emphasis on "translational research" that moves genomic discoveries from the bench to the clinic. The purpose of this chapter is to outline a range of ELSI-related work that might be conducted as part of a large scale genetics or genomics research project, and to provide some practical insights on how a scientific research team might incorporate a strong and effective ELSI program within its broader research mandate. We begin by describing the historical context of ELSI research and the development of GE3LS research in the Canadian context. We then illustrate how some ELSI research might unfold by outlining a variety of GE3LS research questions or content domains and the methodologies that might be employed in studying them. We conclude with some practical suggestions about how to build an effective ELSI/GE3LS team and focus within a broader scientific research program.
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Etchegary H, Pullman D, Simmonds C, Rabie Z, Rahman P. Identifying Aspects of Public Attitudes Toward Whole Genome Sequencing to Inform the Integration of Genomics into Care. Public Health Genomics 2021; 24:229-240. [PMID: 34038902 DOI: 10.1159/000515952] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/16/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION The growth of global sequencing initiatives and commercial genomic test offerings suggests the public will increasingly be confronted with decisions about sequencing. Understanding public attitudes can assist efforts to integrate sequencing into care and inform the development of public education and outreach strategies. METHODS A 48-item online survey was advertised on Facebook in Eastern Canada and hosted on SurveyMonkey in late 2018. The survey measured public interest in whole genome sequencing and attitudes toward various aspects of sequencing using vignettes, scaled, and open-ended items. RESULTS While interest in sequencing was high, critical attitudes were observed. In particular, items measuring features of patient control and choice regarding genomic data were strongly endorsed by respondents. Majority wanted to specify upfront how their data could be used, retain the ability to withdraw their sample at a later date, sign a written consent form, and speak to a genetic counselor prior to sequencing. Concerns about privacy and unauthorized access to data were frequently observed. Education level was the sociodemographic variable most often related to attitude statements such that those with higher levels of education generally displayed more critical attitudes. CONCLUSIONS Attitudes identified here could be used to inform the development of implementation strategies for genomic medicine. Findings suggest health systems must address patient concerns about privacy, consent practices, and the strong desire to control what happens to their genomic data through public outreach and education. Specific oversight procedures and policies that are clearly communicated to the public will be required.
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Affiliation(s)
- Holly Etchegary
- Assistant Professor Clinical Epidemiology, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Daryl Pullman
- Professor of Medicine (Bioethics), Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Charlene Simmonds
- Manager, Health Research Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Zoha Rabie
- Research Assistant, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Proton Rahman
- Professor of Medicine (Rheumatology), Memorial University and Rheumatologist, Eastern Regional Health Authority, St. John's, Newfoundland, Canada
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Abstract
PURPOSE OF REVIEW This review aims to shed light on recent applications of artificial intelligence in urologic oncology. RECENT FINDINGS Artificial intelligence algorithms harness the wealth of patient data to assist in diagnosing, staging, treating, and monitoring genitourinary malignancies. Successful applications of artificial intelligence in urologic oncology include interpreting diagnostic imaging, pathology, and genomic annotations. Many of these algorithms, however, lack external validity and can only provide predictions based on one type of dataset. SUMMARY Future applications of artificial intelligence will need to incorporate several forms of data in order to truly make headway in urologic oncology. Researchers must actively ensure future artificial intelligence developments encompass the entire prospective patient population.
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Rizzo A, Mollica V, Cimadamore A, Santoni M, Scarpelli M, Schiavina R, Cheng L, Lopez-Beltran A, Brunocilla E, Montironi R, Massari F. TNM staging towards a personalized approach in metastatic urothelial carcinoma: what will the future be like?-a narrative review. Transl Androl Urol 2021; 10:1541-1552. [PMID: 33850788 PMCID: PMC8039595 DOI: 10.21037/tau-20-1109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The American Joint Committee of Cancer (AJCC) tumor-node-metastasis (TNM) classification, with its periodical updates and modifications, has represented and still represents the basis of cancer staging. The historical, long-standing limitations of anatomic-based TNM staging have been recently “threatened” by the impressive amount of data derived from molecular analyses, which have led to an unprecedented level of understanding of cancer genomics. In fact, current era of personalized oncology has witnessed important efforts towards the integration between clinical, anatomical and molecular features; however, despite the promises, personalized oncology faces many obstacles, due to the complex relationship between tumor biomarkers, previously unknown cancer subtypes and clinical and anatomical characteristics. With regard to urothelial carcinoma (UC), the characterization of tumors in large cohorts of patients has provided important information concerning genetic alterations, revealing the presence of biologically relevant subtypes of UC. In the current review, we will provide an overview regarding this recent “translation” from the anatomic-based TNM to a novel horizon, aiming at further “tailoring” personalized oncology, especially focusing on recently published data about the molecular landscape of UC with its therapeutic and prognostic implications.
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Affiliation(s)
- Alessandro Rizzo
- Oncologia Medica, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Veronica Mollica
- Oncologia Medica, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Alessia Cimadamore
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, Ancona, Italy
| | | | - Marina Scarpelli
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, Ancona, Italy
| | - Riccardo Schiavina
- Department of Urology, University of Bologna, S-Orsola-Malpighi Hospital, Bologna, Italy
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Eugenio Brunocilla
- Department of Urology, University of Bologna, S-Orsola-Malpighi Hospital, Bologna, Italy
| | - Rodolfo Montironi
- Section of Pathological Anatomy, Polytechnic University of the Marche Region, School of Medicine, United Hospitals, Ancona, Italy
| | - Francesco Massari
- Oncologia Medica, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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Bond DR, Uddipto K, Enjeti AK, Lee HJ. Single-cell epigenomics in cancer: charting a course to clinical impact. Epigenomics 2020; 12:1139-1151. [PMID: 32790506 DOI: 10.2217/epi-2020-0046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cancer is a disease of global epigenetic dysregulation. Mutations in epigenetic regulators are common events in multiple cancer types and epigenetic therapies are emerging as a treatment option in several malignancies. A major challenge for the clinical management of cancer is the heterogeneous nature of this disease. Cancers are composed of numerous cell types and evolve over time. This heterogeneity confounds decisions regarding treatment and promotes disease relapse. The emergence of single-cell epigenomic technologies has introduced the exciting possibility of linking genetic and transcriptional heterogeneity in the context of cancer biology. The next challenge is to leverage these tools for improved patient outcomes. Here we consider how single-cell epigenomic technologies may address the current challenges faced by cancer clinicians.
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Affiliation(s)
- Danielle R Bond
- School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Kumar Uddipto
- School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Anoop K Enjeti
- Department of Haematology, Calvary Mater Newcastle, Waratah 2298, New South Wales, Australia.,School of Medicine & Public Health, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia.,NSW Health Pathology - Hunter, New Lambton Heights 2305, New South Wales, Australia
| | - Heather J Lee
- School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia
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Novel Somatic Genetic Variants as Predictors of Resistance to EGFR-Targeted Therapies in Metastatic Colorectal Cancer Patients. Cancers (Basel) 2020; 12:cancers12082245. [PMID: 32796636 PMCID: PMC7463997 DOI: 10.3390/cancers12082245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/17/2020] [Accepted: 08/06/2020] [Indexed: 12/11/2022] Open
Abstract
Background: About 40% of RAS/BRAF wild-type metastatic colorectal cancer (mCRC) patients undergoing anti-EGFR-based therapy have poor outcomes. Treatment failure is not only associated with poorer prognosis but higher healthcare costs. Our aim was to identify novel somatic genetic variants in the primary tumor and assess their effect on anti-EGFR response. Patients and Methods: Tumor (somatic) and blood (germline) DNA samples were obtained from two well-defined cohorts of mCRC patients, those sensitive and those resistant to EGFR blockade. Genetic variant screening of 43 EGFR-related genes was performed using targeted next-generation sequencing (NGS). Relevant clinical data were collected through chart review to assess genetic results. Results: Among 61 patients, 38 were sensitive and 23 were resistant to treatment. We identified eight somatic variants that predicted non-response. Three were located in insulin-related genes (I668N and E1218K in IGF1R, T1156M in IRS2) and three in genes belonging to the LRIG family (T152T in LRIG1, S697L in LRIG2 and V812M in LRIG3). The remaining two variants were found in NRAS (G115Efs*46) and PDGFRA (T301T). We did not identify any somatic variants related to good response. Conclusions: This study provides evidence that novel somatic genetic variants along the EGFR-triggered pathway could modulate the response to anti-EGFR drugs in mCRC patients. It also highlights the influence of insulin-related genes and LRIG genes on anti-EGFR efficacy. Our findings could help characterize patients who are resistant to anti-EGFR blockade despite harboring RAS/BRAF wild-type tumors.
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Esagian SM, Grigoriadou GΙ, Nikas IP, Boikou V, Sadow PM, Won JK, Economopoulos KP. Comparison of liquid-based to tissue-based biopsy analysis by targeted next generation sequencing in advanced non-small cell lung cancer: a comprehensive systematic review. J Cancer Res Clin Oncol 2020; 146:2051-2066. [PMID: 32462295 PMCID: PMC7456570 DOI: 10.1007/s00432-020-03267-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE To explore whether targeted next generation sequencing (NGS) of liquid biopsy in advanced non-small cell lung cancer (NSCLC) could potentially overcome the innate problems that arise with standard tissue biopsy, like intratumoral heterogeneity and the inability to obtain adequate samples for analysis. METHODS The Scopus, Cochrane Library, and MEDLINE (via PubMed) databases were searched for studies with matched tissue and liquid biopsies from advanced NSCLC patients, analyzed with targeted NGS. The number of mutations detected in tissue biopsy only, liquid biopsy only, or both was assessed and the positive percent agreement (PPA) of the two methods was calculated for every clinically relevant gene. RESULTS A total of 644 unique relevant articles were retrieved and data were extracted from 38 studies fulfilling the inclusion criteria. The sample size was composed of 2000 mutations tested in matched tissue and liquid biopsies derived from 1141 patients. No studies analyzed circulating tumor cells. The calculated PPA rates were 53.6% (45/84) for ALK, 53.9% (14/26) for BRAF, 56.5% (13/23) for ERBB2, 67.8% (428/631) for EGFR, 64.2% (122/190) for KRAS, 58.6% (17/29) for MET, 54.6% (12/22) for RET, and 53.3% (8/15) for ROS1. We additionally recorded data for 65 genes that are not recommended by current guidelines for mutational testing. An extra category containing results of unspecified genes was added, with a PPA rate of 55.7% (122/219). CONCLUSION Despite many advantages, liquid biopsy might be unable to fully substitute its tissue counterpart in detecting clinically relevant mutations in advanced NSCLC patients. However, it may serve as a helpful tool when making therapeutic decisions. More studies are needed to evaluate its role in everyday clinical practice.
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Affiliation(s)
- Stepan M Esagian
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
| | - Georgia Ι Grigoriadou
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
- 1st Department of Medical Oncology, Theageneio Anticancer Hospital, Thessaloníki, Greece
| | - Ilias P Nikas
- School of Medicine, European University of Cyprus, Nicosia, Cyprus
| | - Vasileios Boikou
- Oncology Working Group, Society of Junior Doctors, Athens, Greece
- Athens University of Economics and Business, Athens, Greece
| | - Peter M Sadow
- Department of Pathology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Konstantinos P Economopoulos
- Oncology Working Group, Society of Junior Doctors, Athens, Greece.
- Department of Surgery, Duke University Medical Center, 2301 Erwin Rd, Durham, NC, 27710, USA.
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Melas M, Subbiah S, Saadat S, Rajurkar S, McDonnell KJ. The Community Oncology and Academic Medical Center Alliance in the Age of Precision Medicine: Cancer Genetics and Genomics Considerations. J Clin Med 2020; 9:E2125. [PMID: 32640668 PMCID: PMC7408957 DOI: 10.3390/jcm9072125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
Recent public policy, governmental regulatory and economic trends have motivated the establishment and deepening of community health and academic medical center alliances. Accordingly, community oncology practices now deliver a significant portion of their oncology care in association with academic cancer centers. In the age of precision medicine, this alliance has acquired critical importance; novel advances in nucleic acid sequencing, the generation and analysis of immense data sets, the changing clinical landscape of hereditary cancer predisposition and ongoing discovery of novel, targeted therapies challenge community-based oncologists to deliver molecularly-informed health care. The active engagement of community oncology practices with academic partners helps with meeting these challenges; community/academic alliances result in improved cancer patient care and provider efficacy. Here, we review the community oncology and academic medical center alliance. We examine how practitioners may leverage academic center precision medicine-based cancer genetics and genomics programs to advance their patients' needs. We highlight a number of project initiatives at the City of Hope Comprehensive Cancer Center that seek to optimize community oncology and academic cancer center precision medicine interactions.
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Affiliation(s)
- Marilena Melas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA;
| | - Shanmuga Subbiah
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Glendora, CA 91741, USA;
| | - Siamak Saadat
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Colton, CA 92324, USA;
| | - Swapnil Rajurkar
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Upland, CA 91786, USA;
| | - Kevin J. McDonnell
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte, CA 91010, USA
- Center for Precision Medicine, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
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Etchegary H, Wilson B, Rahman P, Simmonds C, Pullman D. Public interest in whole genome sequencing and information needs: an online survey study. Per Med 2020; 17:283-293. [DOI: 10.2217/pme-2019-0136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aim: To survey the general public about whole genome sequencing interest, including pharmacogenomic testing, and to identify information important for sequencing decisions. Patients & methods: An online survey of 901 members of the general public in an eastern Canadian province. Results: Interest in whole genome sequencing, including pharmacogenomic testing, was high with few differences among demographic variables. Issues identified as very important to sequencing decisions included familial implications of testing, whether treatment was available for conditions tested and knowing who could access genomic information. Most respondents would value support when interpreting sequencing results. Conclusion: Findings reveal the kind of information and support users of sequencing services would value and could inform the implementation of sequencing into care in ways that accord with public preferences and needs.
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Affiliation(s)
- Holly Etchegary
- Faculty of Medicine, Memorial University, St John's, NL, Canada; Craig L. Dobbin Centre for Genetics, Rm 4M210, St John's, NL, A1B 3V6
| | - Brenda Wilson
- Professor of Medicine and Associate Dean, Community Health and Humanities, Memorial University, St John’s, NL A1B 3V6, Canada
| | - Proton Rahman
- Professor of Medicine (Rheumatology), Memorial University and Rheumatologist, Eastern Regional Health Authority, St John’s, NL A1B 3V6, Canada
| | - Charlene Simmonds
- Manager, Health Research Unit, Faculty of Medicine, Memorial University, St. John’s, NL A1B 3V6, Canada
| | - Daryl Pullman
- Professor of Medicine (Bioethics), Faculty of Medicine, Memorial University, St. John’s, NL A1B 3V6, Canada
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Suzuki T, Tsukumo Y, Furihata C, Naito M, Kohara A. Preparation of the standard cell lines for reference mutations in cancer gene-panels by genome editing in HEK 293 T/17 cells. Genes Environ 2020; 42:8. [PMID: 32071619 PMCID: PMC7014756 DOI: 10.1186/s41021-020-0147-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/31/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Next Generation Sequencer (NGS) is a powerful tool for a high-throughput sequencing of human genome. It is important to ensure reliability and sensitivity of the sequence data for a clinical use of the NGS. Various cancer-related gene panels such as Oncomine™ or NCC OncoPanel have been developed and used for clinical studies. Because these panels contain multiple genes, it is difficult to ensure the performance of mutation detection for every gene. In addition, various platforms of NGS are developed and their cross-platform validation has become necessity. In order to create mutant standards in a defined background, we have used CRISPR/Cas9 genome-editing system in HEK 293 T/17 cells. RESULTS Cancer-related genes that are frequently used in NGS-based cancer panels were selected as the target genes. Target mutations were selected based on their frequency reported in database, and clinical significance and on the applicability of CRISPR/Cas9 by considering distance from PAM site, and off-targets. We have successfully generated 88 hetero- and homozygous mutant cell lines at the targeted sites of 36 genes representing a total of 125 mutations. CONCLUSIONS These knock-in HEK293T/17 cells can be used as the reference mutant standards with a steady and continuous supply for NGS-based cancer panel tests from the JCRB cell bank. In addition, these cell lines can provide a tool for the functional analysis of targeted mutations in cancer-related genes in the isogenic background.
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Affiliation(s)
- Takayoshi Suzuki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi-ku, Kawasaki, 210-9501 Japan
| | - Yoshinori Tsukumo
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi-ku, Kawasaki, 210-9501 Japan
| | - Chie Furihata
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi-ku, Kawasaki, 210-9501 Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi-ku, Kawasaki, 210-9501 Japan
| | - Arihiro Kohara
- JCRB Cell Bank, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki City, Osaka, 567-0085 Japan
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Genomic profiling in oncology clinical practice. Clin Transl Oncol 2020; 22:1430-1439. [PMID: 31981077 DOI: 10.1007/s12094-020-02296-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/08/2020] [Indexed: 02/04/2023]
Abstract
The development of high-throughput technologies such as next-generation sequencing for DNA sequencing together with the decrease in their cost has led to the progressive introduction of genomic profiling in our daily practice in oncology. Nowadays, genomic profiling is part of genetic counseling, cancer diagnosis, molecular characterization, and as a biomarker of prognosis and response to treatment. Furthermore, germline or somatic genomic characterization of the tumor may provide new treatment opportunities for patients with cancer. In this review, we will summarize the clinical applications and limitations of genomic profiling in oncology clinical practice, focusing on next-generation sequencing.
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Improved next-generation sequencing pre-capture library yields and sequencing parameters using on-bead PCR. Biotechniques 2020; 68:48-51. [DOI: 10.2144/btn-2019-0059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Tumor DNA sequencing results can have important clinical implications. However, its use is often limited by low DNA input, owing to small tumor biopsy size. To help overcome this limitation we have developed a simple improvement to a commonly used next-generation sequencing (NGS) capture-based library preparation method using formalin-fixed paraffin-embedded-derived tumor DNA. By using on-bead PCR for pre-capture library generation we show that library yields are dramatically increased, resulting in decreased sample failure rates. Improved yields allowed for a reduction in PCR cycles, which translated into improved sequencing parameters without affecting variant calling. This methodology should be applicable to any NGS system in which input DNA is a limiting factor.
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Yin Y, Wu S, Zhao X, Zou L, Luo A, Deng F, Min M, Jiang L, Liu H, Wu X. Whole exome sequencing study of a Chinese concurrent cancer family. Oncol Lett 2019; 18:2619-2627. [PMID: 31452746 DOI: 10.3892/ol.2019.10573] [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: 08/07/2018] [Accepted: 05/22/2019] [Indexed: 11/06/2022] Open
Abstract
Cancer is one of the leading causes of mortality in China, and poses a threat to public health due to its increasing incidence and mortality rates. Concurrent cancer is defined as one or more organs in the same individual having ≥2 primary malignancies occurring simultaneously or successively; however, concurrent cases are rare and poorly studied. The present study recruited a Chinese family presenting multiple cases of concurrent cancer and performed whole exome sequencing in one unaffected and two affected individuals to identify the causative mutations. DNA was extracted from peripheral blood and tumor tissue samples. Following an exome capture and quality test, the qualified library was sequenced as 100 bp paired-end reads on an Ion Torrent platform. Clean data were obtained by filtering out the low-quality reads. Subsequently, bioinformatics analyses were performed using the clean data. After mapping and annotating in 1000 Genomes Project database, the existing SNP database and the Cancer Gene Census (CGC) database, it was revealed that the NADH:ubiquinone oxidoreductase core subunit S7 gene was a candidate gene with somatic mutations, and a subset of 16 genes were candidate genes with germline mutations. The findings of the present study may improve the understanding of the molecular pathogenesis of concurrent cancer.
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Affiliation(s)
- Yifa Yin
- Department of Radiotherapy and Chemotherapy, The Second People's Hospital, Three Gorges University, Yichang, Hubei 443002, P.R. China
| | - Shouxin Wu
- Biotecan Medical Diagnostics Co., Ltd., Zhangjiang Center for Translational Medicine, Shanghai 201203, P.R. China
| | - Xincheng Zhao
- Graduate School of Oncology, Three Gorges University, Yichang, Hubei 443002, P.R. China
| | - Liyong Zou
- Department of Radiotherapy and Chemotherapy, The Second People's Hospital, Three Gorges University, Yichang, Hubei 443002, P.R. China
| | - Aihua Luo
- Department of Radiotherapy and Chemotherapy, The Second People's Hospital, Three Gorges University, Yichang, Hubei 443002, P.R. China
| | - Fei Deng
- Department of Radiotherapy and Chemotherapy, The Second People's Hospital, Three Gorges University, Yichang, Hubei 443002, P.R. China
| | - Mengyun Min
- Graduate School of Oncology, Three Gorges University, Yichang, Hubei 443002, P.R. China
| | - Lisha Jiang
- Biotecan Medical Diagnostics Co., Ltd., Zhangjiang Center for Translational Medicine, Shanghai 201203, P.R. China
| | - Huimin Liu
- Biotecan Medical Diagnostics Co., Ltd., Zhangjiang Center for Translational Medicine, Shanghai 201203, P.R. China
| | - Xiangbai Wu
- Department of General Surgery, The Second People's Hospital, Three Gorges University, Yichang, Hubei 443002, P.R. China
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Bélisle-Pipon JC, Vayena E, Green RC, Cohen IG. Genetic testing, insurance discrimination and medical research: what the United States can learn from peer countries. Nat Med 2019; 25:1198-1204. [PMID: 31388181 DOI: 10.1038/s41591-019-0534-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 06/25/2019] [Indexed: 12/29/2022]
Abstract
While genetic testing may be the gateway to the future of medicine, it also poses challenges for individuals, especially in terms of differentiated treatments on the basis of their genetic characteristics. The fear of unwanted disclosure to insurers and the possibility of genetic discrimination can hamper the recruitment of individuals for clinical research that involves genetic testing. Precision medicine initiatives, such as All of Us, are proliferating in the United States. In order to succeed, however, they must ensure that the millions of Americans recruited to share their genetic data are not penalized with regard to life, disability and long-term insurance coverage. In this Perspective, we discuss several initiatives adopted by countries around the world, such as the United Kingdom and France, that better balance the interests of insurers and research subjects, and explain how the United States might learn from them. We call for regulatory and industry leadership to come together to establish a voluntary moratorium on insurance pricing with the aim of protecting research participants.
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Affiliation(s)
| | - Effy Vayena
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Robert C Green
- Brigham and Women's Hospital, Broad Institute and Harvard Medical School, Boston, MA, USA
| | - I Glenn Cohen
- Petrie-Flom Center for Health Law Policy, Biotechnology, and Bioethics, Harvard Law School, Cambridge, MA, USA.
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