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Sun Y, Zhang X, Yang X, Ma J. Clinical Utility of Circulating Tumor DNA for Detecting Lung Cancer Mutations by Targeted Next-Generation Sequencing With Insufficient Tumor Samples. J Clin Lab Anal 2024:e25099. [PMID: 39315762 DOI: 10.1002/jcla.25099] [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: 02/14/2024] [Revised: 08/07/2024] [Accepted: 08/28/2024] [Indexed: 09/25/2024] Open
Abstract
BACKGROUND Circulating tumor deoxyribonucleic acid (ctDNA) is increasingly applied in clinical practice. This study aimed to explore clinical utility of a minimal invasive and sensitive way of ctDNA for next-generation sequencing in non-small cell lung cancer (NSCLC) with inadequate tumor samples. METHODS Targeted DNA sequencing was performed on tissue biopsies and matched plasma samples from 60 patients with NSCLC. RESULTS A total of 13 driving genes were detected in 60 matched tissue DNA (tDNA) and ctDNA samples. Overall concordance rate was 75.47%, with 77.55% sensitivity and 50% specificity. Epidermal growth factor receptor (EGFR) mutations were the most common in both tDNA and ctDNA samples. Among other mutated genes were tumor protein p53 (TP53), erb-b2 receptor tyrosine kinase 2 (ERBB2), anaplastic lymphoma kinase (ALK), cyclin-dependent kinase inhibitor 2A (CDKN2A), ros proto-oncogene 1, and receptor tyrosine kinase (ROS1). Mutations in b-raf proto-oncogene, serine/threonine kinase (BRAF), cluster of differentiation 274 (CD274), neurotrophin receptor tyrosine kinase 1 (NTRK1), and rearranged during transfection (RET) occurred only in plasma. The majority of mutations in both samples were single-nucleotide variants. Deletions were found in EGFR, BRAF, and TP53 in ctDNA, whereas in tDNA, deletions were only found in EGFR. In ALK, single nucleic acid-site amplification occurred simultaneously in tissue and plasma, but insertions and copy number variations were detected only in plasma. CONCLUSIONS Identifying ctDNA mutations by targeted sequencing in plasma is feasible, showing the clinical value of ctDNA-targeted sequencing in NSCLC patients when tumor tissue sampling is insufficient or even impossible.
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Affiliation(s)
- Yi Sun
- Pediatric, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Xu Zhang
- Department of Molecular Diagnostics, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong Province, China
| | - Xinhua Yang
- Department of Molecular Diagnostics, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong Province, China
| | - Jiangjun Ma
- Department of Molecular Diagnostics, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong Province, China
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2
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Chen X, Jia Y, Ren S, Chen S, Wang X, Gao X, Wang C, Adam FEA, Wang X, Yang Z. Identification of Newcastle disease virus P-gene editing using next-generation sequencing. J Vet Med Sci 2020; 82:1231-1235. [PMID: 32624548 PMCID: PMC7468068 DOI: 10.1292/jvms.18-0707] [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] [Indexed: 12/13/2022] Open
Abstract
Avian paramyxoviruses 1 has the ability to edit its P gene to generate three
amino-coterminal proteins (P, V and W), but its kinetic change is unclear. In this study,
next-generation sequencing (NGS) was used to analyze the P-gene editing of Newcastle
disease virus (NDV). Transcriptome analysis of chicken embryonic tissues and bursa of
fabricius showed the P-gene editing frequencies were 45.46–52.70%. To investigate the
rules of P-gene editing along time, the ratio of PVW was determined by PCR based deep
sequencing at multiple time points in cells infected with velogenic and lentogenic strain
respectively. The results confirmed similar editing frequencies with transcriptome data
and the PVW ratios were stable along time among different NDVs, but had a greater V-gene
transcript on velogenic strain infection (P<0.001), which were
different from previous reports. Also, it was shown that the number of inserted G residues
in P-derived transcripts was not limited to +9G, and +10G transcripts were identified.
These results confirmed the NDV P-gene editing frequencies and provided a novel point of
view on NDV P-gene editing with NDV virulence.
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Affiliation(s)
- Xi Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Yanqing Jia
- Department of Animal Engineering, Yangling Vocational & Technical College, Yangling, Shaanxi Province 712100, P.R. China
| | - Shanhui Ren
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Siqi Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Xiangwei Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Xiaolong Gao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Chongyang Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Fathalrhman E A Adam
- Department of Preventive Medicine and Public Health, Faculty of Veterinary Science, University of Nyala, P.O. Box: 155 Nyala, Sudan
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
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3
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Mateo J, Seed G, Bertan C, Rescigno P, Dolling D, Figueiredo I, Miranda S, Nava Rodrigues D, Gurel B, Clarke M, Atkin M, Chandler R, Messina C, Sumanasuriya S, Bianchini D, Barrero M, Petermolo A, Zafeiriou Z, Fontes M, Perez-Lopez R, Tunariu N, Fulton B, Jones R, McGovern U, Ralph C, Varughese M, Parikh O, Jain S, Elliott T, Sandhu S, Porta N, Hall E, Yuan W, Carreira S, de Bono JS. Genomics of lethal prostate cancer at diagnosis and castration resistance. J Clin Invest 2020; 130:1743-1751. [PMID: 31874108 PMCID: PMC7108902 DOI: 10.1172/jci132031] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
The genomics of primary prostate cancer differ from those of metastatic castration-resistant prostate cancer (mCRPC). We studied genomic aberrations in primary prostate cancer biopsies from patients who developed mCRPC, also studying matching, same-patient, diagnostic, and mCRPC biopsies following treatment. We profiled 470 treatment-naive prostate cancer diagnostic biopsies and, for 61 cases, mCRPC biopsies, using targeted and low-pass whole-genome sequencing (n = 52). Descriptive statistics were used to summarize mutation and copy number profile. Prevalence was compared using Fisher's exact test. Survival correlations were studied using log-rank test. TP53 (27%) and PTEN (12%) and DDR gene defects (BRCA2 7%; CDK12 5%; ATM 4%) were commonly detected. TP53, BRCA2, and CDK12 mutations were markedly more common than described in the TCGA cohort. Patients with RB1 loss in the primary tumor had a worse prognosis. Among 61 men with matched hormone-naive and mCRPC biopsies, differences were identified in AR, TP53, RB1, and PI3K/AKT mutational status between same-patient samples. In conclusion, the genomics of diagnostic prostatic biopsies acquired from men who develop mCRPC differ from those of the nonlethal primary prostatic cancers. RB1/TP53/AR aberrations are enriched in later stages, but the prevalence of DDR defects in diagnostic samples is similar to mCRPC.
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Affiliation(s)
- Joaquin Mateo
- Vall d’Hebron Institute of Oncology (VHIO) and Vall d’Hebron University Hospital, Barcelona, Spain
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - George Seed
- The Institute of Cancer Research, London, United Kingdom
| | - Claudia Bertan
- The Institute of Cancer Research, London, United Kingdom
| | - Pasquale Rescigno
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - David Dolling
- The Institute of Cancer Research, London, United Kingdom
| | | | - Susana Miranda
- The Institute of Cancer Research, London, United Kingdom
| | | | - Bora Gurel
- The Institute of Cancer Research, London, United Kingdom
| | - Matthew Clarke
- The Institute of Cancer Research, London, United Kingdom
| | - Mark Atkin
- The Institute of Cancer Research, London, United Kingdom
| | - Rob Chandler
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Carlo Messina
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Semini Sumanasuriya
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Diletta Bianchini
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Maialen Barrero
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Antonella Petermolo
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Zafeiris Zafeiriou
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Mariane Fontes
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
- Instituto Oncoclinicas-Grupo Oncoclinicas, Rio de Janeiro, Brazil
| | - Raquel Perez-Lopez
- Vall d’Hebron Institute of Oncology (VHIO) and Vall d’Hebron University Hospital, Barcelona, Spain
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Nina Tunariu
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Ben Fulton
- The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Robert Jones
- The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | | | - Christy Ralph
- St James’s University Hospital, Leeds, United Kingdom
| | | | - Omi Parikh
- Royal Blackburn Hospital, Blackburn, United Kingdom
| | - Suneil Jain
- Belfast City Hospital, Belfast, United Kingdom
| | - Tony Elliott
- The Christie Hospital, Manchester, United Kingdom
| | | | - Nuria Porta
- The Institute of Cancer Research, London, United Kingdom
| | - Emma Hall
- The Institute of Cancer Research, London, United Kingdom
| | - Wei Yuan
- The Institute of Cancer Research, London, United Kingdom
| | | | - Johann S. de Bono
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
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Analytical Evaluation of an NGS Testing Method for Routine Molecular Diagnostics on Melanoma Formalin-Fixed, Paraffin-Embedded Tumor-Derived DNA. Diagnostics (Basel) 2019; 9:diagnostics9030117. [PMID: 31547467 PMCID: PMC6787639 DOI: 10.3390/diagnostics9030117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Next Generation Sequencing (NGS) is a promising tool for the improvement of tumor molecular profiling in view of the identification of a personalized treatment in oncologic patients. To verify the potentiality of a targeted NGS (Ion AmpliSeq™ Cancer Hotspot Panel v2), selected melanoma samples (n = 21) were retrospectively analyzed on S5 platform in order to compare NGS performance with the conventional techniques adopted in our routine clinical setting (Sequenom MassARRAY system, Sanger sequencing, allele-specific real-time PCR). The capability in the identification of rare and low-frequency mutations in the main genes involved in melanoma (BRAF and NRAS genes) was verified and integrated with the results deriving from other oncogenes and tumor suppressor genes. The analytical evaluation was carried out by the analysis of DNA derived from control cell lines and FFPE (Formalin-Fixed, Paraffin-Embedded) samples to verify that the achieved resolution of uncommon mutations and low-frequency variants was suitable to meet the technical and clinical requests. Our results demonstrate that the amplicon-based NGS approach can reach the sensitivity proper of the allele-specific assays together with the high specificity of a sequencing method. An overall concordance among the tested methods was observed in the identification of classical and uncommon mutations. The assessment of the quality parameters and the comparison with the orthogonal methods suggest that the NGS method could be implemented in the clinical setting for melanoma molecular characterization.
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Muluhngwi P, Valdes Jr R, Fernandez-Botran R, Burton E, Williams B, Linder MW. Cell-free DNA diagnostics: current and emerging applications in oncology. Pharmacogenomics 2019; 20:357-380. [DOI: 10.2217/pgs-2018-0174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Liquid biopsy is a noninvasive dynamic approach for monitoring disease over time. It offers advantages including limited risks of blood sampling, opportunity for more frequent sampling, lower costs and theoretically non-biased sampling compared with tissue biopsy. There is a high degree of concordance between circulating tumor DNA mutations versus primary tumor mutations. Remote sampling of circulating tumor DNA can serve as viable option in clinical diagnostics. Here, we discuss the progress toward broad adoption of liquid biopsy as a diagnostic tool and discuss knowledge gaps that remain to be addressed.
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Affiliation(s)
- Penn Muluhngwi
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Roland Valdes Jr
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Rafael Fernandez-Botran
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Eric Burton
- Department of Neurology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Brian Williams
- Department of Neurosurgery, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Mark W Linder
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
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6
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Sundar R, Miranda S, Rodrigues DN, Chénard-Poirier M, Dolling D, Clarke M, Figueiredo I, Bertan C, Yuan W, Ferreira A, Chistova R, Boysen G, Perez DR, Tunariu N, Mateo J, Wotherspoon A, Chau I, Cunningham D, Valeri N, Carreira S, de Bono J. Ataxia Telangiectasia Mutated Protein Loss and Benefit From Oxaliplatin-based Chemotherapy in Colorectal Cancer. Clin Colorectal Cancer 2018; 17:280-284. [PMID: 30042009 DOI: 10.1016/j.clcc.2018.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/15/2018] [Accepted: 05/31/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Loss of ataxia telangiectasia mutated (ATM), a key protein regulating DNA repair signaling, has been suggested to increase sensitivity to DNA damaging agents. We conducted a study analyzing the loss of ATM protein expression in colorectal cancer and correlated this with clinical outcomes. MATERIALS AND METHODS The clinical outcomes data and tumor samples from metastatic colorectal cancer patients referred to the Royal Marsden Hospital Drug Development Unit (United Kingdom) from 2012 to 2016 and providing consent for a molecular characterization study were analyzed. Immunohistochemistry (IHC) slides were assessed by a pathologist for nuclear staining intensity of ATM and semiquantitatively scored. ATM loss was defined as a nuclear H-score of ≤ 10. RESULTS Of 223 colorectal cancer samples, ATM IHC loss was identified in 17 (8%). ATM loss was independent of the RAS and RAF mutational status. ATM loss was associated with superior overall survival after first-line oxaliplatin-based therapy (49 vs. 32 months; hazard ratio [HR], 2.52) but not with irinotecan-based therapy (24 vs. 33 months; HR, 0.72). ATM loss was not prognostic for survival from the diagnosis (50 vs. 44 months; HR, 1.43). CONCLUSION ATM could be considered a biomarker for the development of novel DNA repair targeting agents and treatment of colorectal cancer.
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Affiliation(s)
- Raghav Sundar
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Trust, London, UK; Department of Haematology-Oncology, National University Health System, Singapore
| | | | | | | | | | | | | | | | - Wei Yuan
- The Institute of Cancer Research, London, UK
| | | | | | | | | | - Nina Tunariu
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Trust, London, UK
| | | | | | - Ian Chau
- The Royal Marsden NHS Trust, London, UK
| | | | | | | | - Johann de Bono
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Trust, London, UK.
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7
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O'Carrigan B, Lim JSJ, Jalil A, Harris SJ, Papadatos-Pastos D, Banerji U, Lopez J, de Bono JS, Yap TA. Target-based therapeutic matching of phase I trials in patients with metastatic breast cancer in a tertiary referral centre. Br J Cancer 2018; 119:922-927. [PMID: 30318518 PMCID: PMC6203714 DOI: 10.1038/s41416-018-0290-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/07/2018] [Accepted: 09/17/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Greater understanding of the molecular classification of breast cancer has permitted the development of rational drug design strategies. In a phase I clinical trial setting, molecular profiling with next-generation sequencing of individual tumour samples has been employed to guide treatment. METHODS We conducted a retrospective evaluation of clinical outcomes of patients with metastatic breast cancer (MBC) treated in phase I clinical trials at our institution to assess the benefit of molecularly matched compared to non-matched treatments. RESULTS A total of 97 consecutive patients with MBC were enrolled onto ≥1 trial between 2009 and 2015. Fourteen patients participated in multiple trials, and a total of 113 trial encounters were reviewed in this retrospective study. Eighty-three percent of patients with molecular data available were able to participate in trials matched to molecular aberrations. Patients who were treated on matched studies had improved clinical benefit (RR: 1.80, p = 0.005), progression-free (HR: 0.52, p = 0.003) and overall survival (HR: 0.54, p < 0.001). Treatment was well tolerated with low rates of treatment discontinuation for toxicity (8% overall) that did not differ between groups. No toxicity-related deaths were observed. CONCLUSIONS Molecular profiling for MBC patients in a phase I setting is feasible and aids therapeutic decisions with improved patient outcomes.
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Affiliation(s)
| | - Joline Si Jing Lim
- Drug Development Unit, Royal Marsden Hospital, London, UK
- National University Cancer Institute of Singapore, Singapore, Singapore
| | - Awais Jalil
- Drug Development Unit, Royal Marsden Hospital, London, UK
| | | | | | - Udai Banerji
- Drug Development Unit, Royal Marsden Hospital, London, UK
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Juanita Lopez
- Drug Development Unit, Royal Marsden Hospital, London, UK
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Johann Sebastian de Bono
- Drug Development Unit, Royal Marsden Hospital, London, UK
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Timothy Anthony Yap
- Drug Development Unit, Royal Marsden Hospital, London, UK.
- Division of Clinical Studies, The Institute of Cancer Research, London, UK.
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8
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Roy S, Coldren C, Karunamurthy A, Kip NS, Klee EW, Lincoln SE, Leon A, Pullambhatla M, Temple-Smolkin RL, Voelkerding KV, Wang C, Carter AB. Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines. J Mol Diagn 2018; 20:4-27. [DOI: 10.1016/j.jmoldx.2017.11.003] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Accepted: 11/06/2017] [Indexed: 12/17/2022] Open
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9
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Ibarrola-Villava M, Fleitas T, Llorca-Cardeñosa MJ, Mongort C, Alonso E, Navarro S, Burgues O, Vivancos A, Cejalvo JM, Perez-Fidalgo JA, Roselló S, Ribas G, Cervantes A. Determination of somatic oncogenic mutations linked to target-based therapies using MassARRAY technology. Oncotarget 2017; 7:22543-55. [PMID: 26968814 PMCID: PMC5008380 DOI: 10.18632/oncotarget.8002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/24/2016] [Indexed: 12/21/2022] Open
Abstract
Somatic mutation analysis represents a useful tool in selecting personalized therapy. The aim of our study was to determine the presence of common genetic events affecting actionable oncogenes using a MassARRAY technology in patients with advanced solid tumors who were potential candidates for target-based therapies. The analysis of 238 mutations across 19 oncogenes was performed in 197 formalin-fixed paraffin-embedded samples of different tumors using the OncoCarta Panel v1.0 (Sequenom Hamburg, Germany). Of the 197 specimens, 97 (49.2%) presented at least one mutation. Forty-nine different oncogenic mutations in 16 genes were detected. Mutations in KRAS and PIK3CA were detected in 40/97 (41.2%) and 30/97 (30.9%) patients respectively. Thirty-one patients (32.0%) had mutations in two genes, 20 of them (64.5%) initially diagnosed with colorectal cancer. The co-occurrence of mutation involved mainly KRAS, PIK3CA, KIT and RET. Mutation profiles were validated using a customized panel and the Junior Next-Generation Sequencing technology (GS-Junior 454, Roche). Twenty-eight patients participated in early clinical trials or received specific treatments according to the molecular characterization (28.0%). MassARRAY technology is a rapid and effective method for identifying key cancer-driving mutations across a large number of samples, which allows for a more appropriate selection for personalized therapies.
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Affiliation(s)
- Maider Ibarrola-Villava
- Hematology and Medical Oncology Unit, Biomedical Research Institute INCLIVA, Valencia, Spain
| | - Tania Fleitas
- Hematology and Medical Oncology Unit, Biomedical Research Institute INCLIVA, Valencia, Spain
| | | | - Cristina Mongort
- Department of Pathology, Biomedical Research Institute INCLIVA, Valencia, Spain
| | - Elisa Alonso
- Department of Pathology, Biomedical Research Institute INCLIVA, Valencia, Spain
| | - Samuel Navarro
- Department of Pathology, Biomedical Research Institute INCLIVA, Valencia, Spain
| | - Octavio Burgues
- Department of Pathology, Biomedical Research Institute INCLIVA, Valencia, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Juan Miguel Cejalvo
- Hematology and Medical Oncology Unit, Biomedical Research Institute INCLIVA, Valencia, Spain
| | | | - Susana Roselló
- Hematology and Medical Oncology Unit, Clinic University Hospital of Valencia, Valencia, Spain
| | - Gloria Ribas
- Hematology and Medical Oncology Unit, Biomedical Research Institute INCLIVA, Valencia, Spain
| | - Andrés Cervantes
- Hematology and Medical Oncology Unit, Biomedical Research Institute INCLIVA, Valencia, Spain.,Department of Medicine, University of Valencia, Valencia, Spain
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10
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Seed G, Yuan W, Mateo J, Carreira S, Bertan C, Lambros M, Boysen G, Ferraldeschi R, Miranda S, Figueiredo I, Riisnaes R, Crespo M, Rodrigues DN, Talevich E, Robinson DR, Kunju LP, Wu YM, Lonigro R, Sandhu S, Chinnaiyan AM, de Bono JS. Gene Copy Number Estimation from Targeted Next-Generation Sequencing of Prostate Cancer Biopsies: Analytic Validation and Clinical Qualification. Clin Cancer Res 2017; 23:6070-6077. [PMID: 28751446 DOI: 10.1158/1078-0432.ccr-17-0972] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/01/2017] [Accepted: 07/19/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Precise detection of copy number aberrations (CNA) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next-generation sequencing (NGS) is inexpensive, high throughput, and easily feasible, allowing single-nucleotide variant calls, but CNA estimation from this remains challenging.Experimental Design: We evaluated CNVkit for CNA identification from amplicon-based targeted NGS in a cohort of 110 fresh castration-resistant prostate cancer biopsies and used capture-based whole-exome sequencing (WES), array comparative genomic hybridization (aCGH), and FISH to explore the viability of this approach.Results: We showed that this method produced highly reproducible CNA results (r = 0.92), with the use of pooled germline DNA as a coverage reference supporting precise CNA estimation. CNA estimates from targeted NGS were comparable with WES (r = 0.86) and aCGH (r = 0.7); for key selected genes (BRCA2, MYC, PIK3CA, PTEN, and RB1), CNA estimation correlated well with WES (r = 0.91) and aCGH (r = 0.84) results. The frequency of CNAs in our population was comparable with that previously described (i.e., deep deletions: BRCA2 4.5%; RB1 8.2%; PTEN 15.5%; amplification: AR 45.5%; gain: MYC 31.8%). We also showed, utilizing FISH, that CNA estimation can be impacted by intratumor heterogeneity and demonstrated that tumor microdissection allows NGS to provide more precise CNA estimates.Conclusions: Targeted NGS and CNVkit-based analyses provide a robust, precise, high-throughput, and cost-effective method for CNA estimation for the delivery of more precise patient care. Clin Cancer Res; 23(20); 6070-7. ©2017 AACR.
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Affiliation(s)
- George Seed
- The Institute of Cancer Research, London, United Kingdom
| | - Wei Yuan
- The Institute of Cancer Research, London, United Kingdom
| | - Joaquin Mateo
- The Institute of Cancer Research, London, United Kingdom
| | | | - Claudia Bertan
- The Institute of Cancer Research, London, United Kingdom
| | - Maryou Lambros
- The Institute of Cancer Research, London, United Kingdom
| | - Gunther Boysen
- The Institute of Cancer Research, London, United Kingdom
| | - Roberta Ferraldeschi
- The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Susana Miranda
- The Institute of Cancer Research, London, United Kingdom
| | | | - Ruth Riisnaes
- The Institute of Cancer Research, London, United Kingdom
| | - Mateus Crespo
- The Institute of Cancer Research, London, United Kingdom
| | | | - Eric Talevich
- University of California San Francisco, San Francisco, California
| | - Dan R Robinson
- Michigan Centre for Translational Pathology, Ann Arbor, Michigan
| | - Lakshmi P Kunju
- Michigan Centre for Translational Pathology, Ann Arbor, Michigan
| | - Yi-Mi Wu
- Michigan Centre for Translational Pathology, Ann Arbor, Michigan
| | - Robert Lonigro
- Michigan Centre for Translational Pathology, Ann Arbor, Michigan
| | | | | | - Johann S de Bono
- The Institute of Cancer Research, London, United Kingdom. .,The Royal Marsden NHS Foundation Trust, London, United Kingdom
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11
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The AURORA pilot study for molecular screening of patients with advanced breast cancer-a study of the breast international group. NPJ Breast Cancer 2017; 3:23. [PMID: 28685159 PMCID: PMC5491498 DOI: 10.1038/s41523-017-0026-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/04/2017] [Accepted: 06/01/2017] [Indexed: 12/24/2022] Open
Abstract
Several studies have demonstrated the feasibility of molecular screening of tumour samples for matching patients with cancer to targeted therapies. However, most of them have been carried out at institutional or national level. Herein, we report on the pilot phase of AURORA (NCT02102165), a European multinational collaborative molecular screening initiative for advanced breast cancer patients. Forty-one patients were prospectively enroled at four participating centres across Europe. Metastatic tumours were biopsied and profiled using an Ion Torrent sequencing platform at a central facility. Sequencing results were obtained for 63% of the patients in real-time with variable turnaround time stemming from delays between patient consent and biopsy. At least one clinically actionable mutation was identified in 73% of patients. We used the Illumina sequencing technology for orthogonal validation and achieved an average of 66% concordance of substitution calls per patient. Additionally, copy number aberrations inferred from the Ion Torrent sequencing were compared to single nucleotide polymorphism arrays and found to be 59% concordant on average. Although this study demonstrates that powerful next generation genomic techniques are logistically ready for international molecular screening programs in routine clinical settings, technical challenges remain to be addressed in order to ensure the accuracy and clinical utility of the genomic data. A pilot study demonstrated that a large-scale, international screening programme for women with metastatic breast cancer is feasible. The study, coordinated by the Institut Jules Bordet and the Breast International Group, aimed to determine whether biopsies and blood could be collected from women with metastatic breast cancer across Europe and sent to a central laboratory for targeted gene sequencing. Genetic information was successfully obtained for 26 of the 41 participants, 19 of whom had mutations that could be targeted with a known drug, potentially influencing treatment decision-making. They concluded that genomic testing is logistically ready for international molecular screening in routine clinical settings laying the groundwork for the parent European AURORA molecular screening programme which aims at recruiting 1300 metastatic breast cancer patients. However, technical challenges remain to be addressed to ensure the accuracy and robustness across different sequencing platforms.
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Chang YS, Huang HD, Yeh KT, Chang JG. Identification of novel mutations in endometrial cancer patients by whole-exome sequencing. Int J Oncol 2017; 50:1778-1784. [PMID: 28339086 DOI: 10.3892/ijo.2017.3919] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/07/2017] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to identify genomic alterations in Taiwanese endometrial cancer patients. This information is vitally important in Taiwan, where endometrial cancer is the second most common gynecological cancer. We performed whole-exome sequencing on DNA from 14 tumor tissue samples from Taiwanese endometrial cancer patients. We used the Genome Analysis Tool kit software package for data analysis, and the dbSNP, Catalogue of Somatic Mutations in Cancer (COSMIC) and The Cancer Genome Atlas (TCGA) databases for comparisons. Variants were validated via Sanger sequencing. We identified 143 non-synonymous mutations in 756 canonical cancer-related genes and 1,271 non-synonymous mutations in non-canonical cancer-related genes in 14 endometrial samples. PTEN, KRAS and PIK3R1 were the most frequently mutated canonical cancer-related genes. Our results revealed nine potential driver genes (MAPT, IL24, MCM6, TSC1, BIRC2, CIITA, DST, CASP8 and NOTCH2) and 21 potential passenger genes (ARMCX4, IGSF10, VPS13C, DCT, DNAH14, TLN1, ZNF605, ZSCAN29, MOCOS, CMYA5, PCDH17, UGT1A8, CYFIP2, MACF1, NUDT5, JAKMIP1, PCDHGB4, FAM178A, SNX6, IMP4 and PCMTD1). The detected molecular aberrations led to putative activation of the mTOR, Wnt, MAPK, VEGF and ErbB pathways, as well as aberrant DNA repair, cell cycle control and apoptosis pathways. We characterized the mutational landscape and genetic alterations in multiple cellular pathways of endometrial cancer in the Taiwanese population.
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Affiliation(s)
- Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
| | - Hsien-Da Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, R.O.C
| | - Kun-Tu Yeh
- Department of Pathology, Changhua Christian Hospital, Changhua 500, Taiwan, R.O.C
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
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Perakis S, Auer M, Belic J, Heitzer E. Advances in Circulating Tumor DNA Analysis. Adv Clin Chem 2017; 80:73-153. [PMID: 28431643 DOI: 10.1016/bs.acc.2016.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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Pécuchet N, Rozenholc Y, Zonta E, Pietrasz D, Didelot A, Combe P, Gibault L, Bachet JB, Taly V, Fabre E, Blons H, Laurent-Puig P. Analysis of Base-Position Error Rate of Next-Generation Sequencing to Detect Tumor Mutations in Circulating DNA. Clin Chem 2016; 62:1492-1503. [DOI: 10.1373/clinchem.2016.258236] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/15/2016] [Indexed: 12/18/2022]
Abstract
AbstractBACKGROUNDDetecting single-nucleotide variations and insertions/deletions in circulating tumor DNA is challenging because of their low allele frequency. The clinical use of circulating tumor DNA to characterize tumor genetic alterations requires new methods based on next-generation sequencing.METHODSWe developed a method based on quantification of error rate of each base position [position error rate (PER)]. To identify mutations, a binomial test was used to compare the minor-allele frequency to the measured PER at each base position. This process was validated in control samples and in 373 plasma samples from patients with lung or pancreatic cancer.RESULTSMinimal mutated allele frequencies were 0.003 for single-nucleotide variations and 0.001 for insertions/deletions. Independent testing performed by droplet digital PCR (n = 231 plasma samples) showed strong agreement with the base-PER method (κ = 0.90).CONCLUSIONSTargeted next-generation sequencing analyzed with the base-PER method represents a robust and low cost method to detect circulating tumor DNA in patients with cancer.
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Affiliation(s)
- Nicolas Pécuchet
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Medical Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Yves Rozenholc
- MERIT–UMR IRD 216, Paris Sorbonne Cité Université, Paris, France
| | - Eleonora Zonta
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
| | - Daniel Pietrasz
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
| | - Audrey Didelot
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
| | - Pierre Combe
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Medical Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Laure Gibault
- Department of Pathology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Jean-Baptiste Bachet
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Gastro-enterology, Hôpital Pitié-Salpêtrière, Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Valérie Taly
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
| | - Elizabeth Fabre
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Medical Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Hélène Blons
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Biochemistry, Pharmacogenetic and Molecular Oncology Unit, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
| | - Pierre Laurent-Puig
- INSERM UMR-S1147, CNRS SNC 5014, Paris Sorbonne Cité Université, Paris, France–Equipe labélisée Ligue Contre le cancer
- Department of Biochemistry, Pharmacogenetic and Molecular Oncology Unit, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique–Hôpitaux de Paris, Paris, France
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Next-Generation Sequencing in Cancer Diagnostics. J Mol Diagn 2016; 18:813-816. [PMID: 27664753 DOI: 10.1016/j.jmoldx.2016.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/23/2016] [Indexed: 12/14/2022] Open
Abstract
This commentary highlights the article by Misyura et al that underscores the use of next-generation sequencing platforms for detection and verification of somatic variants.
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Neueste technologische Entwicklungen für die Analyse von zirkulierender Tumor-DNA. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zusammenfassung
Die Analyse von zirkulierender Tumor-DNA, zusammen mit der Analyse von zirkulierenden Tumorzellen auch oft Liquid Biopsy genannt, ist ein sich rasch entwickelndes Feld in der medizinischen Forschung. Obwohl es von der Entdeckung der zellfreien DNA bis hin zur Erkenntnis, dass sie sich als Biomarker eignet, Jahrzehnte gedauert hat, wurde der klinische Nutzen der ctDNA hinsichtlich der Überwachung des Therapieansprechens, der Identifizierung von Resistenzmechanismen und neu aufkommenden Therapiezielen sowie der Detektion von minimaler Resterkrankung mittlerweile in unzähligen Studien bewiesen.
Aufgrund der hohen Variabilität, mit der ctDNA in der Zirkulation vorkommt, sowie der starken Fragmentierung, stellt die ctDNA aber einen schwierigen Analyten dar. In den letzten Jahren haben erhebliche technologische Fortschritte dazu beigetragen, dass eine Routineanwendung der ctDNA-Analysen tatsächlich realisierbar wird, sofern eine Reihe von regulatorischen Hürden überwunden wird.
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Abstract
The Pharmacological Audit Trail (PhAT) comprises a set of critical questions that need to be asked during discovery and development of an anticancer drug. Key aspects include: (1) defining a patient population; (2) establishing pharmacokinetic characteristics; (3) providing evidence of target engagement, pathway modulation, and biological effect with proof of concept pharmacodynamic biomarkers; (4) determining intermediate biomarkers of response; (5) assessing tumor response; and (6) determining how to overcome resistance by combination or sequential therapy and new target/drug discovery. The questions asked in the PhAT should be viewed as a continuum and not used in isolation. Different drug development programmes derive different types of benefit from these questions. The PhAT is critical in making go-no-go decisions in the development of currently studied drugs and will continue to be relevant to discovery and development of future generations of anticancer agents.
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Affiliation(s)
- Udai Banerji
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
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Revealing the challenges of low template DNA analysis with the prototype Ion AmpliSeq™ Identity panel v2.3 on the PGM™ Sequencer. Forensic Sci Int Genet 2016; 22:25-36. [DOI: 10.1016/j.fsigen.2015.07.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 06/08/2015] [Accepted: 07/13/2015] [Indexed: 01/18/2023]
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Naka T, Hatanaka Y, Marukawa K, Okada H, Hatanaka KC, Sakakibara-Konishi J, Oizumi S, Hida Y, Kaga K, Mitsuhashi T, Matsuno Y. Comparative genetic analysis of a rare synchronous collision tumor composed of malignant pleural mesothelioma and primary pulmonary adenocarcinoma. Diagn Pathol 2016; 11:38. [PMID: 27091358 PMCID: PMC4836188 DOI: 10.1186/s13000-016-0488-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/02/2016] [Indexed: 12/04/2022] Open
Abstract
Background Although asbestos acts as a potent carcinogen in pleural mesothelial and pulmonary epithelial cells, it still remains unclear whether asbestos causes specific and characteristic gene alterations in these different kinds of target cells, because direct comparison in an identical patient is not feasible. We experienced a rare synchronous collision tumor composed of malignant pleural mesothelioma (MPM) and primary pulmonary adenocarcinoma (PAC) in a 77-year-old man with a history of long-term smoking and asbestos exposure, and compared the DNA copy number alteration (CNA) and somatic mutation in these two independent tumors. Methods Formalin-fixed paraffin-embedded (FFPE) tissues of MPM and PAC lesions from the surgically resected specimen were used. Each of these MPM and PAC lesions exhibited a typical histology and immunophenotype. CNA analysis using SNP array was performed using the Illumina Human Omni Express-12_FFPE (Illumina, San Diego, CA, USA) with DNA extracts from each lesion. Somatic mutation analysis using next-generation sequencing was performed using the TruSeq Amplicon Cancer Panel (Illumina). Results The CNA analysis demonstrated a marked difference in the frequency of gain and loss between MPM and PAC. In PAC, copy number (CN) gain was detected more frequently and widely than CN loss, whereas in MPM there was no such obvious difference. PAC did not harbor CNAs that have been identified in asbestos-associated lung cancer, but did harbor some of the CNAs associated with smoking. MPM exhibited CN loss at 9p21.2-3, which is the most common genetic alteration in mesothelioma. Conclusion In this particular case, asbestos exposure may not have played a primary role in PAC carcinogenesis, but cigarette smoking may have contributed more to the occurrence of CN gains in PAC. This comparative genetic analysis of two different lesions with same amount of asbestos exposure and cigarette smoke exposure has provided information on differences in the cancer genome related to carcinogenesis.
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Affiliation(s)
- Tomoaki Naka
- Department of Surgical Pathology, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8648, Japan
| | - Yutaka Hatanaka
- Department of Surgical Pathology, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8648, Japan.,Research Division of Companion Diagnostics, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8648, Japan
| | - Katsuji Marukawa
- Department of Surgical Pathology, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8648, Japan
| | - Hiromi Okada
- Department of Surgical Pathology, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8648, Japan
| | - Kanako C Hatanaka
- Department of Surgical Pathology, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8648, Japan
| | - Jun Sakakibara-Konishi
- First Department of Medicine, Hokkaido University School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Satoshi Oizumi
- First Department of Medicine, Hokkaido University School of Medicine, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Yasuhiro Hida
- Department of Cardiovascular and Thoracic Surgery, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Kichizo Kaga
- Department of Cardiovascular and Thoracic Surgery, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, Hokkaido, 060-8638, Japan
| | - Tomoko Mitsuhashi
- Department of Surgical Pathology, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8648, Japan
| | - Yoshihiro Matsuno
- Department of Surgical Pathology, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8648, Japan. .,Research Division of Companion Diagnostics, Hokkaido University Hospital, Kita 14, Nishi 5, Kita-ku, Sapporo, Hokkaido, 060-8648, Japan.
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Wisinski KB, Tevaarwerk AJ, Burkard ME, Rampurwala M, Eickhoff J, Bell MC, Kolesar JM, Flynn C, Liu G. Phase I Study of an AKT Inhibitor (MK-2206) Combined with Lapatinib in Adult Solid Tumors Followed by Dose Expansion in Advanced HER2+ Breast Cancer. Clin Cancer Res 2016; 22:2659-67. [PMID: 27026198 DOI: 10.1158/1078-0432.ccr-15-2365] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/21/2016] [Indexed: 01/09/2023]
Abstract
PURPOSE Preclinical data support combining AKT inhibitors with HER2-targeted therapies to overcome resistance to treatment. This phase I study combined the investigational AKT inhibitor, MK-2206, with lapatinib to determine the MTD. EXPERIMENTAL DESIGN The dose escalation cohort enrolled adults with advanced solid tumors, who received MK-2206 dosed 30 to 60 mg every other day and lapatinib 1,000 to 1,500 mg daily continuously, escalated using a 3+3 design. Cycles were 28 days except cycle 1 (35 days, including an initial 8 days of MK-2206 alone to evaluate pharmacokinetic interactions). The dose expansion cohort enrolled adults with advanced HER2(+) breast cancer. RESULTS Twenty-three participants enrolled in the dose escalation cohort. Dose-limiting toxicities were hyponatremia, fatigue, rash, hypocalcemia, and mucositis. Common toxicities included diarrhea, nausea, and rash. The MTD was reached at MK-2206 45 mg orally every other day and lapatinib 1,500 mg orally daily. Two participants maintained stable disease for >4 months, including a colorectal cancer participant with substantial carcinoembryonic antigen decrease. Of 5 participants in the dose expansion cohort, 2 maintained stable disease for >6 months, including one with prior progression on single-agent lapatinib. Plasma MK-2206 concentrations decreased after addition of lapatinib, but in vitro studies indicate lapatinib increases the intracellular levels of MK-2206. CONCLUSIONS MK-2206 combined with lapatinib can be tolerated with both drugs above biologically active single-agent doses. Overlapping toxicities result in significant diarrhea and rash, which can be managed medically. Antitumor activity was promising and supports evaluation of AKT inhibitors combined with HER2-targeted therapies. Clin Cancer Res; 22(11); 2659-67. ©2016 AACR.
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Affiliation(s)
- Kari B Wisinski
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin. University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
| | - Amye J Tevaarwerk
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin. University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Mark E Burkard
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin. University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Murtuza Rampurwala
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin. University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Jens Eickhoff
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin. Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin
| | - Maria C Bell
- Sanford Cancer Center, Sioux Falls, South Dakota
| | - Jill M Kolesar
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin. School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin
| | - Christopher Flynn
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin. University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Glenn Liu
- University of Wisconsin Carbone Cancer Center, Madison, Wisconsin. University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
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Mateo J, de Bono JS. Interrogating the Cancer Genome to Deliver More Precise Cancer Care. Am Soc Clin Oncol Educ Book 2016; 35:e577-e583. [PMID: 27249770 DOI: 10.1200/edbk_156908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aim of precision medicine is to select the best treatment option for each patient at the appropriate time in the natural history of the disease, based on understanding the molecular makeup of the tumor, with the ultimate objective of improving patient survival and quality of life. To achieve it, we must identify functionally distinct subtypes of cancers and, critically, have multiple therapy options available to match to these functional subtypes. As a result of the development of better and less costly next-generation sequencing assays, we can now interrogate the cancer genome, enabling us to use the DNA sequence itself for biomarker studies in drug development. The success of DNA-based biomarkers requires analytical validation and careful clinical qualification in prospective clinical trials. In this article, we review some of the challenges the scientific community is facing as a consequence of this sequencing revolution: reclassifying cancers based on biologic/phenotypic clusters relevant to clinical decision making; adapting how we conduct clinical trials; and adjusting our frameworks for regulatory approvals of biomarker technologies and drugs. Ultimately, we must ensure that this revolution can be safely implemented into routine clinical practice and benefit patients.
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Affiliation(s)
- Joaquin Mateo
- From The Institute of Cancer Research, Sutton, United Kingdom; The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
| | - Johann S de Bono
- From The Institute of Cancer Research, Sutton, United Kingdom; The Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
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22
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Karasaki T, Nagayama K, Kawashima M, Hiyama N, Murayama T, Kuwano H, Nitadori JI, Anraku M, Sato M, Miyai M, Hosoi A, Matsushita H, Kikugawa S, Matoba R, Ohara O, Kakimi K, Nakajima J. Identification of Individual Cancer-Specific Somatic Mutations for Neoantigen-Based Immunotherapy of Lung Cancer. J Thorac Oncol 2015; 11:324-33. [PMID: 26752676 DOI: 10.1016/j.jtho.2015.11.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/19/2015] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Two strategies for selecting neoantigens as targets for non-small cell lung cancer vaccines were compared: (1) an "off-the-shelf" approach starting with shared mutations extracted from global databases and (2) a personalized pipeline using whole-exome sequencing data on each patient's tumor. METHODS The Catalogue of Somatic Mutations in Cancer database was used to create a list of shared missense mutations occurring in more than 1% of patients. These mutations were then assessed for predicted binding affinity to HLA alleles of 15 lung cancer patients, and potential neoantigens (pNeoAgs) for each patient were selected on this basis. In the personalized approach, pNeoAgs were selected from missense mutations detected by whole-exome sequencing of the patient's own samples. RESULTS The list of shared mutations included 22 missense mutations for adenocarcinoma and 18 for squamous cell carcinoma (SCC), resulting in a median of 10 off-the-shelf pNeoAgs for each adenocarcinoma (range 5-13) and 9 (range 5-12) for each SCC. In contrast, a median of 59 missense mutations were identified by whole-exome sequencing (range 33-899) in adenocarcinoma and 164.5 (range 26-232) in SCC. This resulted in a median of 46 pNeoAgs (range 13-659) for adenocarcinoma and 95.5 (range 10-145) for SCC in the personalized set. We found that only one or two off-the-shelf pNeoAgs were included in the set of personalized pNeoAgs-and then in only three patients, with no overlap seen in the remaining 12 patients. CONCLUSIONS Use of an off-the-shelf pipeline is feasible but may not be satisfactory for most patients with non-small cell lung cancer. We recommend identifying personal mutations by comprehensive genome sequencing for developing neoantigen-targeted cancer immunotherapies.
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Affiliation(s)
- Takahiro Karasaki
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Nagayama
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mitsuaki Kawashima
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noriko Hiyama
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomonori Murayama
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Kuwano
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun-ichi Nitadori
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaki Anraku
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaaki Sato
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Manami Miyai
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan; MEDINET Co. Ltd., Yokohama, Japan
| | - Akihiro Hosoi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan; MEDINET Co. Ltd., Yokohama, Japan
| | - Hirokazu Matsushita
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan
| | | | | | - Osamu Ohara
- Department of Human Genome Research, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan.
| | - Jun Nakajima
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Lopez J, Harris S, Roda D, Yap TA. Precision Medicine for Molecularly Targeted Agents and Immunotherapies in Early-Phase Clinical Trials. TRANSLATIONAL ONCOGENOMICS 2015; 7:1-11. [PMID: 26609214 PMCID: PMC4648610 DOI: 10.4137/tog.s30533] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 10/06/2015] [Accepted: 10/09/2015] [Indexed: 12/12/2022]
Abstract
Precision medicine in oncology promises the matching of genomic, molecular, and clinical data with underlying mechanisms of a range of novel anticancer therapeutics to develop more rational and effective antitumor strategies in a timely manner. However, despite the remarkable progress made in the understanding of novel drivers of different oncogenic processes, success rates for the approval of oncology drugs remain low with substantial fiscal consequences. In this article, we focus on how recent rapid innovations in technology have brought greater clarity to the biological and clinical complexities of different cancers and advanced the development of molecularly targeted agents and immunotherapies in clinical trials. We discuss the key challenges of identifying and validating predictive biomarkers of response and resistance using both tumor and surrogate tissues, as well as the hurdles associated with intratumor heterogeneity. Finally, we outline evolving strategies employed in early-phase trial designs that incorporate omics-based technologies.
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Affiliation(s)
- Juanita Lopez
- Royal Marsden NHS Foundation Trust, The Institute of Cancer Research, London, UK
| | - Sam Harris
- Royal Marsden NHS Foundation Trust, The Institute of Cancer Research, London, UK
| | - Desam Roda
- Royal Marsden NHS Foundation Trust, The Institute of Cancer Research, London, UK
| | - Timothy A Yap
- Royal Marsden NHS Foundation Trust, The Institute of Cancer Research, London, UK
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24
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Wan-Ibrahim WI, Singh VA, Hashim OH, Abdul-Rahman PS. Biomarkers for Bone Tumors: Discovery from Genomics and Proteomics Studies and Their Challenges. Mol Med 2015; 21:861-872. [PMID: 26581086 DOI: 10.2119/molmed.2015.00183] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/12/2015] [Indexed: 01/07/2023] Open
Abstract
Diagnosis of bone tumor currently relies on imaging and biopsy, and hence, the need to find less invasive ways for its accurate detection. More recently, numerous promising deoxyribonucleic acid (DNA) and protein biomarkers with significant prognostic, diagnostic and/or predictive abilities for various types of bone tumors have been identified from genomics and proteomics studies. This article reviewed the putative biomarkers for the more common types of bone tumors (that is, osteosarcoma, Ewing sarcoma, chondrosarcoma [malignant] and giant cell tumor [benign]) that were unveiled from the studies. The benefits and drawbacks of these biomarkers, as well as the technology platforms involved in the research, were also discussed. Challenges faced in the biomarker discovery studies and the problems in their translation from the bench to the clinical settings were also addressed.
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Affiliation(s)
- Wan I Wan-Ibrahim
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vivek A Singh
- Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Onn H Hashim
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,University of Malaya Centre of Proteomics Research (UMCPR), University of Malaya, Kuala Lumpur, Malaysia
| | - Puteri S Abdul-Rahman
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,University of Malaya Centre of Proteomics Research (UMCPR), University of Malaya, Kuala Lumpur, Malaysia
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25
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Mateo J, Carreira S, Sandhu S, Miranda S, Mossop H, Perez-Lopez R, Nava Rodrigues D, Robinson D, Omlin A, Tunariu N, Boysen G, Porta N, Flohr P, Gillman A, Figueiredo I, Paulding C, Seed G, Jain S, Ralph C, Protheroe A, Hussain S, Jones R, Elliott T, McGovern U, Bianchini D, Goodall J, Zafeiriou Z, Williamson CT, Ferraldeschi R, Riisnaes R, Ebbs B, Fowler G, Roda D, Yuan W, Wu YM, Cao X, Brough R, Pemberton H, A'Hern R, Swain A, Kunju LP, Eeles R, Attard G, Lord CJ, Ashworth A, Rubin MA, Knudsen KE, Feng FY, Chinnaiyan AM, Hall E, de Bono JS. DNA-Repair Defects and Olaparib in Metastatic Prostate Cancer. N Engl J Med 2015; 373:1697-708. [PMID: 26510020 PMCID: PMC5228595 DOI: 10.1056/nejmoa1506859] [Citation(s) in RCA: 1654] [Impact Index Per Article: 183.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Prostate cancer is a heterogeneous disease, but current treatments are not based on molecular stratification. We hypothesized that metastatic, castration-resistant prostate cancers with DNA-repair defects would respond to poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) inhibition with olaparib. METHODS We conducted a phase 2 trial in which patients with metastatic, castration-resistant prostate cancer were treated with olaparib tablets at a dose of 400 mg twice a day. The primary end point was the response rate, defined either as an objective response according to Response Evaluation Criteria in Solid Tumors, version 1.1, or as a reduction of at least 50% in the prostate-specific antigen level or a confirmed reduction in the circulating tumor-cell count from 5 or more cells per 7.5 ml of blood to less than 5 cells per 7.5 ml. Targeted next-generation sequencing, exome and transcriptome analysis, and digital polymerase-chain-reaction testing were performed on samples from mandated tumor biopsies. RESULTS Overall, 50 patients were enrolled; all had received prior treatment with docetaxel, 49 (98%) had received abiraterone or enzalutamide, and 29 (58%) had received cabazitaxel. Sixteen of 49 patients who could be evaluated had a response (33%; 95% confidence interval, 20 to 48), with 12 patients receiving the study treatment for more than 6 months. Next-generation sequencing identified homozygous deletions, deleterious mutations, or both in DNA-repair genes--including BRCA1/2, ATM, Fanconi's anemia genes, and CHEK2--in 16 of 49 patients who could be evaluated (33%). Of these 16 patients, 14 (88%) had a response to olaparib, including all 7 patients with BRCA2 loss (4 with biallelic somatic loss, and 3 with germline mutations) and 4 of 5 with ATM aberrations. The specificity of the biomarker suite was 94%. Anemia (in 10 of the 50 patients [20%]) and fatigue (in 6 [12%]) were the most common grade 3 or 4 adverse events, findings that are consistent with previous studies of olaparib. CONCLUSIONS Treatment with the PARP inhibitor olaparib in patients whose prostate cancers were no longer responding to standard treatments and who had defects in DNA-repair genes led to a high response rate. (Funded by Cancer Research UK and others; ClinicalTrials.gov number, NCT01682772; Cancer Research UK number, CRUK/11/029.).
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Affiliation(s)
- Joaquin Mateo
- From the Institute of Cancer Research (J.M., S.C., S.S., S.M., H.M., R.P.-L., D.N.R., A.O., N.T., G.B., N.P., P.F., A.G., I.F., C.P., G.S., D.B., J.G., Z.Z., C.T.W., R.F., R.R., B.E., G.F., D. Roda, W.Y., R.B., H.P., R.A., A.S., R.E., G.A., C.J.L., A.A., E.H., J.S.B.), the Royal Marsden NHS Foundation Trust (J.M., S.S., R.P.-L., A.O., N.T., D.B., Z.Z., R.F., D. Roda, R.E., G.A., J.S.B.), and University College London Hospital (U.M.), London, Queen's University, Belfast (S.J.), University of Leeds, Leeds (C.R.), Churchill Hospital, Oxford (A.P.), University of Liverpool, Liverpool (S.H.), Beatson West of Scotland Cancer Centre, Glasgow (R.J.), and Christie Hospital, Manchester (T.E.) - all in the United Kingdom; the University of Michigan, Ann Arbor (D. Robinson, Y.-M.W., X.C., L.P.K., F.Y.F., A.M.C.); Weill Cornell Medical College, New York (M.A.R.); and Thomas Jefferson University, Philadelphia (K.E.K.)
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26
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Frenel JS, Carreira S, Goodall J, Roda D, Perez-Lopez R, Tunariu N, Riisnaes R, Miranda S, Figueiredo I, Nava-Rodrigues D, Smith A, Leux C, Garcia-Murillas I, Ferraldeschi R, Lorente D, Mateo J, Ong M, Yap TA, Banerji U, Gasi Tandefelt D, Turner N, Attard G, de Bono JS. Serial Next-Generation Sequencing of Circulating Cell-Free DNA Evaluating Tumor Clone Response To Molecularly Targeted Drug Administration. Clin Cancer Res 2015; 21:4586-96. [PMID: 26085511 PMCID: PMC4580992 DOI: 10.1158/1078-0432.ccr-15-0584] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/26/2015] [Indexed: 12/25/2022]
Abstract
PURPOSE We evaluated whether next-generation sequencing (NGS) of circulating cell-free DNA (cfDNA) could be used for patient selection and as a tumor clone response biomarker in patients with advanced cancers participating in early-phase clinical trials of targeted drugs. EXPERIMENTAL DESIGN Plasma samples from patients with known tumor mutations who completed at least two courses of investigational targeted therapy were collected monthly, until disease progression. NGS was performed sequentially on the Ion Torrent PGM platform. RESULTS cfDNA was extracted from 39 patients with various tumor types. Treatments administered targeted mainly the PI3K-AKT-mTOR pathway (n = 28) or MEK (n = 7). Overall, 159 plasma samples were sequenced with a mean sequencing coverage achieved of 1,685X across experiments. At trial initiation (C1D1), 23 of 39 (59%) patients had at least one mutation identified in cfDNA (mean 2, range 1-5). Out of the 44 mutations identified at C1D1, TP53, PIK3CA and KRAS were the top 3 mutated genes identified, with 18 (41%), 9 (20%), 8 (18%) different mutations, respectively. Out of these 23 patients, 13 received a targeted drug matching their tumor profile. For the 23 patients with cfDNA mutation at C1D1, the monitoring of mutation allele frequency (AF) in consecutive plasma samples during treatment with targeted drugs demonstrated potential treatment associated clonal responses. Longitudinal monitoring of cfDNA samples with multiple mutations indicated the presence of separate clones behaving discordantly. Molecular changes at cfDNA mutation level were associated with time to disease progression by RECIST criteria. CONCLUSIONS Targeted NGS of cfDNA has potential clinical utility to monitor the delivery of targeted therapies.
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Affiliation(s)
- Jean Sebastien Frenel
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom. Institut de Cancerologie de l'Ouest, Nantes-Saint Herblain, France
| | - Suzanne Carreira
- The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom
| | - Jane Goodall
- The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom
| | - Desam Roda
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | - Raquel Perez-Lopez
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | - Nina Tunariu
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | - Ruth Riisnaes
- The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom
| | - Susana Miranda
- The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom
| | - Ines Figueiredo
- The Institute of Cancer Research, Sutton, Surrey, London, United Kingdom
| | | | - Alan Smith
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | - Christophe Leux
- Département de Santé Publique, CHU de Nantes, Nantes Cedex 1, France
| | - Isaac Garcia-Murillas
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Roberta Ferraldeschi
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | - David Lorente
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | - Joaquin Mateo
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | - Michael Ong
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | - Timothy A Yap
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | - Udai Banerji
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | | | - Nick Turner
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Gerhardt Attard
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom
| | - Johann S de Bono
- The Institute of Cancer Research and the Royal Marsden Hospital, Sutton, Surrey, London, United Kingdom.
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Er TK, Wang YY, Chen CC, Herreros-Villanueva M, Liu TC, Yuan SSF. Molecular characterization of oral squamous cell carcinoma using targeted next-generation sequencing. Oral Dis 2015; 21:872-8. [PMID: 26173098 DOI: 10.1111/odi.12357] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 06/28/2015] [Accepted: 07/01/2015] [Indexed: 01/11/2023]
Abstract
OBJECTIVES Many genetic factors play an important role in the development of oral squamous cell carcinoma. The aim of this study was to assess the mutational profile in oral squamous cell carcinoma using formalin-fixed, paraffin-embedded tumors from a Taiwanese population by performing targeted sequencing of 26 cancer-associated genes that are frequently mutated in solid tumors. METHODS Next-generation sequencing was performed in 50 formalin-fixed, paraffin-embedded tumor specimens obtained from patients with oral squamous cell carcinoma. Genetic alterations in the 26 cancer-associated genes were detected using a deep sequencing (>1000X) approach. RESULTS TP53, PIK3CA, MET, APC, CDH1, and FBXW7 were most frequently mutated genes. Most remarkably, TP53 mutations and PIK3CA mutations, which accounted for 68% and 18% of tumors, respectively, were more prevalent in a Taiwanese population. Other genes including MET (4%), APC (4%), CDH1 (2%), and FBXW7 (2%) were identified in our population. CONCLUSIONS In summary, our study shows the feasibility of performing targeted sequencing using formalin-fixed, paraffin-embedded samples. Additionally, this study also reports the mutational landscape of oral squamous cell carcinoma in the Taiwanese population. We believe that this study will shed new light on fundamental aspects in understanding the molecular pathogenesis of oral squamous cell carcinoma and may aid in the development of new targeted therapies.
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Affiliation(s)
- Tze-Kiong Er
- Division of Molecular Diagnostics, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Yun Wang
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chih-Chieh Chen
- Center for Lipid Biosciences, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Center for Lipid and Glycomedicine Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Marta Herreros-Villanueva
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco UPV/EHU, San Sebastián, Spain
| | - Ta-Chih Liu
- Division of Molecular Diagnostics, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shyng-Shiou F Yuan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Center for Lipid and Glycomedicine Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Translational Research Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
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29
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Mateo J, Gerlinger M, Rodrigues DN, de Bono JS. The promise of circulating tumor cell analysis in cancer management. Genome Biol 2014. [PMID: 25222379 DOI: 10.1186/s13059‐014‐0448‐5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enumeration and molecular characterization of circulating tumor cells isolated from peripheral blood of patients with cancer can aid selection of targeted therapy for patients, monitoring of response to therapies and optimization of drug development, while also providing valuable information about intratumoral heterogeneity.
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30
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Mateo J, Gerlinger M, Rodrigues DN, de Bono JS. The promise of circulating tumor cell analysis in cancer management. Genome Biol 2014; 15:448. [PMID: 25222379 PMCID: PMC4281949 DOI: 10.1186/s13059-014-0448-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Enumeration and molecular characterization of circulating tumor cells isolated from peripheral blood of patients with cancer can aid selection of targeted therapy for patients, monitoring of response to therapies and optimization of drug development, while also providing valuable information about intratumoral heterogeneity.
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Affiliation(s)
- Joaquin Mateo
- />Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG UK
- />Drug Development Unit, The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT UK
| | - Marco Gerlinger
- />Centre for Evolution and Cancer, The Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP UK
- />Gastrointestinal Cancer Unit, Department of Medicine, The Royal Marsden NHS Foundation Trust, Fulham Road, London, SW3 6JJ UK
| | - Daniel Nava Rodrigues
- />Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG UK
- />Drug Development Unit, The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT UK
| | - Johann S de Bono
- />Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG UK
- />Drug Development Unit, The Royal Marsden NHS Foundation Trust, Downs Road, Sutton, Surrey, SM2 5PT UK
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