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Mosleh-Shirazi S, Abbasi M, Moaddeli MR, Vaez A, Shafiee M, Kasaee SR, Amani AM, Hatam S. Nanotechnology Advances in the Detection and Treatment of Cancer: An Overview. Nanotheranostics 2022; 6:400-423. [PMID: 36051855 PMCID: PMC9428923 DOI: 10.7150/ntno.74613] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/25/2022] [Indexed: 12/01/2022] Open
Abstract
Over the last few years, progress has been made across the nanomedicine landscape, in particular, the invention of contemporary nanostructures for cancer diagnosis and overcoming complexities in the clinical treatment of cancerous tissues. Thanks to their small diameter and large surface-to-volume proportions, nanomaterials have special physicochemical properties that empower them to bind, absorb and transport high-efficiency substances, such as small molecular drugs, DNA, proteins, RNAs, and probes. They also have excellent durability, high carrier potential, the ability to integrate both hydrophobic and hydrophilic compounds, and compatibility with various transport routes, making them especially appealing over a wide range of oncology fields. This is also due to their configurable scale, structure, and surface properties. This review paper discusses how nanostructures can function as therapeutic vectors to enhance the therapeutic value of molecules; how nanomaterials can be used as medicinal products in gene therapy, photodynamics, and thermal treatment; and finally, the application of nanomaterials in the form of molecular imaging agents to diagnose and map tumor growth.
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Affiliation(s)
- Sareh Mosleh-Shirazi
- Department of Materials Science and Engineering, Shiraz University of Technology, Shiraz, Iran
| | - Milad Abbasi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad reza Moaddeli
- Assistant Professor, Department of Oral and Maxillofacial Surgery, School of Dentistry, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Ahmad Vaez
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mostafa Shafiee
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Reza Kasaee
- Shiraz Endocrinology and Metabolism Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Mohammad Amani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeid Hatam
- Assistant Lecturer, Azad University, Zarghan Branch, Shiraz, Iran
- ExirBitanic, Science and Technology Park of Fars, Shiraz, Iran
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2
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Wei J, Meng P, Terpstra MM, van Rijk A, Tamminga M, Scherpen F, Ter Elst A, Alimohamed MZ, Johansson LF, Stigt J, Gijtenbeek RPG, van Putten J, Hiltermann TJN, Groen HJM, Kok K, van der Wekken AJ, van den Berg A. Clinical Value of EGFR Copy Number Gain Determined by Amplicon-Based Targeted Next Generation Sequencing in Patients with EGFR-Mutated NSCLC. Target Oncol 2021; 16:215-226. [PMID: 33606136 PMCID: PMC7935828 DOI: 10.1007/s11523-021-00798-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND The clinical relevance of epidermal growth factor receptor (EGFR) copy number gain in patients with EGFR mutated advanced non-small cell lung cancer on first-line tyrosine kinase inhibitor treatment has not been fully elucidated. OBJECTIVE We aimed to estimate EGFR copy number gain using amplicon-based next generation sequencing data and explored its prognostic value. PATIENTS AND METHODS Next generation sequencing data were obtained for 1566 patients with non-small cell lung cancer. EGFR copy number gain was defined based on an increase in EGFR read counts relative to internal reference amplicons and normal controls in combination with a modified z-score ≥ 3.5. Clinical follow-up data were available for 60 patients treated with first-line EGFR-tyrosine kinase inhibitors. RESULTS Specificity and sensitivity of next generation sequencing-based EGFR copy number estimations were above 90%. EGFR copy number gain was observed in 27.9% of EGFR mutant cases and in 7.4% of EGFR wild-type cases. EGFR gain was not associated with progression-free survival but showed a significant effect on overall survival with an adjusted hazard ratio of 3.14 (95% confidence interval 1.46-6.78, p = 0.003). Besides EGFR copy number gain, osimertinib in second or subsequent lines of treatment and the presence of T790M at relapse revealed significant effects in a multivariate analysis with adjusted hazard ratio of 0.43 (95% confidence interval 0.20-0.91, p = 0.028) and 0.24 (95% confidence interval 0.1-0.59, p = 0.001), respectively. CONCLUSIONS Pre-treatment EGFR copy number gain determined by amplicon-based next generation sequencing data predicts worse overall survival in EGFR-mutated patients treated with first-line EGFR-tyrosine kinase inhibitors. T790M at relapse and subsequent treatment with osimertinib predict longer overall survival.
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Affiliation(s)
- Jiacong Wei
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pathology, Cancer Hospital Chinese Academy of Medical Sciences, Beijing, China
| | - Pei Meng
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, HPC: EA10, Room F0-15, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
- Department of Pathology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, Guangdong, China
| | - Miente Martijn Terpstra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anke van Rijk
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, HPC: EA10, Room F0-15, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Menno Tamminga
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank Scherpen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, HPC: EA10, Room F0-15, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Arja Ter Elst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, HPC: EA10, Room F0-15, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Mohamed Z Alimohamed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | - Lennart F Johansson
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jos Stigt
- Department of Pulmonary Diseases, Isala Clinic, Zwolle, The Netherlands
| | - Rolof P G Gijtenbeek
- Department of Pulmonary Diseases, Medical Center Leeuwarden, Leeuwarden, The Netherlands
| | - John van Putten
- Department of Pulmonary Diseases, Martini Hospital, Groningen, The Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anthonie J van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, HPC: EA10, Room F0-15, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
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3
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Park K, Tran H, Eng KW, Ramazanoglu S, Marrero Rolon RM, Scognamiglio T, Borczuk A, Mosquera JM, Pan Q, Sboner A, Rubin MA, Elemento O, Rennert H, Fernandes H, Song W. Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome. Arch Pathol Lab Med 2021; 144:1535-1546. [PMID: 32045275 DOI: 10.5858/arpa.2019-0162-oa] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— An increasing number of molecular laboratories are implementing next-generation sequencing platforms to identify clinically actionable and relevant genomic alterations for precision oncology. OBJECTIVE.— To describe the validation studies as per New York State-Department of Health (NYS-DOH) guidelines for the Oncomine Comprehensive Panel v2, which was originally tailored to the National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH) trial. DESIGN.— Accuracy, precision, and reproducibility were investigated by using 130 DNA and 18 RNA samples from cytology cell blocks; formalin-fixed, paraffin-embedded tissues; and frozen samples. Analytic sensitivity and specificity were tested by using ATCC and HapMap cell lines. RESULTS.— High accuracy and precision/reproducibility were observed for single nucleotide variants and insertion/deletions. We also share our experience in the detection of gene fusions and copy number alterations from an amplicon-based sequencing platform. After sequencing analysis, variant annotation and report generation were performed by using the institutional knowledgebase. CONCLUSIONS.— This study serves as an example for validating a comprehensive targeted next-generation sequencing assay with both DNASeq and RNASeq components for NYS-DOH.
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Affiliation(s)
- Kyung Park
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Hung Tran
- Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Kenneth W Eng
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Sinan Ramazanoglu
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Rebecca M Marrero Rolon
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Theresa Scognamiglio
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Alain Borczuk
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Juan Miguel Mosquera
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Qiulu Pan
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Andrea Sboner
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Mark A Rubin
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Olivier Elemento
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Hanna Rennert
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Helen Fernandes
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Wei Song
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
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Petersen JK, Boldt HB, Sørensen MD, Blach S, Dahlrot RH, Hansen S, Burton M, Thomassen M, Kruse T, Poulsen FR, Andreasen L, Hager H, Ulhøi BP, Lukacova S, Reifenberger G, Kristensen BW. Targeted next-generation sequencing of adult gliomas for retrospective prognostic evaluation and up-front diagnostics. Neuropathol Appl Neurobiol 2020; 47:108-126. [PMID: 32696543 DOI: 10.1111/nan.12645] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/25/2020] [Accepted: 07/13/2020] [Indexed: 01/03/2023]
Abstract
AIMS We aimed to reclassify a population-based cohort of 529 adult glioma patients to evaluate the prognostic impact of the 2016 World Health Organization (WHO) central nervous system tumour classification. Moreover, we evaluated the feasibility of gene panel next-generation sequencing (NGS) in daily diagnostics of 225 prospective glioma patients. METHODS The retrospective cohort was reclassified according to WHO 2016 criteria by immunohistochemistry for IDH-R132H, fluorescence in situ hybridization for 1p/19q-codeletion and gene panel NGS. All tumours of the prospective cohort were subjected to NGS analysis up-front. RESULTS The entire population-based cohort was successfully reclassified according to WHO 2016 criteria. NGS results were obtained for 98% of the prospective patients. Survival analyses in the population-based cohort confirmed three major prognostic subgroups, that is, isocitrate dehydrogenase (IDH)-mutant and 1p/19q-codeleted oligodendrogliomas, IDH-mutant astrocytomas and IDH-wildtype glioblastomas. The distinction between WHO grade II and III was prognostic in patients with IDH-mutant astrocytoma. The survival of patients with IDH-wildtype diffuse astrocytomas carrying TERT promoter mutation and/or EGFR amplification overlapped with the poor survival of IDH-wildtype glioblastoma patients. CONCLUSIONS Gene panel NGS proved feasible in daily diagnostics. In addition, our study confirms the prognostic role of glioma classification according to WHO 2016 in a large population-based cohort. Molecular features of glioblastoma in IDH-wildtype diffuse glioma were linked to poor survival corresponding to IDH-wildtype glioblastoma patients. The distinction between WHO grade II and III retained prognostic significance in patients with IDH-mutant diffuse astrocytic gliomas.
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Affiliation(s)
- J K Petersen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - H B Boldt
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - M D Sørensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - S Blach
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - R H Dahlrot
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark
| | - S Hansen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark
| | - M Burton
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - M Thomassen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - T Kruse
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - F R Poulsen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Neurosurgery, Odense University Hospital, Odense, Denmark
| | - L Andreasen
- Department of Pathology, Vejle Hospital, Vejle, Denmark
| | - H Hager
- Department of Pathology, Vejle Hospital, Vejle, Denmark
| | - B P Ulhøi
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - S Lukacova
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - G Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, Germany.,German Cancer Consortium (DKTK), Partner site Essen/Düsseldorf, Düsseldorf, Germany
| | - B W Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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5
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Steeghs EMP, Kroeze LI, Tops BBJ, van Kempen LC, Ter Elst A, Kastner-van Raaij AWM, Hendriks-Cornelissen SJB, Hermsen MJW, Jansen EAM, Nederlof PM, Schuuring E, Ligtenberg MJL, Eijkelenboom A. Comprehensive routine diagnostic screening to identify predictive mutations, gene amplifications, and microsatellite instability in FFPE tumor material. BMC Cancer 2020; 20:291. [PMID: 32264863 PMCID: PMC7137451 DOI: 10.1186/s12885-020-06785-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/25/2020] [Indexed: 02/08/2023] Open
Abstract
Background Sensitive and reliable molecular diagnostics is needed to guide therapeutic decisions for cancer patients. Although less material becomes available for testing, genetic markers are rapidly expanding. Simultaneous detection of predictive markers, including mutations, gene amplifications and MSI, will save valuable material, time and costs. Methods Using a single-molecule molecular inversion probe (smMIP)-based targeted next-generation sequencing (NGS) approach, we developed an NGS panel allowing detection of predictive mutations in 33 genes, gene amplifications of 13 genes and microsatellite instability (MSI) by the evaluation of 55 microsatellite markers. The panel was designed to target all clinically relevant single and multiple nucleotide mutations in routinely available lung cancer, colorectal cancer, melanoma, and gastro-intestinal stromal tumor samples, but is useful for a broader set of tumor types. Results The smMIP-based NGS panel was successfully validated and cut-off values were established for reliable gene amplification analysis (i.e. relative coverage ≥3) and MSI detection (≥30% unstable loci). After validation, 728 routine diagnostic tumor samples including a broad range of tumor types were sequenced with sufficient sensitivity (2.4% drop-out), including samples with low DNA input (< 10 ng; 88% successful), low tumor purity (5–10%; 77% successful), and cytological material (90% successful). 75% of these tumor samples showed ≥1 (likely) pathogenic mutation, including targetable mutations (e.g. EGFR, BRAF, MET, ERBB2, KIT, PDGFRA). Amplifications were observed in 5.5% of the samples, comprising clinically relevant amplifications (e.g. MET, ERBB2, FGFR1). 1.5% of the tumor samples were classified as MSI-high, including both MSI-prone and non-MSI-prone tumors. Conclusions We developed a comprehensive workflow for predictive analysis of diagnostic tumor samples. The smMIP-based NGS analysis was shown suitable for limited amounts of histological and cytological material. As smMIP technology allows easy adaptation of panels, this approach can comply with the rapidly expanding molecular markers.
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Affiliation(s)
- Elisabeth M P Steeghs
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Bastiaan B J Tops
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.,Department of Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Leon C van Kempen
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Arja Ter Elst
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | - Mandy J W Hermsen
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.
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Backes Y, Seerden TCJ, van Gestel RSFE, Kranenburg O, Ubink I, Schiffelers RM, van Straten D, van der Capellen MS, van de Weerd S, de Leng WWJ, Siersema PD, Offerhaus GJA, Morsink FH, Ramphal W, Terhaar Sive Droste J, van Lent AUG, Geesing JMJ, Vleggaar FP, Elias SG, Lacle MM, Moons LMG. Tumor Seeding During Colonoscopy as a Possible Cause for Metachronous Colorectal Cancer. Gastroenterology 2019; 157:1222-1232.e4. [PMID: 31419435 DOI: 10.1053/j.gastro.2019.07.062] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/16/2019] [Accepted: 07/31/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS In patients who have undergone surgery for colorectal cancer (CRC), 3% have recurrence of (metachronous) CRC. We investigated whether tumor seeding during colonoscopy (iatrogenic implantation of tumor cells in damaged mucosa) increases risk for metachronous CRC. METHODS In a proof of principle study, we collected data from the Dutch National Pathology Registry for patients with a diagnosis of CRC from 2013 through 2015, with a second diagnosis of CRC within 6 months to 3.5 years after surgery. We reviewed pathology reports to identify likely metachronous CRC (histologically proven adenocarcinoma located elsewhere in the colon or rectum from the surgical anastomosis). For 22 patients fulfilling the inclusion criteria, we ascribed the most likely etiology to tumor seeding when endoscopic manipulations, such as biopsies or polypectomy, occurred at the location where the metachronous tumor was subsequently detected, after endoscopic manipulation of the primary tumor. We collected clinical data from patients and compared molecular profiles of the primary and metachronous colorectal tumors using next-generation sequencing. We then examined the source of seeded tumor. We tested whether tumor cells stay behind in the working channel of the endoscope after biopsies of colorectal tumors, and whether these cells maintain viability in organoid cultures. RESULTS In total, tumor seeding was suspected as the most likely etiology of metachronous CRC in 5 patients. Tumor tissues were available from 3 patients. An identical molecular signature was observed in the primary and metachronous colorectal tumors from all 3 patients. In 5 control cases with a different etiology of metachronous CRC, the molecular signature of the primary and metachronous tumor were completely different. Based on review of 2147 patient records, we estimated the risk of tumor seeding during colonoscopy to be 0.3%-0.6%. We demonstrated that the working channel of the colonoscope becomes contaminated with viable tumor cells during biopsy collection. Subsequent instruments introduced through this working channel also became contaminated. These cells were shown to maintain their proliferative potential. CONCLUSIONS In an analysis of primary and secondary tumors from patients with metachronous CRC, we found that primary tumor cells might be seeded in a new location after biopsy of the primary tumor. Although our study does not eliminate other possibilities of transmission, our findings and experiments support the hypothesis that tumor seeding can occur during colonoscopy via the working channel of the endoscope. The possibility of iatrogenic seeding seems low. However, our findings compel awareness on this potentially preventable cause of metachronous CRC.
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Affiliation(s)
- Yara Backes
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tom C J Seerden
- Department of Gastroenterology and Hepatology, Amphia Hospital, Breda, The Netherlands
| | - Rosanne S F E van Gestel
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Onno Kranenburg
- Cancer Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Inge Ubink
- Cancer Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Raymond M Schiffelers
- Laboratory of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Demian van Straten
- Laboratory of Clinical Chemistry and Hematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Malu S van der Capellen
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Simone van de Weerd
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Peter D Siersema
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G Johan A Offerhaus
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Folkert H Morsink
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Winesh Ramphal
- Department of Gastroenterology and Hepatology, Amphia Hospital, Breda, The Netherlands
| | | | - Anja U G van Lent
- Department of Gastroenterology and Hepatology, OLVG, Amsterdam, The Netherlands
| | - Joost M J Geesing
- Department of Gastroenterology and Hepatology, Diakonessenhuis, Utrecht, The Netherlands
| | - Frank P Vleggaar
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sjoerd G Elias
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Miangela M Lacle
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leon M G Moons
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, The Netherlands.
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7
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Moelans CB, de Ligt J, van der Groep P, Prins P, Besselink NJM, Hoogstraat M, Ter Hoeve ND, Lacle MM, Kornegoor R, van der Pol CC, de Leng WWJ, Barbé E, van der Vegt B, Martens J, Bult P, Smit VTHBM, Koudijs MJ, Nijman IJ, Voest EE, Selenica P, Weigelt B, Reis-Filho JS, van der Wall E, Cuppen E, van Diest PJ. The molecular genetic make-up of male breast cancer. Endocr Relat Cancer 2019; 26:779-794. [PMID: 31340200 PMCID: PMC6938562 DOI: 10.1530/erc-19-0278] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/23/2019] [Indexed: 12/17/2022]
Abstract
Male breast cancer (MBC) is extremely rare and accounts for less than 1% of all breast malignancies. Therefore, clinical management of MBC is currently guided by research on the disease in females. In this study, DNA obtained from 45 formalin-fixed paraffin-embedded (FFPE) MBCs with and 90 MBCs (52 FFPE and 38 fresh-frozen) without matched normal tissues was subjected to massively parallel sequencing targeting all exons of 1943 cancer-related genes. The landscape of mutations and copy number alterations was compared to that of publicly available estrogen receptor (ER)-positive female breast cancers (smFBCs) and correlated to prognosis. From the 135 MBCs, 90% showed ductal histology, 96% were ER-positive, 66% were progesterone receptor (PR)-positive, and 2% HER2-positive, resulting in 50, 46 and 4% luminal A-like, luminal B-like and basal-like cases, respectively. Five patients had Klinefelter syndrome (4%) and 11% of patients harbored pathogenic BRCA2 germline mutations. The genomic landscape of MBC to some extent recapitulated that of smFBC, with recurrent PIK3CA (36%) and GATA3 (15%) somatic mutations, and with 40% of the most frequently amplified genes overlapping between both sexes. TP53 (3%) somatic mutations were significantly less frequent in MBC compared to smFBC, whereas somatic mutations in genes regulating chromatin function and homologous recombination deficiency-related signatures were more prevalent. MDM2 amplifications were frequent (13%), correlated with protein overexpression (P = 0.001) and predicted poor outcome (P = 0.007). In conclusion, despite similarities in the genomic landscape between MBC and smFBC, MBC is a molecularly unique and heterogeneous disease requiring its own clinical trials and treatment guidelines.
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Affiliation(s)
- Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joep de Ligt
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Petra van der Groep
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Internal Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pjotr Prins
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nicolle J M Besselink
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Marlous Hoogstraat
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Natalie D Ter Hoeve
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Miangela M Lacle
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Robert Kornegoor
- Department of Pathology, Gelre Ziekenhuizen, Appeldoorn, The Netherlands
| | - Carmen C van der Pol
- Cancer Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ellis Barbé
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Bert van der Vegt
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John Martens
- Department of Medical Oncology, Daniel den Hoed Cancer Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter Bult
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Marco J Koudijs
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Isaac J Nijman
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
| | - Emile E Voest
- Center for Personalized Cancer Treatment, Rotterdam, The Netherlands
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Elsken van der Wall
- Cancer Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Edwin Cuppen
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Cancer Genomics.nl, Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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8
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Driehuis E, Kolders S, Spelier S, Lõhmussaar K, Willems SM, Devriese LA, de Bree R, de Ruiter EJ, Korving J, Begthel H, van Es JH, Geurts V, He GW, van Jaarsveld RH, Oka R, Muraro MJ, Vivié J, Zandvliet MMJM, Hendrickx APA, Iakobachvili N, Sridevi P, Kranenburg O, van Boxtel R, Kops GJPL, Tuveson DA, Peters PJ, van Oudenaarden A, Clevers H. Oral Mucosal Organoids as a Potential Platform for Personalized Cancer Therapy. Cancer Discov 2019; 9:852-871. [PMID: 31053628 DOI: 10.1158/2159-8290.cd-18-1522] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/01/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022]
Abstract
Previous studies have described that tumor organoids can capture the diversity of defined human carcinoma types. Here, we describe conditions for long-term culture of human mucosal organoids. Using this protocol, a panel of 31 head and neck squamous cell carcinoma (HNSCC)-derived organoid lines was established. This panel recapitulates genetic and molecular characteristics previously described for HNSCC. Organoids retain their tumorigenic potential upon xenotransplantation. We observe differential responses to a panel of drugs including cisplatin, carboplatin, cetuximab, and radiotherapy in vitro. Additionally, drug screens reveal selective sensitivity to targeted drugs that are not normally used in the treatment of patients with HNSCC. These observations may inspire a personalized approach to the management of HNSCC and expand the repertoire of HNSCC drugs. SIGNIFICANCE: This work describes the culture of organoids derived from HNSCC and corresponding normal epithelium. These tumoroids recapitulate the disease genetically, histologically, and functionally. In vitro drug screening of tumoroids reveals responses to therapies both currently used in the treatment of HNSCC and those not (yet) used in clinical practice.See related commentary by Hill and D'Andrea, p. 828.This article is highlighted in the In This Issue feature, p. 813.
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Affiliation(s)
- Else Driehuis
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sigrid Kolders
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sacha Spelier
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kadi Lõhmussaar
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lot A Devriese
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Emma J de Ruiter
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeroen Korving
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Harry Begthel
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Johan H van Es
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Veerle Geurts
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gui-Wei He
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Richard H van Jaarsveld
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rurika Oka
- Princess Maxima Center, Utrecht, the Netherlands
| | - Mauro J Muraro
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.,Single Cell Discoveries, Utrecht, the Netherlands
| | - Judith Vivié
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands.,Single Cell Discoveries, Utrecht, the Netherlands
| | - Maurice M J M Zandvliet
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | - Antoni P A Hendrickx
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nino Iakobachvili
- M4I Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Priya Sridevi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Onno Kranenburg
- Utrecht Platform for Organoid Technology (U-PORT), Utrecht Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Peter J Peters
- M4I Division of Nanoscopy, Maastricht University, Maastricht, the Netherlands
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands. .,Princess Maxima Center, Utrecht, the Netherlands
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9
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Eijkelenboom A, Tops BBJ, van den Berg A, van den Brule AJC, Dinjens WNM, Dubbink HJ, Ter Elst A, Geurts-Giele WRR, Groenen PJTA, Groenendijk FH, Heideman DAM, Huibers MMH, Huijsmans CJJ, Jeuken JWM, van Kempen LC, Korpershoek E, Kroeze LI, de Leng WWJ, van Noesel CJM, Speel EJM, Vogel MJ, van Wezel T, Nederlof PM, Schuuring E, Ligtenberg MJL. Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics. Virchows Arch 2019; 474:673-680. [PMID: 30888490 PMCID: PMC6581937 DOI: 10.1007/s00428-019-02555-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/14/2019] [Accepted: 03/03/2019] [Indexed: 01/09/2023]
Abstract
Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity.
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Affiliation(s)
- Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Anke van den Berg
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Arja Ter Elst
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Willemina R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Floris H Groenendijk
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Daniëlle A M Heideman
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Manon M H Huibers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Léon C van Kempen
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Esther Korpershoek
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ernst-Jan M Speel
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Maartje J Vogel
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.
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10
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Strengman E, Barendrecht-Smouter FAS, de Voijs C, de Vree P, Nijman IJ, de Leng WWJ. Amplicon-Based Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue. Methods Mol Biol 2019; 1908:1-17. [PMID: 30649717 DOI: 10.1007/978-1-4939-9004-7_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Next-generation sequencing (NGS) is rapidly becoming the method of choice for mutation analysis in both research and diagnostics. The benefit of targeted NGS compared to whole-genome and whole-exome sequencing is that smaller amounts of input material can be used as well as qualitatively suboptimal tissue samples, like formalin-fixed, paraffin-embedded archival tissue.Here, we describe the protocol for targeted next-generation sequencing using the Ion Torrent PGM platform in combination with Ion Ampliseq NGS gene panels for formalin-fixed, paraffin-embedded tissues. Both the manual and the automated workflow are described as well as the bioinformatics for data analysis.
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Affiliation(s)
- Eric Strengman
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Carmen de Voijs
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paula de Vree
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Isaac J Nijman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands.
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11
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Priesterbach-Ackley LP, Wesseling P, Snijders TJ, de Vos FYFL, de Leng WWJ. Molecular tools for the pathologic diagnosis of central nervous system tumors. Neurooncol Pract 2019; 6:4-16. [PMID: 31386041 PMCID: PMC6656323 DOI: 10.1093/nop/npy041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Molecular diagnostics currently has a crucial role in neuro-oncological patient care. (Epi)genetic assays testing for point mutations, copy number variations, gene fusions, translocations, and methylation status are of main diagnostic interest in neuro-oncology. Multiple assays have been developed for this purpose, ranging from single gene tests to high-throughput, integrated techniques enabling detection of multiple genetic aberrations in a single workflow. This review describes the nature of the simpler and more complex assays for molecular diagnostics of tumors of the central nervous system and briefly discusses their strengths and weaknesses.
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Affiliation(s)
| | - Pieter Wesseling
- Department of Pathology, Princess Máxima Center for Pediatric Oncology and University Medical Center Utrecht, The Netherlands
- Department of Pathology, VU University Medical Center/Brain Tumor Center Amsterdam, The Netherlands
| | - Tom J Snijders
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, The Netherlands
| | - Filip Y F L de Vos
- Department of Medical Oncology, University Medical Center Utrecht, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, The Netherlands
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12
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Crizotinib treatment for patients with EGFR mutation positive NSCLC that acquire cMET amplification after EGFR TKI therapy results in short-lived and heterogeneous responses. Lung Cancer 2018; 124:130-134. [DOI: 10.1016/j.lungcan.2018.07.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/05/2018] [Accepted: 07/20/2018] [Indexed: 12/15/2022]
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13
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Budczies J, Pfarr N, Romanovsky E, Endris V, Stenzinger A, Denkert C. Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data. BMC Bioinformatics 2018; 19:157. [PMID: 29699497 PMCID: PMC5921540 DOI: 10.1186/s12859-018-2159-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research, CNA analysis in a single assay together with somatic mutations is highly desirable. RESULTS Ioncopy is a validated method and easy-to-use software for CNA calling from targeted NGS data. Copy number and significance of CNA are estimated for each gene in each sample. Copy number gains and losses are called after multiple testing corrections controlling FWER or FDR. CONCLUSIONS Ioncopy facilitates calling of CNAs in a cohort of tumors tissues with or without using normal (germline) DNA controls.
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Affiliation(s)
- Jan Budczies
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany. .,German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany.
| | - Nicole Pfarr
- Institute of Pathology, Technical University Munich (TUM), Munich, Germany.,German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany
| | - Eva Romanovsky
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany
| | - Carsten Denkert
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Berlin, Munich and Heidelberg partner sites, Germany
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14
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D'Haene N, Fontanges Q, De Nève N, Blanchard O, Melendez B, Delos M, Dehou MF, Maris C, Nagy N, Rousseau E, Vandenhove J, Gilles A, De Prez C, Verset L, Van Craynest MP, Demetter P, Van Laethem JL, Salmon I, Le Mercier M. Clinical application of targeted next-generation sequencing for colorectal cancer patients: a multicentric Belgian experience. Oncotarget 2018; 9:20761-20768. [PMID: 29755687 PMCID: PMC5945518 DOI: 10.18632/oncotarget.25099] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/17/2018] [Indexed: 01/14/2023] Open
Abstract
International guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-EGFR agents for metastatic colorectal cancer (CRC) patients. Daily, new data emerges on the theranostic and prognostic role of molecular biomarkers; this is a strong incentive for a validated, sensitive, and broadly available molecular screening test. Next-generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. We report here our 2 years of clinical practice using NGS results to guide therapeutic decisions. The Ion Torrent AmpliSeq colon/lung cancer panel, which allows mutation detection in 22 cancer-related genes, was prospectively used in clinical practice (BELAC ISO 15189 accredited method). The DNA of 741 formalin-fixed paraffin-embedded CRC tissues, including primary tumors and metastasis, was obtained from 14 different Belgian institutions and subjected to targeted NGS. Of the tumors tested, 98% (727) were successfully sequenced and 89% (650) harbored at least one mutation. KRAS, BRAF and NRAS mutations were found in 335 (46%), 78 (11%) and 32 (4%) samples, respectively. These mutation frequencies were consistent with those reported in public databases. Moreover, mutations and amplifications in potentially actionable genes were identified in 464 samples (64%), including mutations in PIK3CA (14%), ERBB2 (0.4%), AKT1 (0.6%), and MAP2K1 (0.1%), as well as amplifications of ERBB2 (0.3%) and EGFR (0.3%). The median turnaround time between reception of the sample in the laboratory and report release was 8 calendar days. Overall, the AmpliSeq colon/lung cancer panel was successfully applied in daily practice and provided reliable clinically relevant information for CRC patients.
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Affiliation(s)
- Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Quitterie Fontanges
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Nancy De Nève
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Oriane Blanchard
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Barbara Melendez
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Monique Delos
- Department of Pathology, CHU UCL Namur, Yvoir, Belgium
| | | | - Calliope Maris
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Department of Pathology, Braine l´Alleud Waterloo Hospital, Braine l´Alleud, Belgium
| | - Nathalie Nagy
- Department of Pathology, Charleroi University Hospital, Charleroi, Belgium
| | | | | | - André Gilles
- Department of Pathology, EPICURA Hospital, Frameries, Belgium
| | - Carine De Prez
- Department of Pathology, Brugmann University Hospital, Brussels, Belgium
| | - Laurine Verset
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.,CurePath, Jumet, Belgium
| | | | - Pieter Demetter
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Luc Van Laethem
- Department of Oncology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Le Mercier
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
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15
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Tanzima Nuhat S, Sakata-Yanagimoto M, Komori D, Hattori K, Suehara Y, Fukumoto K, Fujisawa M, Kusakabe M, Matsue K, Wakamatsu H, Shimadzu M, Chiba S. Droplet digital polymerase chain reaction assay and peptide nucleic acid-locked nucleic acid clamp method for RHOA mutation detection in angioimmunoblastic T-cell lymphoma. Cancer Sci 2018; 109:1682-1689. [PMID: 29493850 PMCID: PMC5980118 DOI: 10.1111/cas.13557] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 12/11/2022] Open
Abstract
Angioimmunoblastic T‐cell lymphoma (AITL) is a subtype of nodal peripheral T‐cell lymphoma (PTCL). Somatic RHOA mutations, most frequently found at the hotspot site c.50G > T, p.Gly17Val (G17V RHOA mutation) are a genetic hallmark of AITL. Detection of the G17V RHOA mutations assists prompt and appropriate diagnosis of AITL. However, an optimal detection method for the G17V RHOA mutation remains to be elucidated. We compared the sensitivity and concordance of next‐generation sequencing (NGS), droplet digital PCR (ddPCR) and peptide nucleic acid‐locked nucleic acid (PNA‐LNA) clamp method for detecting the G17V RHOA mutation. G17V RHOA mutations were identified in 27 of 67 (40.3%) PTCL samples using NGS. ddPCR and PNA‐LNA clamp method both detected G17V mutations in 4 samples in addition to those detected with NGS (31 of 67, 46.3%). Additionally, variant allele frequencies with ddPCR and those with NGS showed high concordance (P < .001). Three other RHOA mutations involving the p.Gly17 position (c.[49G > T;50G > T], p.Gly17Leu in PTCL198; c.[50G > T;51A > C], p.Gly17Val in PTCL216; and c.50G > A, p.Gly17Glu in PTCL223) were detected using NGS. These sequence changes could not appropriately be detected using the ddPCR assay and the PNA‐LNA clamp method although both indicated that the samples might have mutations. In total, 34 out of 67 PTCL samples (50.7%) had RHOA mutations at the p.Gly17 position. In conclusion, our results suggested that a combination of ddPCR/PNA‐LNA clamp methods and NGS are best method to assist the diagnosis of AITL by detecting RHOA mutations at the p.Gly17 position.
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Affiliation(s)
- Sharna Tanzima Nuhat
- Department of Hematology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | | | - Daisuke Komori
- Department of Hematology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Keiichiro Hattori
- Department of Hematology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yasuhito Suehara
- Department of Hematology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kota Fukumoto
- Department of Hematology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Manabu Fujisawa
- Department of Hematology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Manabu Kusakabe
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kosei Matsue
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | | | | | - Shigeru Chiba
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.,Life Science Centre of Tsukuba Advanced Research Alliance University of Tsukuba, Tsukuba, Japan
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16
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Venkatesan S, Hoogstraat M, Caljouw E, Pierson T, Spoor JKH, Zeneyedpour L, Dubbink HJ, Dekker LJ, van der Kaaij M, Kloezeman J, Berghauser Pont LME, Besselink NJM, Luider TM, Joore J, Martens JW, Lamfers MLM, Sleijfer S, Leenstra S. TP53 mutated glioblastoma stem-like cell cultures are sensitive to dual mTORC1/2 inhibition while resistance in TP53 wild type cultures can be overcome by combined inhibition of mTORC1/2 and Bcl-2. Oncotarget 2018; 7:58435-58444. [PMID: 27533080 PMCID: PMC5295441 DOI: 10.18632/oncotarget.11205] [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: 01/11/2016] [Accepted: 07/26/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Glioblastoma is the most malignant tumor of the central nervous system and still lacks effective treatment. This study explores mutational biomarkers of 11 drugs targeting either the RTK/Ras/PI3K, the p53 or the Rb pathway using 25 patient-derived glioblastoma stem-like cell cultures (GSCs). RESULTS We found that TP53 mutated GSCs were approximately 3.5 fold more sensitive to dual inhibition of mammalian target of rapamycin complex 1 and 2 (mTORC1/2) compared to wild type GSCs. We identified that Bcl-2(Thr56/Ser70) phosphorylation contributed to the resistance of TP53 wild type GSCs against dual mTORC1/2 inhibition. The Bcl-2 inhibitor ABT-263 (navitoclax) increased sensitivity to the mTORC1/2 inhibitor AZD8055 in TP53 wild type GSCs, while sensitivity to AZD8055 in TP53 mutated GSCs remained unchanged. CONCLUSION Our data suggest that Bcl-2 confers resistance to mTORC1/2 inhibitors in TP53 wild type GSCs and that combined inhibition of both mTORC1/2 and Bcl-2 is worthwhile to explore further in TP53 wild type glioblastomas, whereas in TP53 mutated glioblastomas dual mTORC1/2 inhibitors should be explored.
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Affiliation(s)
| | - Marlous Hoogstraat
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Personalized Cancer Treatment (CPCT), University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Tessa Pierson
- Department of Neurosurgery, Brain Tumor Center Erasmus MC, Rotterdam, The Netherlands
| | - Jochem K H Spoor
- Department of Neurosurgery, Brain Tumor Center Erasmus MC, Rotterdam, The Netherlands
| | - Lona Zeneyedpour
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Lennard J Dekker
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Jenneke Kloezeman
- Department of Neurosurgery, Brain Tumor Center Erasmus MC, Rotterdam, The Netherlands
| | | | - Nicolle J M Besselink
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Personalized Cancer Treatment (CPCT), University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Jos Joore
- Pepscope BV, Utrecht, The Netherlands
| | - John W Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.,Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Martine L M Lamfers
- Department of Neurosurgery, Brain Tumor Center Erasmus MC, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Center for Personalized Cancer Treatment (CPCT), University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.,Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Sieger Leenstra
- Department of Neurosurgery, Brain Tumor Center Erasmus MC, Rotterdam, The Netherlands.,Department of Neurosurgery, St. Elisabeth Hospital Tilburg, Tilburg, The Netherlands
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17
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van Ginkel JH, de Leng WWJ, de Bree R, van Es RJJ, Willems SM. Targeted sequencing reveals TP53 as a potential diagnostic biomarker in the post-treatment surveillance of head and neck cancer. Oncotarget 2018; 7:61575-61586. [PMID: 27528217 PMCID: PMC5308673 DOI: 10.18632/oncotarget.11196] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/28/2016] [Indexed: 02/07/2023] Open
Abstract
Head and neck squamous cell carcinomas (HNSCC) form a large heterogeneous group of tumors and have a relatively poor outcome in advanced cases. Revealing the underlying genetic mutations in HNSCC facilitates the development of diagnostic biomarkers, which might lead to improved diagnosis and post treatment surveillance. We retrospectively analyzed mutational hotspots using targeted next-generation sequencing (NGS) of 239 HNSCC tumor samples in order to examine the mutational profile of HNSCC. Furthermore, we assessed prevalence, co-occurrence, and synonymy of gene mutations in (matched) tumor samples. TP53 was found mutated the most frequent with mutation rates of up to 83% in all tumors, compared to mutation rates of between 0 and 21% of CDKN2A, PIK3CA, HRAS, CDK4, FBXW7 and RB1. Mutational co-occurrence predominantly existed between TP53 and PIK3CA, TP53 and CDKN2A, and HRAS and PIK3CA. Mutational synonymy between primary tumor and associated metastasis and recurrence was present in respectively 88% and 89%. TP53 mutations were concordantly mutated in 95% of metastases and in 91% of recurrences. This indicates TP53 mutations to be highly prevalent and concordant in primary tumors and associated locoregional metastases and recurrences. In turn, this provides ground for further investigating the use of TP53 mutations as diagnostic biomarkers in HNSCC patients.
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Affiliation(s)
- Joost H van Ginkel
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robert J J van Es
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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18
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Budczies J, Pfarr N, Stenzinger A, Treue D, Endris V, Ismaeel F, Bangemann N, Blohmer JU, Dietel M, Loibl S, Klauschen F, Weichert W, Denkert C. Ioncopy: a novel method for calling copy number alterations in amplicon sequencing data including significance assessment. Oncotarget 2017; 7:13236-47. [PMID: 26910888 PMCID: PMC4914355 DOI: 10.18632/oncotarget.7451] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/23/2016] [Indexed: 01/25/2023] Open
Abstract
Recently, it has been demonstrated that calling of copy number alterations (CNAs) from amplicon sequencing (AS) data is feasible. Most approaches, however, require non-tumor (germline) DNA for data normalization. Here, we present the method Ioncopy for CNA detection which requires no normal controls and includes a significance assessment for each detected alteration. Ioncopy was evaluated in a cohort of 184 clinically annotated breast carcinomas. A total number of 252 amplifications were detected, of which 183 (72.6%) could be validated by a call of an additional amplicon interrogating the same gene. Moreover, a total number of 33 deletions were found, whereof 27 (81.8%) could be validated. Analyzing the 16 most frequently amplified genes, validation rates of over 89% could be achieved for 11 of these genes. 11 of the top 16 genes showed significant overexpression in the amplified tumors. 89.5% of the HER2-amplified tumors were GRB7 and STARD3 co-amplified, whereas 68.4% of the HER2-amplified tumors had additional MED1 amplifications. Correlations between CNAs measured by amplicons in HER2 exons 19, 20 and 21 were strong (all R > 0.93). AS based detection of HER2 amplifications had a sensitivity of 90.0% and a specificity of 98.8% compared to the gold standard of HER2 immunohistochemistry combined with in situ hybridization. In summary, we developed and validated a novel method for detection and significance assessment of CNAs in amplicon sequencing data. Using Ioncopy, AS offers a straightforward and efficient approach to simultaneously analyze gene amplifications and gene deletions together with simple somatic mutations in a single assay.
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Affiliation(s)
- Jan Budczies
- Institute of Pathology, Charité University Hospital, Berlin, Germany.,German Cancer Consortium (DKTK), partner sites Berlin, Heidelberg and Munich, Germany
| | - Nicole Pfarr
- German Cancer Consortium (DKTK), partner sites Berlin, Heidelberg and Munich, Germany.,Institute of Pathology, University Hospital, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK), partner sites Berlin, Heidelberg and Munich, Germany.,Institute of Pathology, University Hospital, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Department of Pathology, Center for Integrated Diagnostics (CID), Massachusetts General Hospital/Harvard Medical School, Boston, USA
| | - Denise Treue
- Institute of Pathology, Charité University Hospital, Berlin, Germany
| | - Volker Endris
- German Cancer Consortium (DKTK), partner sites Berlin, Heidelberg and Munich, Germany.,Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Fakher Ismaeel
- Department of Gynecology, Charité University Hospital, Berlin, Germany
| | - Nikola Bangemann
- Interdisciplinary Breast Center, Charité University Hospital, Berlin, Germany
| | - Jens-Uwe Blohmer
- Interdisciplinary Breast Center, Charité University Hospital, Berlin, Germany
| | - Manfred Dietel
- Institute of Pathology, Charité University Hospital, Berlin, Germany.,German Cancer Consortium (DKTK), partner sites Berlin, Heidelberg and Munich, Germany
| | | | | | - Wilko Weichert
- German Cancer Consortium (DKTK), partner sites Berlin, Heidelberg and Munich, Germany.,Institute of Pathology, University Hospital, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Carsten Denkert
- Institute of Pathology, Charité University Hospital, Berlin, Germany.,German Cancer Consortium (DKTK), partner sites Berlin, Heidelberg and Munich, Germany
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19
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Katz‐Summercorn A, Anand S, Ingledew S, Huang Y, Roberts T, Galeano‐Dalmau N, O'Donovan M, Liu H, Fitzgerald RC. Application of a multi-gene next-generation sequencing panel to a non-invasive oesophageal cell-sampling device to diagnose dysplastic Barrett's oesophagus. J Pathol Clin Res 2017; 3:258-267. [PMID: 29085666 PMCID: PMC5653927 DOI: 10.1002/cjp2.80] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/30/2017] [Accepted: 07/13/2017] [Indexed: 12/14/2022]
Abstract
The early detection and endoscopic treatment of patients with the dysplastic stage of Barrett's oesophagus is a key to preventing progression to oesophageal adenocarcinoma. However, endoscopic surveillance protocols are hampered by the invasiveness of repeat endoscopy, sampling bias, and a subjective histopathological diagnosis of dysplasia. In this case-control study, we investigated the use of a non-invasive, pan-oesophageal cell-sampling device, the Cytosponge™, coupled with a cancer hot-spot panel to identify patients with dysplastic Barrett's oesophagus. Formalin-fixed, paraffin-embedded (FFPE) Cytosponge™ samples from 31 patients with non-dysplastic and 28 with dysplastic Barrett's oesophagus with good available clinical annotation were selected for inclusion. Samples were microdissected and amplicon sequencing performed using a panel covering >2800 COSMIC hot-spot mutations in 50 oncogenes and tumour suppressor genes. Strict mutation criteria were determined and duplicates were run to confirm any mutations with an allele frequency <12%. When compared with endoscopy and biopsy as the gold standard the panel achieved a 71.4% sensitivity (95% CI 51.3-86.8) and 90.3% (95% CI 74.3-98.0) specificity for diagnosing dysplasia. TP53 had the highest rate of mutation in 14/28 dysplastic samples (50%). CDKN2A was mutated in 6/28 (21.4%), ERBB2 in 3/28 (10.7%), and 5 other genes at lower frequency. The only gene from this panel found to be mutated in the non-dysplastic cases was CDKN2A in 3/31 cases (9.7%) in keeping with its known loss early in the natural history of the disease. Hence, it is possible to apply a multi-gene cancer hot-spot panel and next-generation sequencing to microdissected, FFPE samples collected by the Cytosponge™, in order to distinguish non-dysplastic from dysplastic Barrett's oesophagus. Further work is required to maximize the panel sensitivity.
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Affiliation(s)
- Annalise Katz‐Summercorn
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research CentreBox 197, Cambridge Biomedical CampusCambridgeUK
| | - Shubha Anand
- Molecular Malignancy Laboratory, Haematology and Oncology Diagnostic ServiceAddenbrooke's Hospital, Cambridge University Hospitals NHS Foundation TrustCambridgeUK
| | - Sophie Ingledew
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research CentreBox 197, Cambridge Biomedical CampusCambridgeUK
| | - Yuanxue Huang
- Molecular Malignancy Laboratory, Haematology and Oncology Diagnostic ServiceAddenbrooke's Hospital, Cambridge University Hospitals NHS Foundation TrustCambridgeUK
| | - Thomas Roberts
- Molecular Malignancy Laboratory, Haematology and Oncology Diagnostic ServiceAddenbrooke's Hospital, Cambridge University Hospitals NHS Foundation TrustCambridgeUK
| | - Nuria Galeano‐Dalmau
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research CentreBox 197, Cambridge Biomedical CampusCambridgeUK
| | - Maria O'Donovan
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research CentreBox 197, Cambridge Biomedical CampusCambridgeUK
| | - Hongxiang Liu
- Molecular Malignancy Laboratory, Haematology and Oncology Diagnostic ServiceAddenbrooke's Hospital, Cambridge University Hospitals NHS Foundation TrustCambridgeUK
| | - Rebecca C Fitzgerald
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research CentreBox 197, Cambridge Biomedical CampusCambridgeUK
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20
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van Winkel E, de Leng W, Witteveen P, Jonges T, Willems S, Langenberg M. Next-Generation Sequencing in Gynaecological Tumours: The Prognostic and Predictive Value of the Most Common Mutations Found in Ovarian, Endometrial, and Cervical Tumours: Literature Review and the University Medical Centre Utrecht Next-Generation Sequencing Data. Pathobiology 2017. [DOI: 10.1159/000479797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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21
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Wing MR, Reeser JW, Smith AM, Reeder M, Martin D, Jewell BM, Datta J, Miya J, Monk JP, Mortazavi A, Otterson GA, Goldberg RM, VanDeusen JB, Cole S, Dittmar K, Jaiswal S, Kinzie M, Waikhom S, Freud AG, Zhou XP, Chen W, Bhatt D, Roychowdhury S. Analytic validation and real-time clinical application of an amplicon-based targeted gene panel for advanced cancer. Oncotarget 2017; 8:75822-75833. [PMID: 29100271 PMCID: PMC5652665 DOI: 10.18632/oncotarget.20616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 08/14/2017] [Indexed: 12/20/2022] Open
Abstract
Multiplex somatic testing has emerged as a strategy to test patients with advanced cancer. We demonstrate our analytic validation approach for a gene hotspot panel and real-time prospective clinical application for any cancer type. The TruSight Tumor 26 assay amplifies 85 somatic hotspot regions across 26 genes. Using cell line and tumor mixes, we observed that 100% of the 14,715 targeted bases had at least 1000x raw coverage. We determined the sensitivity (100%, 95% CI: 96-100%), positive predictive value (100%, 95% CI: 96-100%), reproducibility (100% concordance), and limit of detection (3% variant allele frequency at 1000x read depth) of this assay to detect single nucleotide variants and small insertions and deletions. Next, we applied the assay prospectively in a clinical tumor sequencing study to evaluate 174 patients with metastatic or advanced cancer, including frozen tumors, formalin-fixed tumors, and enriched peripheral blood mononuclear cells in hematologic cancers. We reported one or more somatic mutations in 89 (53%) of the sequenced tumors (167 passing quality filters). Forty-three of these patients (26%) had mutations that would enable eligibility for targeted therapies. This study demonstrates the validity and feasibility of applying TruSight Tumor 26 for pan-cancer testing using multiple specimen types.
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Affiliation(s)
- Michele R Wing
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Julie W Reeser
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Amy M Smith
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Matthew Reeder
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Dorrelyn Martin
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Benjamin M Jewell
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jharna Datta
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jharna Miya
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - J Paul Monk
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Amir Mortazavi
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Gregory A Otterson
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Richard M Goldberg
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | | | | | - Kristin Dittmar
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Sunny Jaiswal
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Matthew Kinzie
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Suraj Waikhom
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Aharon G Freud
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Xiao-Ping Zhou
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA.,University Pathologists, LLC, Department of Pathology, Roger Williams Medical Center, Providence, RI, USA
| | - Wei Chen
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Darshna Bhatt
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Sameek Roychowdhury
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
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22
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van Ginkel JH, Huibers MMH, van Es RJJ, de Bree R, Willems SM. Droplet digital PCR for detection and quantification of circulating tumor DNA in plasma of head and neck cancer patients. BMC Cancer 2017. [PMID: 28629339 PMCID: PMC5477260 DOI: 10.1186/s12885-017-3424-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background During posttreatment surveillance of head and neck cancer patients, imaging is insufficiently accurate for the early detection of relapsing disease. Free circulating tumor DNA (ctDNA) may serve as a novel biomarker for monitoring tumor burden during posttreatment surveillance of these patients. In this exploratory study, we investigated whether low level ctDNA in plasma of head and neck cancer patients can be detected using Droplet Digital PCR (ddPCR). Methods TP53 mutations were determined in surgically resected primary tumor samples from six patients with high stage (II-IV), moderate to poorly differentiated head and neck squamous cell carcinoma (HNSCC). Subsequently, mutation specific ddPCR assays were designed. Pretreatment plasma samples from these patients were examined on the presence of ctDNA by ddPCR using the mutation-specific assays. The ddPCR results were evaluated alongside clinicopathological data. Results In all cases, plasma samples were found positive for targeted TP53 mutations in varying degrees (absolute quantification of 2.2–422 mutational copies/ml plasma). Mutations were detected in wild-type TP53 background templates of 7667–156,667 copies/ml plasma, yielding fractional abundances of down to 0.01%. Conclusions Our results show that detection of tumor specific TP53 mutations in low level ctDNA from HNSCC patients using ddPCR is technically feasible and provide ground for future research on ctDNA quantification for the use of diagnostic biomarkers in the posttreatment surveillance of HNSCC patients. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3424-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joost H van Ginkel
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands. .,Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.
| | - Manon M H Huibers
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Robert J J van Es
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Head and Neck Surgical Oncology, UMC Utrecht Cancer Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, UMC Utrecht Cancer Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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23
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Kluk MJ, Lindsley RC, Aster JC, Lindeman NI, Szeto D, Hall D, Kuo FC. Validation and Implementation of a Custom Next-Generation Sequencing Clinical Assay for Hematologic Malignancies. J Mol Diagn 2017; 18:507-15. [PMID: 27339098 DOI: 10.1016/j.jmoldx.2016.02.003] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/30/2015] [Accepted: 02/02/2016] [Indexed: 11/19/2022] Open
Abstract
Targeted next-generation sequencing panels to identify genetic alterations in cancers are increasingly becoming an integral part of clinical practice. We report here the design, validation, and implementation of a comprehensive 95-gene next-generation sequencing panel targeted for hematologic malignancies that we named rapid heme panel. Rapid heme panel is amplicon based and covers hotspot regions of oncogenes and most of the coding regions of tumor suppressor genes. It is composed of 1330 amplicons and covers 175 kb of genomic sequence in total. Rapid heme panel's average coverage is 1500× with <5% of the amplicons with <50× coverage, and it reproducibly detects single nucleotide variants and small insertions/deletions at allele frequencies of ≥5%. Comparison with a capture-based next-generation sequencing assay showed that there is >95% concordance among a wide array of variants across a range of allele frequencies. Read count analyses that used rapid heme panel showed high concordance with karyotypic results when tumor content was >30%. The average turnaround time was 7 days over a 6-month span with an average volume of ≥40 specimens per week and a low sample fail rate (<1%), demonstrating its suitability for clinical application.
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Affiliation(s)
- Michael J Kluk
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, Massachusetts
| | - R Coleman Lindsley
- Department of Medical Oncology, Division of Hematological Malignancies, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jon C Aster
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Neal I Lindeman
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, Massachusetts
| | - David Szeto
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Dimity Hall
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Frank C Kuo
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, Massachusetts.
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Single-Center Experience with a Targeted Next Generation Sequencing Assay for Assessment of Relevant Somatic Alterations in Solid Tumors. Neoplasia 2017; 19:196-206. [PMID: 28161563 PMCID: PMC5293722 DOI: 10.1016/j.neo.2017.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/18/2017] [Accepted: 01/18/2017] [Indexed: 02/07/2023] Open
Abstract
Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material. Cohort I consisted of 59 diagnostic clinical samples from the daily routine submitted for molecular testing over a 4-month time period. Cohort II consisted of 39 archival melanoma samples that were up to 15years old. Libraries were prepared from isolated nucleic acids and sequenced on the Ion Torrent PGM sequencer. Sequencing datasets were analyzed using the Ion Reporter software. Genomic alterations were identified and validated by orthogonal conventional assays including pyrosequencing and immunohistochemistry. Sequencing results of both cohorts, including archival formalin-fixed, paraffin-embedded material stored up to 15years, were consistent with published variant frequencies. A concordance of 100% between established assays and OFA targeted NGS was observed. The OFA workflow enabled a turnaround of 3½ days. Taken together, OFA was found to be a convenient tool for fast, reliable, broadly applicable and cost-effective targeted NGS of tumor samples in routine diagnostics. Thus, OFA has strong potential to become an important asset for precision oncology.
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Han Y, Li J. Sample types applied for molecular diagnosis of therapeutic management of advanced non-small cell lung cancer in the precision medicine. ACTA ACUST UNITED AC 2017; 55:1817-1833. [DOI: 10.1515/cclm-2017-0112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/07/2017] [Indexed: 12/17/2022]
Abstract
AbstractIn this era of precision medicine, molecular biology is becoming increasingly significant for the diagnosis and therapeutic management of non-small cell lung cancer. The specimen as the primary element of the whole testing flow is particularly important for maintaining the accuracy of gene alteration testing. Presently, the main sample types applied in routine diagnosis are tissue and cytology biopsies. Liquid biopsies are considered as the most promising alternatives when tissue and cytology samples are not available. Each sample type possesses its own strengths and weaknesses, pertaining to the disparity of sampling, preparation and preservation procedures, the heterogeneity of inter- or intratumors, the tumor cellularity (percentage and number of tumor cells) of specimens, etc., and none of them can individually be a “one size to fit all”. Therefore, in this review, we summarized the strengths and weaknesses of different sample types that are widely used in clinical practice, offered solutions to reduce the negative impact of the samples and proposed an optimized strategy for choice of samples during the entire diagnostic course. We hope to provide valuable information to laboratories for choosing optimal clinical specimens to achieve comprehensive functional genomic landscapes and formulate individually tailored treatment plans for NSCLC patients that are in advanced stages.
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Atanesyan L, Steenkamer MJ, Horstman A, Moelans CB, Schouten JP, Savola SP. Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA. Am J Clin Pathol 2017; 147:60-68. [PMID: 28122725 PMCID: PMC5848216 DOI: 10.1093/ajcp/aqw205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES Molecular genetic analysis of formalin-fixed, paraffin-embedded (FFPE) tissues is of great importance both for research and diagnostics. Multiplex ligation-dependent probe amplification (MLPA) is a widely used technique for gene copy number determination, and it has been successfully used for FFPE tissue-extracted DNA analysis. However, there have been no studies addressing the effect of tissue fixation procedures and DNA extraction methods on MLPA. This study therefore focuses on selecting optimal preanalytic conditions such as FFPE tissue preparation conditions and DNA extraction methods. METHODS Healthy tissues were fixed in buffered or nonbuffered formalin for 1 hour, 12 to 24 hours, or 48 to 60 hours at 4 °C or at room temperature. DNA extracted from differently fixed and subsequently paraffin-embedded tissues was used for MLPA. Four commercial DNA extraction kits and one in-house method were compared. RESULTS Tissues fixed for 12 to 24 hours in buffered formalin at room temperature produced DNA with the most optimal quality for MLPA. The in-house FFPE DNA extraction method was shown to perform as efficient as or even superior to other methods in terms of suitability for MLPA, time and cost-efficiency, and ease of performance. CONCLUSIONS FFPE-extracted DNA is well suitable for MLPA analysis, given that optimal tissue fixation and DNA extraction methods are chosen.
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Affiliation(s)
- Lilit Atanesyan
- From the MRC-Holland BV, Amsterdam, the Netherlands
- Corresponding author: Lilit Atanesyan, PhD, MRC-Holland, Willem Schoutenstraat 1, Amsterdam, the Netherlands; . Disclaimer: Lilit Atanesyan, Maryvonne Steenkamer, Suvi Savola, and Jan Schouten are employees of MRC-Holland
| | | | | | - Cathy B. Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
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Serratì S, De Summa S, Pilato B, Petriella D, Lacalamita R, Tommasi S, Pinto R. Next-generation sequencing: advances and applications in cancer diagnosis. Onco Targets Ther 2016; 9:7355-7365. [PMID: 27980425 PMCID: PMC5144906 DOI: 10.2147/ott.s99807] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Technological advances have led to the introduction of next-generation sequencing (NGS) platforms in cancer investigation. NGS allows massive parallel sequencing that affords maximal tumor genomic assessment. NGS approaches are different, and concern DNA and RNA analysis. DNA sequencing includes whole-genome, whole-exome, and targeted sequencing, which focuses on a selection of genes of interest for a specific disease. RNA sequencing facilitates the detection of alternative gene-spliced transcripts, posttranscriptional modifications, gene fusion, mutations/single-nucleotide polymorphisms, small and long noncoding RNAs, and changes in gene expression. Most applications are in the cancer research field, but lately NGS technology has been revolutionizing cancer molecular diagnostics, due to the many advantages it offers compared to traditional methods. There is greater knowledge on solid cancer diagnostics, and recent interest has been shown also in the field of hematologic cancer. In this review, we report the latest data on NGS diagnostic/predictive clinical applications in solid and hematologic cancers. Moreover, since the amount of NGS data produced is very large and their interpretation is very complex, we briefly discuss two bioinformatic aspects, variant-calling accuracy and copy-number variation detection, which are gaining a lot of importance in cancer-diagnostic assessment.
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Affiliation(s)
- Simona Serratì
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Simona De Summa
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Brunella Pilato
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Daniela Petriella
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Rosanna Lacalamita
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Stefania Tommasi
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Rosamaria Pinto
- Molecular Genetics Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
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28
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Eijkelenboom A, Kamping EJ, Kastner-van Raaij AW, Hendriks-Cornelissen SJ, Neveling K, Kuiper RP, Hoischen A, Nelen MR, Ligtenberg MJ, Tops BB. Reliable Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue Using Single Molecule Tags. J Mol Diagn 2016; 18:851-863. [DOI: 10.1016/j.jmoldx.2016.06.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/04/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022] Open
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de Haart SJ, Willems SM, Mutis T, Koudijs MJ, van Blokland MT, Lokhorst HM, de Weger RA, Minnema MC. Comparison of intramedullary myeloma and corresponding extramedullary soft tissue plasmacytomas using genetic mutational panel analyses. Blood Cancer J 2016; 6:e426. [PMID: 27206246 PMCID: PMC4916304 DOI: 10.1038/bcj.2016.35] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- S J de Haart
- Department of Clinical Chemistry and Hematology, UMC Utrecht, Utrecht, The Netherlands
| | - S M Willems
- Department of Molecular Pathology, UMC Utrecht, Utrecht, The Netherlands
| | - T Mutis
- Department of Hematology, VU Medical Center, Amsterdam, The Netherlands
| | - M J Koudijs
- Medical Genetics, UMC Utrecht, Utrecht, The Netherlands
| | - M T van Blokland
- Department of Molecular Pathology, UMC Utrecht, Utrecht, The Netherlands
| | - H M Lokhorst
- Department of Hematology, VU Medical Center, Amsterdam, The Netherlands
| | - R A de Weger
- Department of Molecular Pathology, UMC Utrecht, Utrecht, The Netherlands
| | - M C Minnema
- Department of Hematology, Cancer Center UMC Utrecht, Utrecht, The Netherlands
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Zito Marino F, Rocco G, Morabito A, Mignogna C, Intartaglia M, Liguori G, Botti G, Franco R. A new look at the ALK gene in cancer: copy number gain and amplification. Expert Rev Anticancer Ther 2016; 16:493-502. [PMID: 26943457 DOI: 10.1586/14737140.2016.1162098] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To date, ALK-rearrangement is a molecular target in several cancers, i.e. NSCLC. The dramatic benefits of crizotinib have prompted research into identifying other possible patients carrying ALK gene alterations with possible clinical significance. The ALK gene is involved not only in several rearrangements but also in other alterations such as amplification. ALK-amplification (ALK-A) is a common genetic event in several cancers, generally associated with poor outcome and more aggressive behaviour. Here we review the role of ALK-A in cancer as a prognostic and predictive biomarker. Furthermore, several critical issues regarding ALK-A in relation to; methods of detection, acquired resistance and ALK second generation inhibitors are analyzed. We conclude that ALK-A could be an intriguing alteration in the context of targeted therapy.
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Affiliation(s)
- Federica Zito Marino
- a Pathology Unit , Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS , Naples , Italy
| | - Gaetano Rocco
- b Division of Thoracic Surgery, Department of Thoracic Surgical and Medical Oncology , Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS , Naples , Italy
| | - Alessandro Morabito
- c Medical Oncology Unit, Department of Thoracic Surgical and Medical Oncology , Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS , Naples , Italy
| | - Chiara Mignogna
- d Department of Heath Science, Pathology Unit , University 'Magna Graecia' of Catanzaro , Catanzaro , Italy
| | - Martina Intartaglia
- a Pathology Unit , Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS , Naples , Italy
| | - Giuseppina Liguori
- a Pathology Unit , Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS , Naples , Italy
| | - Gerardo Botti
- a Pathology Unit , Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS , Naples , Italy
| | - Renato Franco
- a Pathology Unit , Istituto Nazionale Tumori 'Fondazione G. Pascale'-IRCCS , Naples , Italy.,e Pathology Unit , Second University of Naples - SUN , Naples , Italy
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Randomized phase II study of axitinib versus physicians best alternative choice of therapy in patients with recurrent glioblastoma. J Neurooncol 2016; 128:147-155. [PMID: 26935577 DOI: 10.1007/s11060-016-2092-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/25/2016] [Indexed: 01/14/2023]
Abstract
We conducted a randomized, non-comparative, multi center, phase II clinical trial in order to investigate the efficacy of axitinib, an oral small molecule tyrosine kinase inhibitor with high affinity and specificity for the vascular endothelial growth factor receptors, in patients with recurrent glioblastoma following prior treatment with radiation and temozolomide. Forty-four patients were randomly assigned to receive treatment with axitinib (5 mg BID starting dose; N = 22) or "physicians best alternative choice of therapy" that consisted of bevacizumab (N = 20) or lomustine (N = 2). Six-month progression-free survival served as the primary endpoint. The estimated 6-month progression-free survival rate was 34 % (95 % CI 14-54) for patients treated with axitinib and 28 % (95 % CI 8-48) with best alternative treatment; median overall survival was 29 and 17 weeks, respectively. Objective responses according to RANO criteria were documented in 28 % of patients treated with axitinib and 23 % of patients treated with best alternative therapy. A decrease in maximal uptake of 18F-fluoro-ethyL-tyrosine (18F-FET) by the glioblastoma on PET imaging was documented in 85 % of patients at the time of response on axitinib. Corticosteroid treatment could be stopped in four and tapered in seven out of the 15 patients who were treated with steroids at baseline in the axitinib cohort. Most frequent axitinib related grade ≥3 adverse events consisted of fatigue (9 %), diarrhea (9 %), and oral hyperesthesia (4.5 %). We conclude that axitinib has single-agent clinical activity and a manageable toxicity profile in patients with recurrent glioblastoma.
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de Leng WWJ, Gadellaa-van Hooijdonk CG, Barendregt-Smouter FAS, Koudijs MJ, Nijman I, Hinrichs JWJ, Cuppen E, van Lieshout S, Loberg RD, de Jonge M, Voest EE, de Weger RA, Steeghs N, Langenberg MHG, Sleijfer S, Willems SM, Lolkema MP. Targeted Next Generation Sequencing as a Reliable Diagnostic Assay for the Detection of Somatic Mutations in Tumours Using Minimal DNA Amounts from Formalin Fixed Paraffin Embedded Material. PLoS One 2016; 11:e0149405. [PMID: 26919633 PMCID: PMC4769293 DOI: 10.1371/journal.pone.0149405] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 02/01/2016] [Indexed: 12/26/2022] Open
Abstract
Background Targeted Next Generation Sequencing (NGS) offers a way to implement testing of multiple genetic aberrations in diagnostic pathology practice, which is necessary for personalized cancer treatment. However, no standards regarding input material have been defined. This study therefore aimed to determine the effect of the type of input material (e.g. formalin fixed paraffin embedded (FFPE) versus fresh frozen (FF) tissue) on NGS derived results. Moreover, this study aimed to explore a standardized analysis pipeline to support consistent clinical decision-making. Method We used the Ion Torrent PGM sequencing platform in combination with the Ion AmpliSeq Cancer Hotspot Panel v2 to sequence frequently mutated regions in 50 cancer related genes, and validated the NGS detected variants in 250 FFPE samples using standard diagnostic assays. Next, 386 tumour samples were sequenced to explore the effect of input material on variant detection variables. For variant calling, Ion Torrent analysis software was supplemented with additional variant annotation and filtering. Results Both FFPE and FF tissue could be sequenced reliably with a sensitivity of 99.1%. Validation showed a 98.5% concordance between NGS and conventional sequencing techniques, where NGS provided both the advantage of low input DNA concentration and the detection of low-frequency variants. The reliability of mutation analysis could be further improved with manual inspection of sequence data. Conclusion Targeted NGS can be reliably implemented in cancer diagnostics using both FFPE and FF tissue when using appropriate analysis settings, even with low input DNA.
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Affiliation(s)
- Wendy W. J. de Leng
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Christa G. Gadellaa-van Hooijdonk
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Françoise A. S. Barendregt-Smouter
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Marco J. Koudijs
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Ies Nijman
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - John W. J. Hinrichs
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Edwin Cuppen
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Stef van Lieshout
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Robert D. Loberg
- Medical Sciences, Amgen Inc., Thousand Oaks, CA, 91320–1799, United States of America
| | - Maja de Jonge
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
| | - Emile E. Voest
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Roel A. de Weger
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Neeltje Steeghs
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
| | - Marlies H. G. Langenberg
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Stefan Sleijfer
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
| | - Stefan M. Willems
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
| | - Martijn P. Lolkema
- Netherlands Center for Personalized Cancer Treatment, Utrecht, The Netherlands
- Department of Medical Oncology, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, 3075 EA Rotterdam, The Netherlands
- * E-mail:
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Hovelson DH, McDaniel AS, Cani AK, Johnson B, Rhodes K, Williams PD, Bandla S, Bien G, Choppa P, Hyland F, Gottimukkala R, Liu G, Manivannan M, Schageman J, Ballesteros-Villagrana E, Grasso CS, Quist MJ, Yadati V, Amin A, Siddiqui J, Betz BL, Knudsen KE, Cooney KA, Feng FY, Roh MH, Nelson PS, Liu CJ, Beer DG, Wyngaard P, Chinnaiyan AM, Sadis S, Rhodes DR, Tomlins SA. Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors. Neoplasia 2016; 17:385-99. [PMID: 25925381 PMCID: PMC4415141 DOI: 10.1016/j.neo.2015.03.004] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 03/27/2015] [Indexed: 12/21/2022] Open
Abstract
Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible with < 20 ng of DNA/RNA from formalin-fixed paraffin-embedded (FFPE) tissues], coupled with an informatics pipeline to specifically identify relevant predefined variants and created a knowledge base of related potential treatments, current practice guidelines, and open clinical trials. We validated OCP using molecular standards and more than 300 FFPE tumor samples, achieving >95% accuracy for KRAS, epidermal growth factor receptor, and BRAF mutation detection as well as for ALK and TMPRSS2:ERG gene fusions. Associating positive variants with potential targeted treatments demonstrated that 6% to 42% of profiled samples (depending on cancer type) harbored alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies. As a translational research tool, OCP identified adaptive CTNNB1 amplifications/mutations in treated prostate cancers. Through predefining somatic variants in solid tumors and compiling associated potential treatment strategies, OCP represents a simplified, broadly applicable targeted NGS system with the potential to advance precision oncology efforts.
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Affiliation(s)
- Daniel H Hovelson
- Michigan Center for Translational Pathology, Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Andrew S McDaniel
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Andi K Cani
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Kate Rhodes
- Thermo Fisher Scientific, Ann Arbor, MI, USA
| | | | | | | | - Paul Choppa
- Thermo Fisher Scientific, Ann Arbor, MI, USA
| | | | | | - Guoying Liu
- Thermo Fisher Scientific, Ann Arbor, MI, USA
| | | | | | | | - Catherine S Grasso
- Department of Pathology, Oregon Health and Sciences University, Portland, OR, USA
| | - Michael J Quist
- Department of Pathology, Oregon Health and Sciences University, Portland, OR, USA
| | - Venkata Yadati
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anmol Amin
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Javed Siddiqui
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Bryan L Betz
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA; Department of Urology, Thomas Jefferson University, Philadelphia, PA, USA; Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Kathleen A Cooney
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael H Roh
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chia-Jen Liu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David G Beer
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Seth Sadis
- Thermo Fisher Scientific, Ann Arbor, MI, USA
| | - Daniel R Rhodes
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Thermo Fisher Scientific, Ann Arbor, MI, USA
| | - Scott A Tomlins
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
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