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Appel S, Bar J, Saad A, Marom EM, Urban D, Onn A, Gantz-Sorotsky H, Kremer RY, Ben-Nun A, Perelman M, Ofek E, Yacobi R, Daher S, Rasco A, Symon Z, Lawrence YR, Goldstein J. Effects of EGFR driver mutations on pathologic regression in resectable locally advanced non-small cell lung cancer treated with neoadjuvant chemoradiation and completion surgery. Br J Radiol 2023; 96:20220763. [PMID: 37751214 PMCID: PMC10646649 DOI: 10.1259/bjr.20220763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 06/26/2023] [Accepted: 08/21/2023] [Indexed: 09/27/2023] Open
Abstract
OBJECTIVE We hypothesized that driver mutations in epidermal growth factor receptor (EGFR) are associated with decreased pathologic response to neoadjuvant chemoradiation (NA-ChRT) in locally advanced non-small cell lung cancer (LA-NSCLC). METHODS Patients with Stage IIB-IIIA NSCLC treated with NA-ChRT, completion surgery, and underwent molecular profile testing were identified in a lung cancer database. Pathologic response was quantified using: (i) major pathologic response (MPR), (ii) complete pathologic response (pCR), and (iii) mean residual viable tumor cells (MRTC). Two groups were formed based on the presence or absence of driver mutations. Clinical and pathological correlations between the groups were studied. RESULTS Forty-seven patients underwent tumor molecular profile testing, NA-ChRT, and completion surgery. Compared to the no-driver mutation group, the driver mutation group had lower MPR (23% vs 71%, p = 0.003), pCR (0% vs 26%, p = 0.02), and higher MRTC (43.4% vs 15.8%, p = 0.009). Univariate analysis showed an increased MPR rate for smokers, squamous cell histology, ChRT-surgery interval >65 days, and no-driver mutations. Multivariate analysis showed that only no-driver mutations (OR 0.39, p = 0.02) remained significant for MPR. PD-L1 status did not affect MPR. At 2 years, the driver mutation group had lower rates of local control (Hazard ration [HR] 0.67, p = 0.17) and disease-free survival (HR 0.5, p = 0.001). Overall survival was similar for both groups (HR = 1.04, p = 0.86). CONCLUSION Following 60 Gray NA-ChRT, tumors with a driver mutation had lower MPR and pCR rates than tumors without a driver mutation. PD-L1 was not associated with tumor regression. ADVANCES IN KNOWLEDGE Patients with resectable LA-NSCLC and an EGFR driver mutation treated with neoadjuvant-ChRT and completion surgery have reduced pathologic regression, lower local control rates, and shorter disease-free survival than patients without a driver mutation. Evaluation of molecular testing should be introduced in LA-NSCLC intended for prognostication and treatment decisions.
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Affiliation(s)
- Sarit Appel
- Department of Radiation Oncology, Chaim Sheba Medical Center, Tel- Hashomer, Israel
| | | | - Akram Saad
- Department of Medical Oncology, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Damien Urban
- Department of Medical Oncology, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Hadas Gantz-Sorotsky
- Department of Medical Oncology, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Ran Yosef Kremer
- Department of Thoracic Surgery, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Alon Ben-Nun
- Department of Thoracic Surgery, Assuta Medical Center, Tel Aviv, Israel
| | - Marina Perelman
- Department of Pathology, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Efrat Ofek
- Department of Pathology, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Rinat Yacobi
- Department of Pathology, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Sameh Daher
- Thoracic Cancer Unit Cancer Division, Rambam Health Care Campus, Haifa, Israel
| | - Adi Rasco
- Department of Medical Oncology, Kaplan Medical Center, Rehovot, Israel
| | | | | | - Jeffrey Goldstein
- Department of Radiation Oncology, Tel-Aviv Medical Center, Tel-Aviv, Israel
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Tieng FYF, Baharudin R, Abu N, Mohd Yunos RI, Lee LH, Ab Mutalib NS. Single Cell Transcriptome in Colorectal Cancer-Current Updates on Its Application in Metastasis, Chemoresistance and the Roles of Circulating Tumor Cells. Front Pharmacol 2020; 11:135. [PMID: 32174835 PMCID: PMC7056698 DOI: 10.3389/fphar.2020.00135] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is among the most common cancer worldwide, a challenge for research, and a model for studying the molecular mechanisms involved in its development. Previously, bulk transcriptomics analyses were utilized to classify CRC based on its distinct molecular and clinicopathological features for prognosis and diagnosis of patients. The introduction of single-cell transcriptomics completely turned the table by enabling the examination of the expression levels of individual cancer cell within a single tumor. In this review, we highlighted the importance of these single-cell transcriptomics analyses as well as suggesting circulating tumor cells (CTCs) as the main focus of single-cell RNA sequencing. Characterization of these cells might reveal the intratumoral heterogeneity present in CRC while providing critical insights into cancer metastasis. To summarize, we believed the analysis of gene expression patterns of CTC from CRC at single-cell resolution holds the potential to provide key information for identification of prognostic and diagnostic markers as well as the development of precise and personalized cancer treatment.
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Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rashidah Baharudin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Ryia-Illani Mohd Yunos
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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3
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Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution. Nat Ecol Evol 2020; 4:437-452. [PMID: 32094541 DOI: 10.1038/s41559-020-1103-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/08/2020] [Indexed: 01/28/2023]
Abstract
Evolutionary dynamics in large asexual populations is strongly influenced by multiple competing beneficial lineages, most of which segregate at very low frequencies. However, technical barriers to tracking a large number of these rare lineages in bacterial populations have so far prevented a detailed elucidation of evolutionary dynamics. Here, we overcome this hurdle by developing a chromosomal-barcoding technique that allows simultaneous tracking of approximately 450,000 distinct lineages in Escherichia coli, which we use to test the effect of sub-inhibitory concentrations of common antibiotics on the evolutionary dynamics of low-frequency lineages. We find that populations lose lineage diversity at distinct rates that correspond to their antibiotic regimen. We also determine that some lineages have similar fates across independent experiments. By analysing the trajectory dynamics, we attribute the reproducible fates of these lineages to the presence of pre-existing beneficial mutations, and we demonstrate how the relative contribution of pre-existing and de novo mutations varies across drug regimens. Finally, we reproduce the observed lineage dynamics by simulations. Altogether, our results provide a valuable methodology for studying bacterial evolution as well as insights into evolution under sub-inhibitory antibiotic levels.
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4
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Bessi S, Pepe F, Ottaviantonio M, Pisapia P, Malapelle U, Troncone G, Biancalani M. Comparison between two different next generation sequencing platforms for clinical relevant gene mutation test in solid tumours. J Clin Pathol 2020; 73:602-604. [PMID: 32060075 DOI: 10.1136/jclinpath-2019-206422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 11/03/2022]
Abstract
In the present study, we analysed 44 formalin fixed paraffin embedded (FFPE) from different solid tumours by adopting two different next generation sequencing platforms: GeneReader (QIAGEN, Hilden, Germany) and Ion Torrent (Thermo Fisher Scientific, Waltham, Massachusetts, USA). We highlighted a 100% concordance between the platforms. In addition, focusing on variant detection, we evaluated a very good agreement between the two tests (Cohen's kappa=0.84) and, when taking into account variant allele fraction value for each variant, a very high concordance was obtained (Pearson's r=0.94). Our results underlined the high performance rate of GeneReader on FFPE samples and its suitability in routine molecular predictive practice.
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Affiliation(s)
- Silvia Bessi
- Azienda USL Toscana Centro, Complex Unit of Pathological Anatomy Empoli-Prato, S. Stefano Hospital, Prato, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Marco Ottaviantonio
- Azienda USL Toscana Centro, Complex Unit of Pathological Anatomy Empoli-Prato, S. Stefano Hospital, Prato, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mauro Biancalani
- Azienda USL Toscana Centro, Complex Unit of Pathological Anatomy Empoli-Prato, S. Stefano Hospital, Prato, Italy
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5
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Simarro J, Murria R, Pérez-Simó G, Llop M, Mancheño N, Ramos D, Juan ID, Barragán E, Laiz B, Cases E, Ansótegui E, Gómez-Codina J, Aparicio J, Salvador C, Juan Ó, Palanca S. Development, Implementation and Assessment of Molecular Diagnostics by Next Generation Sequencing in Personalized Treatment of Cancer: Experience of a Public Reference Healthcare Hospital. Cancers (Basel) 2019; 11:E1196. [PMID: 31426418 PMCID: PMC6721584 DOI: 10.3390/cancers11081196] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
The establishment of precision medicine in cancer patients requires the study of several biomarkers. Single-gene testing approaches are limited by sample availability and turnaround time. Next generation sequencing (NGS) provides an alternative for detecting genetic alterations in several genes with low sample requirements. Here we show the implementation to routine diagnostics of a NGS assay under International Organization for Standardization (UNE-EN ISO 15189:2013) accreditation. For this purpose, 106 non-small cell lung cancer (NSCLC) and 102 metastatic colorectal cancer (mCRC) specimens were selected for NGS analysis with Oncomine Solid Tumor (ThermoFisher). In NSCLC the most prevalently mutated gene was TP53 (49%), followed by KRAS (31%) and EGFR (13%); in mCRC, TP53 (50%), KRAS (48%) and PIK3CA (16%) were the most frequently mutated genes. Moreover, NGS identified actionable genetic alterations in 58% of NSCLC patients, and 49% of mCRC patients did not harbor primary resistance mechanisms to anti-EGFR treatment. Validation with conventional approaches showed an overall agreement >90%. Turnaround time and cost analysis revealed that NGS implementation is feasible in the public healthcare context. Therefore, NGS is a multiplexed molecular diagnostic tool able to overcome the limitations of current molecular diagnosis in advanced cancer, allowing an improved and economically sustainable molecular profiling.
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Affiliation(s)
- Javier Simarro
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Rosa Murria
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Gema Pérez-Simó
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Marta Llop
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Nuria Mancheño
- Department of Pathology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - David Ramos
- Department of Pathology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Inmaculada de Juan
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Eva Barragán
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Begoña Laiz
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Enrique Cases
- Department of Pulmonology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Emilio Ansótegui
- Department of Pulmonology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - José Gómez-Codina
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Jorge Aparicio
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Carmen Salvador
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Óscar Juan
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Sarai Palanca
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain.
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain.
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Zhang X, Liang Z, Wang S, Lu S, Song Y, Cheng Y, Ying J, Liu W, Hou Y, Li Y, Liu Y, Hou J, Liu X, Shao J, Tai Y, Wang Z, Fu L, Li H, Zhou X, Bai H, Wang M, Lu Y, Yang J, Zhong W, Zhou Q, Yang X, Wang J, Huang C, Liu X, Zhou X, Zhang S, Tian H, Chen Y, Ren R, Liao N, Wu C, Zhu Z, Pan H, Gu Y, Wang L, Liu Y, Zhang S, Liu T, Chen G, Shao Z, Xu B, Zhang Q, Xu R, Shen L, Wu Y, Tumor Biomarker Committee OBOCSOCO(CSCO. Application of next-generation sequencing technology to precision medicine in cancer: joint consensus of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology. Cancer Biol Med 2019; 16:189-204. [PMID: 31119060 PMCID: PMC6528448 DOI: 10.20892/j.issn.2095-3941.2018.0142] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 12/20/2018] [Indexed: 02/05/2023] Open
Abstract
Next-generation sequencing (NGS) technology is capable of sequencing millions or billions of DNA molecules simultaneously. Therefore, it represents a promising tool for the analysis of molecular targets for the initial diagnosis of disease, monitoring of disease progression, and identifying the mechanism of drug resistance. On behalf of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology (CSCO) and the China Actionable Genome Consortium (CAGC), the present expert group hereby proposes advisory guidelines on clinical applications of NGS technology for the analysis of cancer driver genes for precision cancer therapy. This group comprises an assembly of laboratory cancer geneticists, clinical oncologists, bioinformaticians, pathologists, and other professionals. After multiple rounds of discussions and revisions, the expert group has reached a preliminary consensus on the need of NGS in clinical diagnosis, its regulation, and compliance standards in clinical sample collection. Moreover, it has prepared NGS criteria, the sequencing standard operation procedure (SOP), data analysis, report, and NGS platform certification and validation.
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Affiliation(s)
- Xuchao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Shengyue Wang
- National Research Center for Translational Medicine, Shanghai, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Shun Lu
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Song
- Division of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210029, China
| | - Ying Cheng
- Department of Oncology, Jilin Cancer Hospital, Changchun 132002, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Yangqiu Li
- Department of Hematology, First Affiliated Hospital, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 519000, China
| | - Yi Liu
- Laboratory of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Jun Hou
- Department of Oncology, First Clinical College of South China University of Technology/Guangdong Lung Cancer Institute, Guangzhou 510060, China
| | - Xiufeng Liu
- People's Liberation Army Cancer Center of Bayi Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Jianyong Shao
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou 519000, China
| | - Yanhong Tai
- Department of Pathology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Zheng Wang
- Department of Pathology, Beijing Hospital, Beijing 100071, China
| | - Li Fu
- Department of Breast Cancer Pathology and Research Laboratory of Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
| | - Hui Li
- Department of Oncology, Jilin Cancer Hospital, Changchun 132002, China
| | - Xiaojun Zhou
- Department of Pathology, Jinling Hospital Nanjing University School of Medicine, Nanjing 210029, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Mengzhao Wang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100006, China
| | - You Lu
- Department of Oncology, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Jinji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Wenzhao Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xuening Yang
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Jie Wang
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Cheng Huang
- Department of Thoracic Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350001, China
| | - Xiaoqing Liu
- Department of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiaoyan Zhou
- Department of Pathology, Shanghai Cancer Center, Fudan University, Shanghai 200433, China
| | - Shirong Zhang
- Center for Translational Medicine, Hangzhou First People's Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Hongxia Tian
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Yu Chen
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Ruibao Ren
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Ning Liao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangzhou 510080, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200240, China
| | - Zhongzheng Zhu
- Department of Oncology, No. 113 Hospital of People's Liberation Army, Ningbo 315040, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310020, China
| | - Yanhong Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China
| | - Liwei Wang
- Department of Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Yunpeng Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110016, China
| | - Suzhan Zhang
- Department of Oncology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310020, China
| | - Tianshu Liu
- Department of Oncology, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Gong Chen
- Department of Colorectal, Sun Yat-sen University Cancer Center, Guangzhou 519000, China
| | - Zhimin Shao
- Department of Breast Surgery, Shanghai Cancer Center, Fudan University, Shanghai 200433, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Qingyuan Zhang
- Department of Internal Medicine, The Third Affiliated Hospital of Harbin Medical University, Harbin 150030, China
| | - Ruihua Xu
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 519000, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yilong Wu
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
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7
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Ghosh S, Prasad M, Kundu K, Cohen L, Yegodayev KM, Zorea J, Joshua BZ, Lasry B, Dimitstein O, Bahat-Dinur A, Mizrachi A, Lazar V, Elkabets M, Porgador A. Tumor Tissue Explant Culture of Patient-Derived Xenograft as Potential Prioritization Tool for Targeted Therapy. Front Oncol 2019; 9:17. [PMID: 30723707 PMCID: PMC6350270 DOI: 10.3389/fonc.2019.00017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
Despite of remarkable progress made in the head and neck cancer (HNC) therapy, the survival rate of this metastatic disease remain low. Tailoring the appropriate therapy to patients is a major challenge and highlights the unmet need to have a good preclinical model that will predict clinical response. Hence, we developed an accurate and time efficient drug screening method of tumor ex vivo analysis (TEVA) system, which can predict patient-specific drug responses. In this study, we generated six patient derived xenografts (PDXs) which were utilized for TEVA. Briefly, PDXs were cut into 2 × 2 × 2 mm3 explants and treated with clinically relevant drugs for 24 h. Tumor cell proliferation and death were evaluated by immunohistochemistry and TEVA score was calculated. Ex vivo and in vivo drug efficacy studies were performed on four PDXs and three drugs side-by-side to explore correlation between TEVA and PDX treatment in vivo. Efficacy of drug combinations was also ventured. Optimization of the culture timings dictated 24 h to be the time frame to detect drug responses and drug penetrates 2 × 2 × 2 mm3 explants as signaling pathways were significantly altered. Tumor responses to drugs in TEVA, significantly corresponds with the drug efficacy in mice. Overall, this low cost, robust, relatively simple and efficient 3D tissue-based method, employing material from one PDX, can bypass the necessity of drug validation in immune-incompetent PDX-bearing mice. Our data provides a potential rationale for utilizing TEVA to predict tumor response to targeted and chemo therapies when multiple targets are proposed.
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Affiliation(s)
- Susmita Ghosh
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Manu Prasad
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Kiran Kundu
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Limor Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ksenia M. Yegodayev
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jonathan Zorea
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ben-Zion Joshua
- Department of Otolaryngology-Head and Neck Surgery, Soroka Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Batel Lasry
- Department of Otolaryngology-Head and Neck Surgery, Soroka Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Orr Dimitstein
- Department of Otolaryngology-Head and Neck Surgery, Soroka Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anat Bahat-Dinur
- Department of Otolaryngology-Head and Neck Surgery, Soroka Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Aviram Mizrachi
- Department of Otolaryngology-Head and Neck Surgery and The Center for Translational Research in Head and Neck Cancer, Rabin Medical Center, Petah Tikva and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Vladimir Lazar
- Worldwide Innovative Network Association-WIN Consortium, Villejuif, France
| | - Moshe Elkabets
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Angel Porgador
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel
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8
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Simultaneous identification of clinically relevant single nucleotide variants, copy number alterations and gene fusions in solid tumors by targeted next-generation sequencing. Oncotarget 2018; 9:22749-22768. [PMID: 29854313 PMCID: PMC5978263 DOI: 10.18632/oncotarget.25229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/05/2018] [Indexed: 01/19/2023] Open
Abstract
In this study, we have set-up a routine pipeline to evaluate the clinical application of Oncomine™ Focus Assay, a panel that allows the simultaneous detection of single nucleotide hotspot mutations in 35 genes, copy number alterations (CNAs) in 19 genes and gene fusions involving 23 genes in cancer samples. For this study we retrospectively selected 106 patients that were submitted to surgical resection for lung, gastric, colon or rectal cancer. We found that 56 patients out of 106 showed at least one alteration (53%), with 47 patients carrying at least one relevant nucleotide variant, 10 patients carrying at least one CNA and 3 patients carrying one gene fusion. On the basis of the mutational profiles obtained, we have identified 22 patients (20.7%) that were potentially eligible for targeted therapy. The most frequently mutated genes across all tumor types included KRAS (30 patients), PIK3CA (16 patients), BRAF (6 patients), EGFR (5 patients), NRAS (4 patients) and ERBB2 (3 patients) whereas CCND1, ERBB2, EGFR and MYC were the genes most frequently subjected to copy number gain. Finally, gene fusions were identified only in lung cancer patients and involved MET [MET(13)–MET(15) fusion] and FGFR3 [FGFR3(chr 17)–TACC3(chr 11)]. In conclusion, we demonstrate that the analysis with a multi-biomarker panel of cancer patients after surgery, may present several potential advantages in clinical daily practice, including the simultaneous detection of different potentially druggable alterations, reasonable costs, short time of testing and automated interpretation of results.
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9
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Wilson JL, Altman RB. Biomarkers: Delivering on the expectation of molecularly driven, quantitative health. Exp Biol Med (Maywood) 2018; 243:313-322. [PMID: 29199461 PMCID: PMC5813871 DOI: 10.1177/1535370217744775] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Biomarkers are the pillars of precision medicine and are delivering on expectations of molecular, quantitative health. These features have made clinical decisions more precise and personalized, but require a high bar for validation. Biomarkers have improved health outcomes in a few areas such as cancer, pharmacogenetics, and safety. Burgeoning big data research infrastructure, the internet of things, and increased patient participation will accelerate discovery in the many areas that have not yet realized the full potential of biomarkers for precision health. Here we review themes of biomarker discovery, current implementations of biomarkers for precision health, and future opportunities and challenges for biomarker discovery. Impact statement Precision medicine evolved because of the understanding that human disease is molecularly driven and is highly variable across patients. This understanding has made biomarkers, a diverse class of biological measurements, more relevant for disease diagnosis, monitoring, and selection of treatment strategy. Biomarkers' impact on precision medicine can be seen in cancer, pharmacogenomics, and safety. The successes in these cases suggest many more applications for biomarkers and a greater impact for precision medicine across the spectrum of human disease. The authors assess the status of biomarker-guided medical practice by analyzing themes for biomarker discovery, reviewing the impact of these markers in the clinic, and highlight future and ongoing challenges for biomarker discovery. This work is timely and relevant, as the molecular, quantitative approach of precision medicine is spreading to many disease indications.
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Affiliation(s)
- Jennifer L Wilson
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Russ B Altman
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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10
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D'Gama AM, Woodworth MB, Hossain AA, Bizzotto S, Hatem NE, LaCoursiere CM, Najm I, Ying Z, Yang E, Barkovich AJ, Kwiatkowski DJ, Vinters HV, Madsen JR, Mathern GW, Blümcke I, Poduri A, Walsh CA. Somatic Mutations Activating the mTOR Pathway in Dorsal Telencephalic Progenitors Cause a Continuum of Cortical Dysplasias. Cell Rep 2017; 21:3754-3766. [PMID: 29281825 PMCID: PMC5752134 DOI: 10.1016/j.celrep.2017.11.106] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 10/02/2017] [Accepted: 11/29/2017] [Indexed: 01/16/2023] Open
Abstract
Focal cortical dysplasia (FCD) and hemimegalencephaly (HME) are epileptogenic neurodevelopmental malformations caused by mutations in mTOR pathway genes. Deep sequencing of these genes in FCD/HME brain tissue identified an etiology in 27 of 66 cases (41%). Radiographically indistinguishable lesions are caused by somatic activating mutations in AKT3, MTOR, and PIK3CA and germline loss-of-function mutations in DEPDC5, NPRL2, and TSC1/2, including TSC2 mutations in isolated HME demonstrating a "two-hit" model. Mutations in the same gene cause a disease continuum from FCD to HME to bilateral brain overgrowth, reflecting the progenitor cell and developmental time when the mutation occurred. Single-cell sequencing demonstrated mTOR activation in neurons in all lesions. Conditional Pik3ca activation in the mouse cortex showed that mTOR activation in excitatory neurons and glia, but not interneurons, is sufficient for abnormal cortical overgrowth. These data suggest that mTOR activation in dorsal telencephalic progenitors, in some cases specifically the excitatory neuron lineage, causes cortical dysplasia.
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Affiliation(s)
- Alissa M D'Gama
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Mollie B Woodworth
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Amer A Hossain
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Nicole E Hatem
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Imad Najm
- Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zhong Ying
- Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Radiology, Harvard Medical School, Boston, MA 02115, USA
| | - A James Barkovich
- Departments of Radiology and Diagnostic Imaging, Neurology, Pediatrics, and Neurosurgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Harry V Vinters
- Departments of Pathology and Laboratory Medicine (Neuropathology) and Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joseph R Madsen
- Department of Neurosurgery, Boston Children's Hospital, Boston, MA, USA
| | - Gary W Mathern
- Departments of Neurosurgery and Psychiatry and Biobehavioral Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ingmar Blümcke
- Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Neuropathology, University Hospital Erlangen, Schwabachanlage 6, 91054 Erlangen, Germany
| | - Annapurna Poduri
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Epilepsy Genetics Program, Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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11
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Zhao L, Deng L, Li G, Jin H, Cai J, Shang H, Li Y, Wu H, Xu W, Zeng L, Zhang R, Zhao H, Wu P, Zhou Z, Zheng J, Ezanno P, Yang AX, Yan Q, Deem MW, He J. Single molecule sequencing of the M13 virus genome without amplification. PLoS One 2017; 12:e0188181. [PMID: 29253901 PMCID: PMC5734777 DOI: 10.1371/journal.pone.0188181] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 11/02/2017] [Indexed: 01/01/2023] Open
Abstract
Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias.
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Affiliation(s)
- Luyang Zhao
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Liwei Deng
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Gailing Li
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Huan Jin
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Jinsen Cai
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Huan Shang
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Yan Li
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Haomin Wu
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Weibin Xu
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Lidong Zeng
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Renli Zhang
- Reproductive Medical Center of Guangdong General Hospital & Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Huan Zhao
- Shenzhen Armed Police Hospital Reproductive Center, Luohu District, Shenzhen, China
| | - Ping Wu
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Zhiliang Zhou
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Jiao Zheng
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Pierre Ezanno
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Andrew X. Yang
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, China
| | - Qin Yan
- Direct Genomics Co., Ltd., Shenzhen, Guangdong, China
| | - Michael W. Deem
- Departments of Bioengineering and Physics & Astronomy, Rice University, Houston, TX, United States of America
| | - Jiankui He
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, China
- * E-mail:
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12
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Chia S, Low JL, Zhang X, Kwang XL, Chong FT, Sharma A, Bertrand D, Toh SY, Leong HS, Thangavelu MT, Hwang JSG, Lim KH, Skanthakumar T, Tan HK, Su Y, Hui Choo S, Hentze H, Tan IBH, Lezhava A, Tan P, Tan DSW, Periyasamy G, Koh JLY, Gopalakrishna Iyer N, DasGupta R. Phenotype-driven precision oncology as a guide for clinical decisions one patient at a time. Nat Commun 2017; 8:435. [PMID: 28874669 PMCID: PMC5585361 DOI: 10.1038/s41467-017-00451-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/30/2017] [Indexed: 12/22/2022] Open
Abstract
Genomics-driven cancer therapeutics has gained prominence in personalized cancer treatment. However, its utility in indications lacking biomarker-driven treatment strategies remains limited. Here we present a "phenotype-driven precision-oncology" approach, based on the notion that biological response to perturbations, chemical or genetic, in ex vivo patient-individualized models can serve as predictive biomarkers for therapeutic response in the clinic. We generated a library of "screenable" patient-derived primary cultures (PDCs) for head and neck squamous cell carcinomas that reproducibly predicted treatment response in matched patient-derived-xenograft models. Importantly, PDCs could guide clinical practice and predict tumour progression in two n = 1 co-clinical trials. Comprehensive "-omics" interrogation of PDCs derived from one of these models revealed YAP1 as a putative biomarker for treatment response and survival in ~24% of oral squamous cell carcinoma. We envision that scaling of the proposed PDC approach could uncover biomarkers for therapeutic stratification and guide real-time therapeutic decisions in the future.Treatment response in patient-derived models may serve as a biomarker for response in the clinic. Here, the authors use paired patient-derived mouse xenografts and patient-derived primary culture models from head and neck squamous cell carcinomas, including metastasis, as models for high-throughput screening of anti-cancer drugs.
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Affiliation(s)
- Shumei Chia
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Joo-Leng Low
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Xiaoqian Zhang
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Xue-Lin Kwang
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Fui-Teen Chong
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Ankur Sharma
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Denis Bertrand
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Shen Yon Toh
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Hui-Sun Leong
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Matan T Thangavelu
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Jacqueline S G Hwang
- Department of Anatomical Pathology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Kok-Hing Lim
- Department of Anatomical Pathology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Thakshayeni Skanthakumar
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Hiang-Khoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Yan Su
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Siang Hui Choo
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Hannes Hentze
- Biological Resource Centre (BRC), A*STAR, 20 Biopolis Way, #07-01 Centros, Singapore, 138668, Singapore
| | - Iain B H Tan
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Alexander Lezhava
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Daniel S W Tan
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Giridharan Periyasamy
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - Judice L Y Koh
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore
| | - N Gopalakrishna Iyer
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, 11 Hospital Drive, Singapore, 169610, Singapore.
| | - Ramanuj DasGupta
- Genome Institute of Singapore, A*STAR, Cancer Therapeutics & Stratified Oncology, PerkinElmer-GIS Centre for Precision Oncology, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore.
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