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Nindra U, Pal A, Bray V, Yip PY, Tognela A, Roberts TL, Becker TM, Williamson J, Farzin M, Li JJ, Lea V, Hagelamin A, Ng W, Wang B, Lee CS, Chua W. Utility of multigene panel next-generation sequencing in routine clinical practice for identifying genomic alterations in newly diagnosed metastatic nonsmall cell lung cancer. Intern Med J 2024; 54:596-601. [PMID: 37713593 DOI: 10.1111/imj.16224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/17/2023] [Indexed: 09/17/2023]
Abstract
BACKGROUND The standard of care in newly diagnosed metastatic non-small cell lung cancer (NSCLC) is to test for aberrations in three genes for driver mutations - ALK, ROS1 and epidermal growth factor receptor (EGFR) - and also for immunohistochemistry to be performed for programmed death-ligand 1 expression level. Next-generation sequencing (NGS), with or without RNA fusion testing, is increasingly used in standard clinical practice to identify patients with potentially actionable mutations. Stratification of NGS mutation tiers is currently based on the European Society of Medical Oncology Scale for Clinical Actionability of Molecular Targets (ESCAT) Tiers I-V and X. AIM Our aim was to analyse NSCLC tumour samples for the prevalence of Tiers I-V mutations to establish guidance for current and novel treatments in patients with metastatic disease. METHODS NGS was performed employing the Oncomine Precision Assay (without RNA fusion testing) that interrogates DNA hotspot variants across 45 genes to screen 210 NSCLC tissue samples obtained across six Sydney hospitals between June 2021 and March 2022. RESULTS In our cohort, 161 of 210 (77%) had at least one gene mutation identified, with 41 of 210 (20%) having two or more concurrent mutations. Tier I mutations included 42 of 210 (20%) EGFR mutations (EIA) and five of 210 (3%) MET exon 14 skipping mutations (EIB). Non-Tier I variants included 22 of 210 (11%) KRAS G12C hotspot mutations (EIIB), with a further 47 of 210 (22%) having non-G12C KRAS (EX) mutations. NGS testing revealed an additional 15% of cases with Tier II ESCAT mutations in NSCLC. Forty-six percent of patients also demonstrated potential Tier III and IV mutations that are currently under investigation in early-phase clinical trials. CONCLUSIONS In addition to identifying patients with genomic alterations suitable for clinically proven standard-of-care therapeutic options, the 45-gene NGS panel has significant potential in identifying potentially actionable non-Tier 1 mutations that may become future standard clinical practice in NSCLC.
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Affiliation(s)
- Udit Nindra
- Department of Medical Oncology, Liverpool Hospital, Sydney, New South Wales, Australia
- Department of Medical Oncology, Macarthur Cancer Therapy Centre, Campbelltown Hospital, Sydney, New South Wales, Australia
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
| | - Abhijit Pal
- Department of Medical Oncology, Liverpool Hospital, Sydney, New South Wales, Australia
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Sydney, New South Wales, Australia
| | - Victoria Bray
- Department of Medical Oncology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Po Y Yip
- Department of Medical Oncology, Macarthur Cancer Therapy Centre, Campbelltown Hospital, Sydney, New South Wales, Australia
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - Annette Tognela
- Department of Medical Oncology, Macarthur Cancer Therapy Centre, Campbelltown Hospital, Sydney, New South Wales, Australia
| | - Tara L Roberts
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- South Western Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Therese M Becker
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- South Western Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Jonathon Williamson
- Department of Respiratory Medicine, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Mahtab Farzin
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Jing J Li
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Vivienne Lea
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Abeer Hagelamin
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Weng Ng
- Department of Medical Oncology, Liverpool Hospital, Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- South Western Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Bin Wang
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - C Soon Lee
- Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- South Western Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Wei Chua
- Department of Medical Oncology, Liverpool Hospital, Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- South Western Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ghanem P, Fatteh M, Kamson DO, Balan A, Chang M, Tao J, Blakeley J, Canzoniero J, Grossman SA, Marrone K, Schreck KC, Anagnostou V. Druggable genomic landscapes of high-grade gliomas. Front Med (Lausanne) 2023; 10:1254955. [PMID: 38143440 PMCID: PMC10749203 DOI: 10.3389/fmed.2023.1254955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/06/2023] [Indexed: 12/26/2023] Open
Abstract
Background Despite the putatively targetable genomic landscape of high-grade gliomas, the long-term survival benefit of genomically-tailored targeted therapies remains discouraging. Methods Using glioblastoma (GBM) as a representative example of high-grade gliomas, we evaluated the clonal architecture and distribution of hotspot mutations in 388 GBMs from the Cancer Genome Atlas (TCGA). Mutations were matched with 54 targeted therapies, followed by a comprehensive evaluation of drug biochemical properties in reference to the drug's clinical efficacy in high-grade gliomas. We then assessed clinical outcomes of a cohort of patients with high-grade gliomas with targetable mutations reviewed at the Johns Hopkins Molecular Tumor Board (JH MTB; n = 50). Results Among 1,156 sequence alterations evaluated, 28.6% represented hotspots. While the frequency of hotspot mutations in GBM was comparable to cancer types with actionable hotspot alterations, GBMs harbored a higher fraction of subclonal mutations that affected hotspots (7.0%), compared to breast cancer (4.9%), lung cancer (4.4%), and melanoma (1.4%). In investigating the biochemical features of targeted therapies paired with recurring alterations, we identified a trend toward higher lipid solubility and lower IC50 in GBM cell lines among drugs with clinical efficacy. The drugs' half-life, molecular weight, surface area and binding to efflux transporters were not associated with clinical efficacy. Among the JH MTB cohort of patients with IDH1 wild-type high-grade gliomas who received targeted therapies, trametinib monotherapy or in combination with dabrafenib conferred radiographic partial response in 75% of patients harboring BRAF or NF1 actionable mutations. Cabozantinib conferred radiographic partial response in two patients harboring a MET and a PDGFRA/KDR amplification. Patients with IDH1 wild-type gliomas that harbored actionable alterations who received genotype-matched targeted therapy had longer progression-free (PFS) and overall survival (OS; 7.37 and 14.72 respectively) than patients whose actionable alterations were not targeted (2.83 and 4.2 months respectively). Conclusion While multiple host, tumor and drug-related features may limit the delivery and efficacy of targeted therapies for patients with high-grade gliomas, genotype-matched targeted therapies confer favorable clinical outcomes. Further studies are needed to generate more data on the impact of biochemical features of targeted therapies on their clinical efficacy for high-grade gliomas.
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Affiliation(s)
- Paola Ghanem
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Maria Fatteh
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David Olayinka Kamson
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Archana Balan
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Michael Chang
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jessica Tao
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jaishri Blakeley
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jenna Canzoniero
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Stuart A. Grossman
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kristen Marrone
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Karisa C. Schreck
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Valsamo Anagnostou
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Matrone A, Citro F, Gambale C, Prete A, Minaldi E, Ciampi R, Ramone T, Materazzi G, Torregrossa L, Elisei R. BRAF K601E Mutation in Oncocytic Carcinoma of the Thyroid: A Case Report and Literature Review. J Clin Med 2023; 12:6970. [PMID: 38002585 PMCID: PMC10672186 DOI: 10.3390/jcm12226970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Thyroid carcinoma (TC) is the most common endocrine cancer, with papillary thyroid carcinoma (PTC) being the most common subtype. BRAF and RAS oncogene were characterized as the most frequently altered genes in PTC, with a strong association between genotype and histotype. The most common mutation in BRAF gene is V600E and is prevalent in classic and aggressive variants of PTC, while BRAF K601E mutation is the most common among the other rare BRAF mutations. BRAF K601E mutated thyroid carcinomas are usually characterized by low aggressiveness, except for anecdotal cases of poorly differentiated TC. CASE PRESENTATION We described a case of oncocytic carcinoma of the thyroid (OCA) with an aggressive clinical course, including widespread metastasis and resistance to radioiodine treatment. Molecular analysis revealed the exclusive presence of the BRAF K601E mutation in both primary tumor and metastatic lesions. Accordingly, a revision of the literature about aggressive TC cases carrying BRAF K601E mutation was performed. CONCLUSION Although rare, this case emphasizes the relevance of considering BRAF K601E mutation in advanced non-PTC thyroid carcinomas, since it can be considered an actionable mutation for target therapies.
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Affiliation(s)
- Antonio Matrone
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, Pisa University Hospital, 56124 Pisa, Italy; (F.C.); (C.G.); (A.P.); (E.M.); (R.C.); (T.R.); (R.E.)
| | - Fabrizia Citro
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, Pisa University Hospital, 56124 Pisa, Italy; (F.C.); (C.G.); (A.P.); (E.M.); (R.C.); (T.R.); (R.E.)
| | - Carla Gambale
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, Pisa University Hospital, 56124 Pisa, Italy; (F.C.); (C.G.); (A.P.); (E.M.); (R.C.); (T.R.); (R.E.)
| | - Alessandro Prete
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, Pisa University Hospital, 56124 Pisa, Italy; (F.C.); (C.G.); (A.P.); (E.M.); (R.C.); (T.R.); (R.E.)
| | - Elisa Minaldi
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, Pisa University Hospital, 56124 Pisa, Italy; (F.C.); (C.G.); (A.P.); (E.M.); (R.C.); (T.R.); (R.E.)
| | - Raffaele Ciampi
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, Pisa University Hospital, 56124 Pisa, Italy; (F.C.); (C.G.); (A.P.); (E.M.); (R.C.); (T.R.); (R.E.)
| | - Teresa Ramone
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, Pisa University Hospital, 56124 Pisa, Italy; (F.C.); (C.G.); (A.P.); (E.M.); (R.C.); (T.R.); (R.E.)
| | - Gabriele Materazzi
- Endocrine Surgery Unit, Department of Surgical, Medical, Molecular Pathology and Critical Area, Pisa University Hospital, 56126 Pisa, Italy;
| | - Liborio Torregrossa
- Department of Surgical, Medical, Molecular Pathology and Critical Area, Anatomic Pathology Section, Pisa University Hospital, 56126 Pisa, Italy;
| | - Rossella Elisei
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, Pisa University Hospital, 56124 Pisa, Italy; (F.C.); (C.G.); (A.P.); (E.M.); (R.C.); (T.R.); (R.E.)
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Hosono N, Chi S, Yamauchi T, Fukushima K, Shibayama H, Katagiri S, Gotoh A, Eguchi M, Morishita T, Ogasawara R, Kondo T, Yanada M, Yamamoto K, Kobayashi T, Kuroda J, Usuki K, Utsu Y, Yoshimitsu M, Ishitsuka K, Ono T, Takahashi N, Iyama S, Kojima K, Nakamura Y, Fukuhara S, Izutsu K, Abutani H, Yamauchi N, Yuda J, Minami Y. Clinical utility of genomic profiling of AML using paraffin-embedded bone marrow clots: HM-SCREEN-Japan 01. Cancer Sci 2023; 114:2098-2108. [PMID: 36793248 PMCID: PMC10154825 DOI: 10.1111/cas.15746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/20/2023] [Accepted: 01/29/2023] [Indexed: 02/17/2023] Open
Abstract
Next-generation sequencing of AML has identified specific genetic mutations in AML patients. Hematologic Malignancies (HM)-SCREEN-Japan 01 is a multicenter study to detect actionable mutations using paraffin-embedded bone marrow (BM) clot specimens rather than BM fluid in AML patients for whom standard treatment has not been established. The purpose of this study is to evaluate the presence of potentially therapeutic target gene mutations in patients with newly diagnosed unfit AML and relapsed/refractory AML (R/R-AML) using BM clot specimens. In this study, 188 patients were enrolled and targeted sequencing was undertaken on DNA from 437 genes and RNA from 265 genes. High-quality DNA and RNA were obtained using BM clot specimens, with genetic alterations successfully detected in 177 patients (97.3%), and fusion transcripts in 41 patients (23.2%). The median turnaround time was 13 days. In the detection of fusion genes, not only common fusion products such as RUNX1-RUX1T1 and KMT2A rearrangements, but also NUP98 rearrangements and rare fusion genes were observed. Among 177 patients (72 with unfit AML, 105 with R/R-AML), mutations in KIT and WT1 were independent factors for overall survival (hazard ratio = 12.6 and 8.88, respectively), and patients with high variant allele frequency (≥40%) of TP53 mutations had a poor prognosis. As for the detection of actionable mutations, 38% (n = 69) of patients had useful genetic mutation (FLT3-ITD/TKD, IDH1/2, and DNMT3AR822 ) for treatment selection. Comprehensive genomic profiling using paraffin-embedded BM clot specimens successfully identified leukemic-associated genes that can be used as therapeutic targets.
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Affiliation(s)
- Naoko Hosono
- Department of Hematology and Oncology, University of Fukui Hospital, Fukui, Japan
| | - SungGi Chi
- Department of Hematology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Takahiro Yamauchi
- Department of Hematology and Oncology, University of Fukui Hospital, Fukui, Japan
| | - Kentaro Fukushima
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hirohiko Shibayama
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Seiichiro Katagiri
- Department of Hematology, Tokyo Medical University Hospital, Tokyo, Japan
| | - Akihiko Gotoh
- Department of Hematology, Tokyo Medical University Hospital, Tokyo, Japan
| | - Motoki Eguchi
- Division of Hematology, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Japan
| | - Takanobu Morishita
- Division of Hematology, Japanese Red Cross Aichi Medical Center Nagoya Daiichi Hospital, Nagoya, Japan
| | | | - Takeshi Kondo
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | - Masamitsu Yanada
- Department of Hematology and Cell Therapy, Aichi Cancer Center, Nagoya, Japan
| | - Kazuhito Yamamoto
- Department of Hematology and Cell Therapy, Aichi Cancer Center, Nagoya, Japan
| | - Tsutomu Kobayashi
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kensuke Usuki
- Department of Hematology, NTT Medical Center Tokyo, Tokyo, Japan
| | - Yoshikazu Utsu
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Narita, Japan
| | - Makoto Yoshimitsu
- Department of Hematology, Kagoshima University Hospital, Kagoshima, Japan
| | - Kenji Ishitsuka
- Department of Hematology, Kagoshima University Hospital, Kagoshima, Japan
| | - Takaaki Ono
- Department of Hematology, Hamamatsu University Hospital, Hamamatsu, Japan
| | - Naoto Takahashi
- Department of Hematology, Nephrology, and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Satoshi Iyama
- Department of Hematology, Sapporo Medical University, Sapporo, Japan
| | - Kensuke Kojima
- Department of Hematology, Kochi Medical School Hospital, Nankoku, Japan
| | - Yukinori Nakamura
- Third Department of Internal Medicine, Yamaguchi University Hospital, Ube, Japan
| | - Suguru Fukuhara
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Koji Izutsu
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | | | - Nobuhiko Yamauchi
- Department of Hematology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Junichiro Yuda
- Department of Hematology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Kashiwa, Japan
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Huang CC, Liu CY, Huang CJ, Hsu YC, Lien HH, Wong JU, Tai FC, Ku WH, Hung CF, Lin JT, Huang CS, Chiang HS. Deciphering Genetic Alterations of Taiwanese Patients with Pancreatic Adenocarcinoma through Targeted Sequencing. Int J Mol Sci 2022; 23:1579. [PMID: 35163506 PMCID: PMC8835797 DOI: 10.3390/ijms23031579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
Pancreatic adenocarcinoma (PAC) is the 8th leading cause of cancer-related deaths in Taiwan, and its incidence is increasing. The development of PAC involves successive accumulation of multiple genetic alterations. Understanding the molecular pathogenesis and heterogeneity of PAC may facilitate personalized treatment for PAC and identify therapeutic agents. We performed tumor-only next-generation sequencing (NGS) with targeted panels to explore the molecular changes underlying PAC patients in Taiwan. The Ion Torrent Oncomine Comprehensive Panel (OCP) was used for PAC metastatic lesions, and more PAC samples were sequenced with the Ion AmpliSeq Cancer Hot Spot (CHP) v2 panel. Five formalin-fixed paraffin-embedded (FFPE) metastatic PAC specimens were successfully assayed with OCP, and KRAS was the most prevalent alteration, which might contraindicate the use of anti-EGFR therapy. One PAC patient harbored a FGFR2 p. C382R mutation, which might benefit from FGFR tyrosine kinase inhibitors. An additional 38 samples assayed with CHP v2 showed 100 hotspot variants, collapsing to 54 COSMID IDs. The most frequently mutated genes were TP53, KRAS, and PDGFRA (29, 23, 10 hotspot variants), impacting 11, 23, and 10 PAC patients. Highly pathogenic variants, including COSM22413 (PDGFRA, FATHMM predicted score: 0.88), COSM520, COSM521, and COSM518 (KRAS, FATHMM predicted score: 0.98), were reported. By using NGS with targeted panels, somatic mutations with therapeutic potential were identified. The combination of clinical and genetic information is useful for decision making and precise selection of targeted medicine.
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Affiliation(s)
- Chi-Cheng Huang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | - Chih-Yi Liu
- Department of Pathology, Cathay General Hospital SiJhih, New Taipei 221, Taiwan;
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei 106, Taiwan;
- Department of Biochemistry, National Defense Medical Center, Taipei 114, Taiwan
| | - Yao-Chun Hsu
- Division of Gastroenterology, Department of Internal Medicine, E-da Hospital, Kaohsiung 82445, Taiwan;
| | - Heng-Hui Lien
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei 106, Taiwan; (H.-H.L.); (F.-C.T.)
- School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei 242, Taiwan;
| | - Jia-Uei Wong
- Division of General Surgery, Department of Surgery, Fu-Jen Catholic University Hospital, New Taipei 243, Taiwan;
| | - Feng-Chuan Tai
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei 106, Taiwan; (H.-H.L.); (F.-C.T.)
| | - Wen-Hui Ku
- Department of Clinical Pathology and Molecular Medicine, Taipei Institute of Pathology, Taipei 10374, Taiwan;
| | - Chi-Feng Hung
- School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei 242, Taiwan;
| | - Jaw-Town Lin
- Digestive Medicine Center, China Medical University Hospital, Taichung 404, Taiwan;
| | - Ching-Shui Huang
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei 106, Taiwan; (H.-H.L.); (F.-C.T.)
- School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Han-Sun Chiang
- School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei 242, Taiwan;
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7
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Dongre HN, Haave H, Fromreide S, Erland FA, Moe SEE, Dhayalan SM, Riis RK, Sapkota D, Costea DE, Aarstad HJ, Vintermyr OK. Targeted Next-Generation Sequencing of Cancer-Related Genes in a Norwegian Patient Cohort With Head and Neck Squamous Cell Carcinoma Reveals Novel Actionable Mutations and Correlations With Pathological Parameters. Front Oncol 2021; 11:734134. [PMID: 34631566 PMCID: PMC8497964 DOI: 10.3389/fonc.2021.734134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/27/2021] [Indexed: 12/11/2022] Open
Abstract
Background Targeted next-generation sequencing (NGS) is increasingly applied in clinical oncology to advance personalized treatment. Despite success in many other tumour types, use of targeted NGS panels for assisting diagnosis and treatment of head and neck squamous cell carcinomas (HNSCC) is still limited. Aim The focus of this study was to establish a robust NGS panel targeting most frequent cancer mutations in long-term preserved formalin-fixed paraffin-embedded (FFPE) tissue samples of HNSCC from routine diagnostics. Materials and Methods Tumour DNA obtained from archival FFPE tissue blocks of HNSCC patients treated at Haukeland University Hospital between 2003-2016 (n=111) was subjected to mutational analysis using a custom made AmpliSeq Library PLUS panel targeting 31 genes (Illumina). Associations between mutational burden and clinical and pathological parameters were investigated. Mutation and corresponding clinicopathological data from HNSCC were extracted for selected genes from the Cancer Genome Atlas (TCGA) and used for Chi-square and Kaplan-Meier analysis. Results The threshold for sufficient number of reads was attained in 104 (93.7%) cases. Although the specific number of PCR amplified reads detected decreased, the number of NGS-annotated mutations did not significantly change with increased tissue preservation time. In HPV-negative carcinomas, mutations were detected mainly in TP53 (73.3%), FAT1 (26.7%) and FLG (16.7%) whereas in HPV-positive, the common mutations were in FLG (24.3%) FAT1 (17%) and FGFR3 (14.6%) genes. Other less common pathogenic mutations, including well reported SNPs were reproducibly identified. Presence of at least one cancer-specific mutations was found to be positively associated with an extensive desmoplastic stroma (p=0.019), and an aggressive type of invasive front (p=0.035), and negatively associated with the degree of differentiation (p=0.041). Analysis of TCGA data corroborated the association between cancer-specific mutations and tumour differentiation and survival analysis showed that tumours with at least one mutation had shorter disease-free and overall survival (p=0.005). Conclusions A custom made targeted NGS panel could reliably detect several specific mutations in archival samples of HNSCCs preserved up to 17 years. Using this method novel associations between mutational burden and clinical and pathological parameters were detected and actionable mutations in HPV-positive HNSCC were discovered.
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Affiliation(s)
- Harsh N Dongre
- Department of Pathology, Haukeland University Hospital, Bergen, Norway.,Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway.,Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hilde Haave
- Department of Otolaryngology/Head and Neck Surgery, Haukeland University Hospital, Bergen, Norway.,Otolaryngology, Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Siren Fromreide
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway.,Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Fredrik A Erland
- Department of Otolaryngology/Head and Neck Surgery, Haukeland University Hospital, Bergen, Norway.,Otolaryngology, Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Svein Erik Emblem Moe
- Department of Otolaryngology/Head and Neck Surgery, Haukeland University Hospital, Bergen, Norway.,Otolaryngology, Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | | | | | - Dipak Sapkota
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Daniela Elena Costea
- Department of Pathology, Haukeland University Hospital, Bergen, Norway.,Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway.,Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans Jorgen Aarstad
- Department of Otolaryngology/Head and Neck Surgery, Haukeland University Hospital, Bergen, Norway.,Otolaryngology, Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Olav K Vintermyr
- Department of Pathology, Haukeland University Hospital, Bergen, Norway.,Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
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8
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Yao H, Liang Q, Qian X, Wang J, Sham PC, Li MJ. Methods and resources to access mutation-dependent effects on cancer drug treatment. Brief Bioinform 2020; 21:1886-1903. [PMID: 31750520 DOI: 10.1093/bib/bbz109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/13/2022] Open
Abstract
In clinical cancer treatment, genomic alterations would often affect the response of patients to anticancer drugs. Studies have shown that molecular features of tumors could be biomarkers predictive of sensitivity or resistance to anticancer agents, but the identification of actionable mutations are often constrained by the incomplete understanding of cancer genomes. Recent progresses of next-generation sequencing technology greatly facilitate the extensive molecular characterization of tumors and promote precision medicine in cancers. More and more clinical studies, cancer cell lines studies, CRISPR screening studies as well as patient-derived model studies were performed to identify potential actionable mutations predictive of drug response, which provide rich resources of molecularly and pharmacologically profiled cancer samples at different levels. Such abundance of data also enables the development of various computational models and algorithms to solve the problem of drug sensitivity prediction, biomarker identification and in silico drug prioritization by the integration of multiomics data. Here, we review the recent development of methods and resources that identifies mutation-dependent effects for cancer treatment in clinical studies, functional genomics studies and computational studies and discuss the remaining gaps and future directions in this area.
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Affiliation(s)
- Hongcheng Yao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Qian Liang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xinyi Qian
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Junwen Wang
- Department of Health Sciences Research & Center for Individualized Medicine, Mayo Clinic, Scottsdale, USA
| | - Pak Chung Sham
- Center for Genomic Sciences, The University of Hong Kong, Hong Kong SAR, China.,Departments of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mulin Jun Li
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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9
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Hirotsu Y, Yokoyama H, Amemiya K, Hagimoto T, Hosaka K, Oyama T, Mochizuki H, Omata M. Genomic Profiling Identified ERCC2 E606Q Mutation in Helicase Domain Respond to Platinum-Based Neoadjuvant Therapy in Urothelial Bladder Cancer. Front Oncol 2020; 10:1643. [PMID: 32984035 PMCID: PMC7480179 DOI: 10.3389/fonc.2020.01643] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/27/2020] [Indexed: 11/13/2022] Open
Abstract
Genomic profiling of tumors enables therapeutic decisions, and identifying drug-matched mutations will prolong survival and prognosis. Here, we generated a custom panel for detecting genetic alterations in 19 patients with urothelial bladder cancer. This panel targeted 71 genes associated with urological cancer. Targeted sequencing was performed on formalin-fixed paraffin-embedded tumor tissues. Paired patient-matched tumor and blood samples were subjected to this analysis. A total of 142 somatic mutations were detected in 19 tumor tissues. At least one non-synonymous mutation was detected in all tumor tissues, and KDM6A, KMT2D, TP53, KMT2C, PIK3CA, and ERCC2 were recurrently mutated. Chromatin remodeling and epigenetic modifier genes are frequently mutated. Of 142 mutations, 69 mutations (49%) were annotated to have oncogenic potential. Furthermore, 74% of patients were expected to receive targeted therapy due to drug-matched mutations being identified in their tumors. Among this cohort, a patient harbored an ERCC2 helicase domain mutation and would be expected to respond to platinum-based therapy. As expected, the patient received carboplatin-containing neoadjuvant therapy with a remarkable response. Furthermore, tumor-derived mutations in urine were rapidly decreased after neoadjuvant therapy. These results suggested targeted sequencing could help to detect drug-matched somatic mutations and indicate single or combination therapy for cancer patients.
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Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Japan.,Department of Urology, Yamanashi Central Hospital, Kofu, Japan.,Department of Pathology, Yamanashi Central Hospital, Kofu, Japan.,Department of Gastroenterology, Yamanashi Central Hospital, Kofu, Japan.,The University of Tokyo, Bunkyo-ku, Japan
| | | | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Japan
| | | | - Kyoko Hosaka
- Department of Urology, Yamanashi Central Hospital, Kofu, Japan
| | - Toshio Oyama
- Department of Pathology, Yamanashi Central Hospital, Kofu, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Japan.,Department of Gastroenterology, Yamanashi Central Hospital, Kofu, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Japan.,Department of Gastroenterology, Yamanashi Central Hospital, Kofu, Japan.,The University of Tokyo, Bunkyo-ku, Japan
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10
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Jin S, Zhou C, Hou X, Fan Z, Zhao J, Ai X, Chu Y, Chen R, Guo R, Chen L. A multicenter real-world study of tumor-derived DNA from pleural effusion supernatant in genomic profiling of advanced lung cancer. Transl Lung Cancer Res 2020; 9:1507-1515. [PMID: 32953522 PMCID: PMC7481626 DOI: 10.21037/tlcr-20-882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background Pleural effusion (PE) is commonly observed in advanced lung cancer. Research has suggested that molecular profiling of PE could be used to detect tumor driver mutations, thus informing clinical decision-making. However, the performance of PE samples in a real-world setting has yet to be examined. Methods A total of 678 metastatic lung cancer patients with pleural effusion were enrolled in this study. Cohort 1 included 22 patients whose PE and matched plasma samples were simultaneously collected as a pilot study. Cohort 2 comprised 656 patients, from whom 734 samples were collected in a real world setting. These samples were subjected to targeted next-generation sequencing (NGS) of 1,021 cancer-related genes. Results PE supernatant was the preferred choice for genetic profiling. While the maximal somatic allele frequency (MSAF) of plasma in patients with M1a stage was significantly lower than that in patients with M1b/c stages (4.4%±9.6% vs. 9.0%±14.1%, P<0.01), the MSAF of PE supernatant was similar between M1a and M1b/c stages. PE supernatant demonstrated higher sensitivity than plasma in detecting actionable mutations in cohort 1 (81.8% vs. 45.5%, P=0.01) as well as in M1a disease (84.7% vs. 42.1%, P<0.01), but not in M1b/c disease, in cohort 2. Known resistant mutations were identified in 72 of the 117 patients who were resistant to first- or second-generation EGFR-TKIs, 22 of the 42 patients who were resistant to osimertinib, and 9 of the 13 patients who were resistant to crizotinib. Remarkably, PE supernatant outperformed plasma in identifying mutations that confer resistance to first- and second-generation EGFR-TKIs (75.4% vs. 29.8%, P<0.001). Conclusions This real-world large cohort study verified that PE supernatant had higher sensitivity than plasma for identifying actionable mutations, including resistance mutations. PE supernatant would be preferred by physicians for assessing tumor genomics in advanced lung cancer when tumor tissue is not available.
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Affiliation(s)
- Shidai Jin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chengzhi Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of the Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xue Hou
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zaiwen Fan
- Department of Medical Oncology, Air Force Medical Center, PLA, Beijing, China
| | - Jun Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing Cancer Hospital, Beijing, China
| | - Xinghao Ai
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | | | | | - Renhua Guo
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Likun Chen
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
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11
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Wang S, Chen R, Tang Y, Yu Y, Fang Y, Huang H, Wu D, Fang H, Bai Y, Sun C, Yu A, Fan Q, Gu D, Yi X, Li N. Comprehensive Genomic Profiling of Rare Tumors: Routes to Targeted Therapies. Front Oncol 2020; 10:536. [PMID: 32373528 PMCID: PMC7186305 DOI: 10.3389/fonc.2020.00536] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/25/2020] [Indexed: 01/24/2023] Open
Abstract
Comprehensive Genomic Profiling may be informative for novel treatment strategies and to improve outcomes for patients with rare tumors. This study aims to discover opportunities for use of targeted therapies already approved for routine use in patients with rare tumors. Solid tumors with an incidence lower than 2.5/100,000 per year was defined as rare tumors in China after comprehensive analysis based on epidemiological data and current availability of standardized treatment. Genomic data of rare tumors from the public database cBioPortal were compared with that of the Chinese population for targetable genomic alterations (TGAs). TGAs were defined as mutations of ALK, ATM, BRAF, BRCA1, BRCA2, CDKN2A, EGFR, ERBB2, FGFR1,2,3, KIT, MET, NF1, NTRK1,2,3, PIK3CA, PTEN, RET, and ROS1 with level 1 to 4 of evidence according to the OncoKB knowledge database. Genomic data of 4,901 patients covering 63 subtypes of rare tumor from cBioPortal were used as the western cohort. The Chinese cohort was comprised of next generation sequencing (NGS) data of 1,312 patients from across China covering 67 subtypes. Forty-one subtypes were common between the two cohorts. The accumulative prevalence of TGAs was 20.40% (1000/4901) in cBioPortal cohort, and 53.43% (701/1312) in Chinese cohort (p < 0.001). Among those 41 overlapping subtypes, it was still significantly higher in Chinese cohort compared with cBioPortal cohort (54.1%% vs. 26.1%, p < 0.001). Generally, targetable mutations in BRAF, BRCA2, CDKN2A, EGFR, ERBB2, KIT, MET, NF1, ROS1 were ≥3 times more frequent in Chinese cohort compared with that of the cBioPortal cohort. Cancer of unknown primary tumor type, gastrointestinal stromal tumor, gallbladder cancer, intrahepatic cholangiocarcinoma, and sarcomatoid carcinoma of the lung were the top 5 tumor types with the highest number of TGAs per tumor. The incidence of TGAs in rare tumors was substantial worldwide and was even higher in our Chinese rare tumor population. Comprehensive genomic profiling may offer novel treatment paradigms to address the limited options for patients with rare tumors.
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Affiliation(s)
- Shuhang Wang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rongrong Chen
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Yu Tang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Yu
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Fang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huiyao Huang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dawei Wu
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong Fang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Bai
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Sun
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Anqi Yu
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Fan
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dejian Gu
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Xin Yi
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Ning Li
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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12
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Yang HT, Shah RH, Tegay D, Onel K. Precision oncology: lessons learned and challenges for the future. Cancer Manag Res 2019; 11:7525-7536. [PMID: 31616176 PMCID: PMC6698584 DOI: 10.2147/cmar.s201326] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
The decreasing cost of and increasing capacity of DNA sequencing has led to vastly increased opportunities for population-level genomic studies to discover novel genomic alterations associated with both Mendelian and complex phenotypes. To translate genomic findings clinically, a number of health care institutions have worked collaboratively or individually to initiate precision medicine programs. These precision medicine programs involve designing patient enrollment systems, tracking electronic health records, building biobank repositories, and returning results with actionable matched therapies. As cancer is a paradigm for genetic diseases and new therapies are increasingly tailored to attack genetic susceptibilities in tumors, these precision medicine programs are largely driven by the urgent need to perform genetic profiling on cancer patients in real time. Here, we review the current landscape of precision oncology and highlight challenges to be overcome and examples of benefits to patients. Furthermore, we make suggestions to optimize future precision oncology programs based upon the lessons learned from these "first generation" early adopters.
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Affiliation(s)
- Hsih-Te Yang
- Medical Genetics and Human Genomics, Department of Pediatrics, Northwell Health, New York, NY, USA
| | - Ronak H Shah
- Medical Genetics and Human Genomics, Department of Pediatrics, Northwell Health, New York, NY, USA
- Center for Research Informatics and Innovation, The Feinstein Institute for Medical Research, Northwell Health, New York, NY, USA
| | - David Tegay
- Medical Genetics and Human Genomics, Department of Pediatrics, Northwell Health, New York, NY, USA
| | - Kenan Onel
- The Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
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13
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Abstract
In oncology, actionable mutations (alterations) in cancer-associated genes are critical in terms of the selection of therapeutic approaches. Next-generation sequencing of tumor sample DNA (ie, clinical sequencing) can guide clinical management by providing diagnostic or prognostic data, and facilitating the identification of potential treatment regimens, such as molecular-targeted and immune checkpoint blockade therapies. In the USA, a variety of tumor-profiling multiplex gene panels have been developed and implemented for this purpose. In Japan, several academic institutions have now carried out detailed investigations of the feasibility and value of clinical sequencing, and cancer societies have issued consensus clinical practice guidance for next-generation sequencing-based gene panel tests. These efforts will facilitate the implementation of cancer genome medicine in Japan.
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Affiliation(s)
- Takashi Kohno
- Division of Genome BiologyNational Cancer Center Research InstituteTokyoJapan
- Division of Translational GenomicsExploratory Oncology Research and Clinical Trial CenterNational Cancer CenterTokyoJapan
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14
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Liu L, Liu H, Shao D, Liu Z, Wang J, Deng Q, Tang H, Yang H, Zhang Y, Qiu Y, Cui F, Tan M, Zhang P, Li Z, Liu J, Liang W, Wang Y, Peng Z, Wang J, Yang H, Mao M, Kristiansen K, Ye M, He J. Development and clinical validation of a circulating tumor DNA test for the identification of clinically actionable mutations in nonsmall cell lung cancer. Genes Chromosomes Cancer 2018; 57:211-220. [PMID: 29277949 DOI: 10.1002/gcc.22522] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 12/31/2022] Open
Abstract
Molecular analysis of potentially actionable mutations has become routine practice in oncological pathology. However, testing a wide range of oncogenes and mutations can be technically challenging because of limitations associated with tumor biopsy. Circulating tumor DNA (ctDNA) is a potential tool for the noninvasive profiling of tumors. In this study, we developed a next-generation sequencing (NGS)-based test for the detection of clinically relevant mutations in ctDNA and evaluated the feasibility of using this ctDNA NGS-based assay as an alternative to tissue genotyping. Tissue and matched blood samples were obtained from 72 patients with advanced nonsmall cell lung cancer (NSCLC). NGS-based testing was performed using plasma cell-free DNA (cfDNA) samples of all 72 patients as well as tumor DNA samples of 46 patients. Of the remaining 26 patients, tDNA was tested by amplification refractory mutation system PCR (ARMS-PCR) because of insufficient tissue sample or quality for NGS. Of the 46 patients who had tDNA and cfDNA NGS performed, we found 20 patients were concordant between tDNA and ctDNA alterations and 21 sample pairs were discordant because of additional alterations found in tDNA. Considering all clinically relevant alterations, the concordance rate between tDNA and ctDNA alterations was 54.9% with a sensitivity of 53.2% and a specificity of 75.0%. Our findings demonstrate that targeted NGS using cfDNA is a feasible approach for rapid and accurate identification of actionable mutations in patients with advanced NSCLC, and may provide a safe and robust alternative approach to tissue biopsy.
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Affiliation(s)
- Liping Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China.,The Translational Medicine Laboratory, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Han Liu
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Di Shao
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, DK 2200, Denmark
| | - Zu Liu
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Jingjing Wang
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Qiuhua Deng
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China.,The Translational Medicine Laboratory, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Hailing Tang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China.,The Translational Medicine Laboratory, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Haihong Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Yalei Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Yuan Qiu
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Fei Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Meihua Tan
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Pan Zhang
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Zhilong Li
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Jilong Liu
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China
| | - Wenhua Liang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Yuying Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Mao Mao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, DK 2200, Denmark.,BGI-Shenzhen, Shenzhen, 518083, China
| | - Mingzhi Ye
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, 510006, China.,BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, DK 2200, Denmark
| | - Jianxing He
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Disease, Guangzhou, 510120, China.,Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
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15
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Dhakal P, Gundabolu K, Amador C, Rayamajhi S, Bhatt VR. Atypical chronic myeloid leukemia: a rare entity with management challenges. Future Oncol 2017; 14:177-185. [PMID: 29226717 DOI: 10.2217/fon-2017-0334] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The aim of our study was to review the clinicopathologic features and management of atypical chronic myeloid leukemia (aCML). Relevant manuscripts published in English were searched using PubMed. aCML is diagnosed as per WHO 2016 classification in the presence of leukocytosis ≥13 × 109/l with circulating neutrophil precursors ≥10%, monocytes less than 10%, minimal basophils, hypercellular bone marrow with granulocytic proliferation and dysplasia, bone marrow blast less than 20% and absence of BCR/ABL fusion gene. Common cytogenetic features and mutations include trisomy 8, and mutations in SETBP1 and ETNK1. Median survival is 1-2 years. Hematopoietic stem cell transplant may be the only curative option. Ruxolitinib and dasatinib are emerging therapeutic options. Thus, aCML is a rare entity with poor survival. Novel therapies are needed.
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Affiliation(s)
- Prajwal Dhakal
- Department of Medicine, Michigan State University, 788 Service Rd, East Lansing, MI 48824, USA
| | - Krishna Gundabolu
- Department of Internal Medicine, Division of Hematology & Oncology, University of Nebraska Medical Center, NE 68198, USA
| | - Catalina Amador
- Department of Pathology & Microbiology, University of Nebraska Medical Center, NE 68198, USA
| | - Supratik Rayamajhi
- Department of Medicine, Michigan State University, 788 Service Rd, East Lansing, MI 48824, USA
| | - Vijaya Raj Bhatt
- Department of Internal Medicine, Division of Hematology & Oncology, University of Nebraska Medical Center, NE 68198, USA
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Kou T, Kanai M, Matsumoto S, Okuno Y, Muto M. The possibility of clinical sequencing in the management of cancer. Jpn J Clin Oncol 2016; 46:399-406. [PMID: 26917600 DOI: 10.1093/jjco/hyw018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 01/31/2016] [Indexed: 02/07/2023] Open
Abstract
Comprehensive genomic profiling using next-generation sequencing technologies provides insights into understanding the genomic architecture of human cancer. This new understanding of the cancer genome allows us to identify many more genomic alterations occurring within tumors than before, some of which could be potential therapeutic targets through molecular targeted agents. Currently, a large number of molecular targeted agents are being developed, and consequently, cancer treatment is rapidly shifting from empiric therapy employing cytotoxic anticancer drugs to genotype-directed therapy using molecular targeted agents. In current daily clinical practice, hotspot-based single-gene assays that detect RAS mutations in colorectal cancer or EGFR mutations in non-small cell lung cancer are widely used to identify variants. However, it is becoming evident that more comprehensive genomic analysis is crucial in identifying the patient population that may benefit from molecular targeted therapy and the accelerated development of novel drugs for early clinical trials. For these purposes, an increasing number of gene panel-based targeted sequencing is commercially available in clinical practice from sequencing companies. Despite several challenges in implementing this approach, comprehensive genomic profiling and identification of actionable mutations is likely to become one of the standard options in the management of cancer in the near future. The use of clinical sequencing has the potential to usher a new era in precision medicine for cancer diagnosis and treatment. In this review, we discuss the application of comprehensive genomic profiling using next-generation sequencing technologies in clinical oncology and address the current challenges for its implementation.
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Affiliation(s)
- Tadayuki Kou
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto Department of Clinical Oncology, Kyoto University Hospital Cancer Center, Kyoto
| | - Masashi Kanai
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto Department of Clinical Oncology, Kyoto University Hospital Cancer Center, Kyoto
| | - Shigemi Matsumoto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto Department of Clinical Oncology, Kyoto University Hospital Cancer Center, Kyoto
| | - Yasushi Okuno
- Department of Clinical System Onco-Informatics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Muto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto Department of Clinical Oncology, Kyoto University Hospital Cancer Center, Kyoto
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