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Sun M, Ji X, Xie M, Chen X, Zhang B, Luo X, Feng Y, Liu D, Wang Y, Li Y, Liu B, Xia L, Huang W. Identification of necroptosis-related subtypes, development of a novel signature, and characterization of immune infiltration in colorectal cancer. Front Immunol 2022; 13:999084. [PMID: 36544770 PMCID: PMC9762424 DOI: 10.3389/fimmu.2022.999084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Necroptosis, a type of programmed cell death, has recently been extensively studied as an important pathway regulating tumor development, metastasis, and immunity. However, the expression patterns of necroptosis-related genes (NRGs) in colorectal cancer (CRC) and their potential roles in the tumor microenvironment (TME) have not been elucidated. Methods We explored the expression patterns of NRGs in 1247 colorectal cancer samples from genetics and transcriptional perspective. Based on a consensus clustering algorithm, we identified NRG molecular subtypes and gene subtypes, respectively. Furthermore, we constructed a necroptosis-related signature for predicting overall survival time and verified the predictive ability of the model. Using the ESTIMATE, CIBERSORT, and ssGSEA algorithms, we assessed the association between the above subtypes, scores and immune infiltration. Results Most NRGs were differentially expressed between CRC tissues and normal tissues. We found that distinct subtypes exhibited different NRGs expression, patients' prognosis, immune checkpoint gene expression, and immune infiltration characteristics. The scores calculated from the necroptosis-related signature can be used to classify patients into high-risk and low-risk groups, with the high-risk group corresponding to reduced immune cell infiltration and immune function, and a greater risk of immune dysfunction and immune escape. Discussion Our comprehensive analysis of NRGs in CRC demonstrated their potential role in clinicopathological features, prognosis, and immune infiltration in the TME. These findings help us deepen our understanding of NRGs and the tumor microenvironment landscape, and lay a foundation for effectively assessing patient outcomes and promoting more effective immunotherapy.
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Affiliation(s)
- Mengyu Sun
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoyu Ji
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meng Xie
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoping Chen
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, China
| | - Bixiang Zhang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, China
| | - Xiangyuan Luo
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yangyang Feng
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Danfei Liu
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yijun Wang
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Bifeng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics and Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Limin Xia
- Department of Gastroenterology, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, China
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Siegmund SE, Manning DK, Davineni PK, Dong F. Deriving tumor purity from cancer next generation sequencing data: applications for quantitative ERBB2 (HER2) copy number analysis and germline inference of BRCA1 and BRCA2 mutations. Mod Pathol 2022; 35:1458-1467. [PMID: 35902772 DOI: 10.1038/s41379-022-01083-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 11/09/2022]
Abstract
Tumor purity, or the relative contribution of tumor cells out of all cells in a pathological specimen, influences mutation identification and clinical interpretation of cancer panel next generation sequencing results. Here, we describe a method of calculating tumor purity using pathologist-guided copy number analysis from sequencing data. Molecular calculation of tumor purity showed strong linear correlation with purity derived from driver KRAS or BRAF variant allele fractions in colorectal cancers (R2 = 0.79) compared to histological estimation in the same set of colorectal cancers (R2 = 0.01) and in a broader dataset of cancers with various diagnoses (R2 = 0.35). We used calculated tumor purity to quantitate ERBB2 copy number in breast carcinomas with equivocal immunohistochemical staining and demonstrated strong correlation with fluorescence in situ hybridization (R2 = 0.88). Finally, we used calculated tumor purity to infer the germline status of variants in breast and ovarian carcinomas with concurrent germline testing. Tumor-only next generation sequencing correctly predicted the somatic versus germline nature of 26 of 26 (100%) pathogenic TP53, BRCA1 and BRCA2 variants. In this article, we describe a framework for calculating tumor purity from cancer next generation sequencing data. Accurate tumor purity assessment can be assimilated into interpretation pipelines to derive clinically useful information from cancer genomic panels.
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Affiliation(s)
| | | | - Phani K Davineni
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
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Werner TV, Kock S, Weber I, Kayser G, Werner M, Lassmann S. Validation of a DNA-Based Next-Generation Sequencing Test for Molecular Diagnostic Variant and Fusion Detection in Formalin-Fixed, Paraffin-Embedded Tissue Specimens and Liquid Biopsy Plasma/Cell-Free DNA Samples. J Mol Diagn 2022; 24:784-802. [PMID: 35787794 DOI: 10.1016/j.jmoldx.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/26/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
This study evaluated two DNA-based next-generation sequencing approaches for detection of single-nucleotide variants (SNVs) and fusions in formalin-fixed, paraffin-embedded (FFPE) tissue specimens and liquid biopsies (AVENIO Targeted and Surveillance Panels). Reference standards (n = 7 with SNVs and structural variants) and real-world FFPE tissue specimens (n = 26 lung, colorectal, pancreas, ovary, breast, prostate, melanoma, and soft tissue cancer cases with n = 27 samples), liquid biopsies [n = 29 cases with n = 40 plasma/cell-free DNA (cfDNA) samples], and one pleural effusion (lung cancer) were analyzed by the AVENIO workflow for known SNVs (BRAF, BRCA1/2, CTNNB1, EGFR, KRAS, MET exon 14 skipping, NRAS, PIK3CA, and TP53), insertions and deletions (ERBB2 and KIT), and fusions (ALK and ROS1). Detection of SNVs, insertions and deletions, and fusions was reliable in 24 of 26 FFPE tissue specimen cases and at 1% allele frequency in 5 of 5 cfDNA reference standards and 37 of 40 plasma/cfDNA samples. Pitfalls were identified for the AVENIO workflow in calling and listing of clinically relevant variants, requiring additional manual inspection. Moreover, laboratory workflows are distinct for FFPE tissue specimens and liquid biopsies as well as time-consuming for sample quality control assays. In summary, the DNA-based next-generation sequencing approaches may be suitable for routine molecular pathology diagnostics on careful data interpretation and further optimization of the technical and laboratory workflows.
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Affiliation(s)
- Tamara V Werner
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Sylvia Kock
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Isabel Weber
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Gian Kayser
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany.
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Iwaya K, Arai H, Takatou N, Morita Y, Ozeki R, Nakaoka H, Sakamoto M, Kouno T, Soma M. A sheet pocket to prevent cross-contamination of formalin-fixed paraffin-embedded block for application in next generation sequencing. PLoS One 2022; 17:e0266947. [PMID: 35507545 PMCID: PMC9067696 DOI: 10.1371/journal.pone.0266947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/31/2022] [Indexed: 11/23/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) blocks are used as biomaterials for next-generation sequencing of cancer panels. Cross-contamination is detected in approximately 5% of the DNA extracted from FFPE samples, which reduces the detection rate of genetic abnormalities. There are no effective methods available for processing FFPE blocks that prevent cells from mixing with other specimens. The present study evaluated 897 sheets that could potentially prevent cell transmission but allow for the movement of various solvents used in FFPE blocks. According to the International Organization for Standardization and Japanese Industrial Standards, six requirements were established for the screening of packing sheets: 1) filter opening ≤5 μm, 2) thickness ≤100 μm, 3) chemical resistance, 4) permeability ≥1.0 × 10−3 cm/s, 5) water retention rate <200%, and 6) cell transit test (≤2 cells/10 high-power fields). Polyamide, polyethylene terephthalate, and polypropylene/polyethylene composite sheets met all criteria. A pocket, which was designed to wrap the tissue uniformly, was made of these sheets and was found to effectively block the entry of all cell types during FFPE block processing. Using a sheet pocket, no single cell from the cell pellet could pass through the outer layer. The presence or absence of the sheet pocket did not affect hematoxylin and eosin staining. When processing FFPE blocks as a biomaterial for next-generation sequencing, the sheet pocket was effective in preventing cross-contamination. This technology will in part support the precise translation of histopathological data into genome sequencing data in general pathology laboratories.
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Affiliation(s)
- Keiichi Iwaya
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
- * E-mail:
| | - Hisae Arai
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Nanao Takatou
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Yuka Morita
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Rinko Ozeki
- Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Hirofumi Nakaoka
- Department of Cancer Genome Research, SASAKI Institute, Chiyoda-ku, Tokyo, Japan
| | - Masaru Sakamoto
- Department of Gynecology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Tsutomu Kouno
- Department of Medical Oncology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
| | - Masayoshi Soma
- Department of Internal Medicine, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan
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Vicente-Garcés C, Esperanza-Cebollada E, Montesdeoca S, Torrebadell M, Rives S, Dapena JL, Català A, Conde N, Camós M, Vega-García N. Technical Validation and Clinical Utility of an NGS Targeted Panel to Improve Molecular Characterization of Pediatric Acute Leukemia. Front Mol Biosci 2022; 9:854098. [PMID: 35463953 PMCID: PMC9021638 DOI: 10.3389/fmolb.2022.854098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/18/2022] [Indexed: 12/03/2022] Open
Abstract
Development of next-generation sequencing (NGS) has provided useful genetic information to redefine diagnostic, prognostic, and therapeutic strategies for the management of acute leukemia (AL). However, the application in the clinical setting is still challenging. Our aim was to validate the AmpliSeq™ for Illumina® Childhood Cancer Panel, a pediatric pan-cancer targeted NGS panel that includes the most common genes associated with childhood cancer, and assess its utility in the daily routine of AL diagnostics. In terms of sequencing metrics, the assay reached all the expected values. We obtained a mean read depth greater than 1000×. The panel demonstrated a high sensitivity for DNA (98.5% for variants with 5% variant allele frequency (VAF)) and RNA (94.4%), 100% of specificity and reproducibility for DNA and 89% of reproducibility for RNA. Regarding clinical utility, 49% of mutations and 97% of the fusions identified were demonstrated to have clinical impact. Forty-one percent of mutations refined diagnosis, while 49% of them were considered targetable. Regarding RNA, fusion genes were more clinically impactful in terms of refining diagnostic (97%). Overall, the panel found clinically relevant results in the 43% of patients tested in this cohort. To sum up, we validated a reliable and reproducible method to refine pediatric AL diagnosis, prognosis, and treatment, and demonstrated the feasibility of incorporating a targeted NGS panel into pediatric hematology practice.
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Affiliation(s)
- Clara Vicente-Garcés
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Elena Esperanza-Cebollada
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Sara Montesdeoca
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Montserrat Torrebadell
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Susana Rives
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Pediatric Hematology and Oncology Department, Hospital Sant Joan de Déu Barcelona, University of Barcelona, Barcelona, Spain
| | - José Luis Dapena
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Pediatric Hematology and Oncology Department, Hospital Sant Joan de Déu Barcelona, University of Barcelona, Barcelona, Spain
| | - Albert Català
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Pediatric Hematology and Oncology Department, Hospital Sant Joan de Déu Barcelona, University of Barcelona, Barcelona, Spain
| | - Nuria Conde
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Pediatric Hematology and Oncology Department, Hospital Sant Joan de Déu Barcelona, University of Barcelona, Barcelona, Spain
| | - Mireia Camós
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Nerea Vega-García
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- *Correspondence: Nerea Vega-García,
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Hummel M, Hegewisch-Becker S, Neumann JHL, Vogel A. BRAF testing in metastatic colorectal carcinoma and novel, chemotherapy-free therapeutic options. DER PATHOLOGE 2021; 42:98-109. [PMID: 34259881 PMCID: PMC8571135 DOI: 10.1007/s00292-021-00946-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 11/25/2022]
Abstract
In the past 25 years, treatment of metastatic colorectal cancer (mCRC) has undergone profound changes. The approval of newer chemotherapeutics such as irinotecan and oxaliplatin was followed in 2005 by the first targeted therapies, for example, monoclonal antibodies directed against the epidermal growth factor receptor (EGFR), as cetuximab and panitumumab, or the angiogenesis inhibitors bevacizumab, ramucirumab, and aflibercept. With the rapidly progressing molecular characterization of mCRC in the last 10 years and the classification of the disease in four consensus subtypes, further changes are emerging, which will promote, among other things, the introduction of protein-kinase inhibitors developed for specific molecular aberrations as well as immune checkpoint inhibitors into the treatment algorithm.Thorough molecular pathologic testing is indispensable today for guideline-compliant treatment of mCRC patients. In addition to RAS testing as a precondition for the therapy decision with regard to cetuximab and panitumumab, BRAF testing is of considerable relevance to allow decision making with regard to the newly approved chemotherapy-free combination of the BRAF inhibitor encorafenib and cetuximab in cases where a BRAF-V600E mutation is detected. Additional diagnostic tests should also include genome instability (microsatellite instability). Overall, more and more molecular alterations need to be investigated simultaneously, so that the use of focused next-generation sequencing is increasingly recommended.This overview describes the prognostic relevance of BRAF testing in the context of molecular pathologic diagnostics of mCRC, presents new treatment options for BRAF-mutated mCRC patients, and explains which modern DNA analytical and immunohistochemical methods are available to detect BRAF mutations in mCRC patients.
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Affiliation(s)
- Michael Hummel
- Institut für Pathologie der Charité, Universitätsmedizin, Campus Charité Mitte, Virchowweg 16/17a, 10117, Berlin, Germany.
| | | | - Jens H L Neumann
- Pathologisches Institut der Medizinischen Fakultät, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Arndt Vogel
- Klinik für Gastroenterologie, Hepatologie und Endokrinologie, Medizinische Hochschule Hannover, Hannover, Germany
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Hummel M, Hegewisch-Becker S, Neumann J, Vogel A. [BRAF-V600E testing in metastatic colorectal cancer and new, chemotherapy-free therapy options. German version]. DER PATHOLOGE 2021; 42:578-590. [PMID: 33956173 PMCID: PMC8536591 DOI: 10.1007/s00292-021-00942-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 11/24/2022]
Abstract
In the past 25 years, treatment of metastatic colorectal cancer (mCRC) has undergone profound changes. The approval of newer chemotherapeutics such as irinotecan and oxaliplatin was followed in 2005 by the first targeted therapies, for example, monoclonal antibodies directed against the epidermal growth factor receptor (EGFR), as cetuximab and panitumumab, or the angiogenesis inhibitors bevacizumab, ramucirumab, and aflibercept. With the rapidly progressing molecular characterization of mCRC in the last 10 years and the classification of the disease in four consensus subtypes, further changes are emerging, which will promote, among other things, the introduction of protein-kinase inhibitors developed for specific molecular aberrations as well as immune checkpoint inhibitors into the treatment algorithm.Thorough molecular pathologic testing is indispensable today for guideline-compliant treatment of mCRC patients. In addition to RAS testing as a precondition for the therapy decision with regard to cetuximab and panitumumab, BRAF testing is of considerable relevance to allow decision making with regard to the newly approved chemotherapy-free combination of the BRAF inhibitor encorafenib and cetuximab in cases where a BRAF-V600E mutation is detected. Additional diagnostic tests should also include genome instability (microsatellite instability). Overall, more and more molecular alterations need to be investigated simultaneously, so that the use of focused next-generation sequencing is increasingly recommended.This overview describes the prognostic relevance of BRAF testing in the context of molecular pathologic diagnostics of mCRC, presents new treatment options for BRAF-mutated mCRC patients, and explains which modern DNA analytical and immunohistochemical methods are available to detect BRAF mutations in mCRC patients.
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Affiliation(s)
- Michael Hummel
- Institut für Pathologie, Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Virchowweg 16/17a, 10117, Berlin, Deutschland.
| | | | - Jens Neumann
- Pathologisches Institut, Medizinische Fakultät, Ludwig-Maximilians-Universität München, München, Deutschland
| | - Arndt Vogel
- Klinik für Gastroenterologie, Hepatologie und Endokrinologie, Medizinische Hochschule Hannover, Hannover, Deutschland
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Neuroblastoma Risk Assessment and Treatment Stratification with Hybrid Capture-Based Panel Sequencing. J Pers Med 2021; 11:jpm11080691. [PMID: 34442335 PMCID: PMC8398598 DOI: 10.3390/jpm11080691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022] Open
Abstract
For many years, the risk-based therapy stratification of children with neuroblastoma has relied on clinical and molecular covariates. In recent years, genome analysis has revealed further alterations defining risk, tumor biology, and therapeutic targets. The implementation of a robust and scalable method for analyzing traditional and new molecular markers in routine diagnostics is an urgent clinical need. Here, we investigated targeted panel sequencing as a diagnostic approach to analyze all relevant genomic neuroblastoma risk markers in one assay. Our "neuroblastoma hybrid capture sequencing panel" (NB-HCSP) assay employs a technology for the high-coverage sequencing (>1000×) of 55 selected genes and neuroblastoma-relevant genomic regions, which allows for the detection of single nucleotide changes, structural rearrangements, and copy number alterations. We validated our assay by analyzing 15 neuroblastoma cell lines and a cohort of 20 neuroblastomas, for which reference routine diagnostic data and genome sequencing data were available. We observed a high concordance for risk markers identified by the NB-HSCP assay, clinical routine diagnostics, and genome sequencing. Subsequently, we demonstrated clinical applicability of the NB-HCSP assay by analyzing routine clinical samples. We conclude that the NB-HCSP assay may be implemented into routine diagnostics as a single assay that covers all essential covariates for initial neuroblastoma classification, extended risk stratification, and targeted therapy selection.
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Hofman P. Next-Generation Sequencing with Liquid Biopsies from Treatment-Naïve Non-Small Cell Lung Carcinoma Patients. Cancers (Basel) 2021; 13:2049. [PMID: 33922637 PMCID: PMC8122958 DOI: 10.3390/cancers13092049] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/11/2021] [Accepted: 04/20/2021] [Indexed: 12/16/2022] Open
Abstract
Recently, the liquid biopsy (LB), a non-invasive and easy to repeat approach, has started to compete with the tissue biopsy (TB) for detection of targets for administration of therapeutic strategies for patients with advanced stages of lung cancer at tumor progression. A LB at diagnosis of late stage non-small cell lung carcinoma (NSCLC) is also being performed. It may be asked if a LB can be complementary (according to the clinical presentation or systematics) or even an alternative to a TB for treatment-naïve advanced NSCLC patients. Nucleic acid analysis with a TB by next-generation sequencing (NGS) is gradually replacing targeted sequencing methods for assessment of genomic alterations in lung cancer patients with tumor progression, but also at baseline. However, LB is still not often used in daily practice for NGS. This review addresses different aspects relating to the use of LB for NGS at diagnosis in advanced NSCLC, including its advantages and limitations.
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Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Université Côte d’Azur, CHU Nice, FHU OncoAge, Pasteur Hospital, 30 avenue de la voie romaine, BP69, CEDEX 01, 06001 Nice, France; ; Tel.: +33-4-92-03-88-55 or +33-4-92-03-87-49; Fax: +33-4-92-88-50
- Hospital-Integrated Biobank BB-0033-00025, Université Côte d’Azur, CHU Nice, FHU OncoAge, 06001 Nice, France
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Wenzel C, Herold S, Wermke M, E. Aust D, B. Baretton G. Routine Molecular Pathology Diagnostics in Precision Oncology. DEUTSCHES ARZTEBLATT INTERNATIONAL 2021; 118:arztebl.m2021.0025. [PMID: 33536117 PMCID: PMC8287073 DOI: 10.3238/arztebl.m2021.0025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/01/2020] [Indexed: 11/27/2022]
Abstract
BACKGROUND Technical advances in the field of molecular genetics permit precise genomic characterization of malignant tumors. This has not only improved our understanding of tumor biology but also paved the way for molecularly stratified treatment strategies in routine clinical practice. METHODS A selective search of PubMed to identify literature on molecular pathology methods, their indications, the challenges associated with molecular findings, and future developments. RESULTS Tumors can be characterized with the aid of immunohistochemistry, in-situ hybridization, and sequencing of DNA or RNA. The benefits of molecularly stratified tumor treatment have been demonstrated by randomized clinical trials on numerous tumor entities, e.g., non-small-cell lung cancer, colorectal cancer, and breast cancer. Therefore, initiation of specific treatment for these entities should be preceded by molecular pathology biomarker analyses, generally carried out on tumor tissue. Randomized controlled trials and non-controlled studies show that enhanced progression-free survival ensues if the pharmacological treatment is oriented on the findings of molecular pathology diagnostics. In next-generation sequencing, numerous relevant gene sequences or even whole genes can be sequenced in parallel, dispensing with complex staged diagnostics and reducing the use of biomaterials. These new methods also complement the currently relevant predictive biomarkers by permitting the investigation of genetic alterations presently of interest in the context of clinical studies. Prior to widespread routine clinical application, however, sequencing of large gene panels or whole genomes or exomes need to be even more stringently validated. CONCLUSION Quality-assured molecular pathology assays are universally available for the determination of currently relevant predictive biomarkers. However, the integration of extensive genomic analyses into routine molecular pathology diagnostics represents a future challenge in precision oncology.
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Affiliation(s)
- Carina Wenzel
- Institute of Pathology, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden
| | - Sylvia Herold
- Institute of Pathology, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden
| | - Martin Wermke
- Medical Department I, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden: Dr. med. Martin Wermke
| | - Daniela E. Aust
- Institute of Pathology, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden
| | - Gustavo B. Baretton
- Institute of Pathology, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden
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Sutton LA, Ljungström V, Enjuanes A, Cortese D, Skaftason A, Tausch E, Stano Kozubik K, Nadeu F, Armand M, Malcikova J, Pandzic T, Forster J, Davis Z, Oscier D, Rossi D, Ghia P, Strefford JC, Pospisilova S, Stilgenbauer S, Davi F, Campo E, Stamatopoulos K, Rosenquist R, On Behalf Of The European Research Initiative On Cll Eric. Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study. Haematologica 2021; 106:682-691. [PMID: 32273480 PMCID: PMC7927885 DOI: 10.3324/haematol.2019.234716] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) has transitioned from research to clinical routine, yet the comparability of different technologies for mutation profiling remains an open question. We performed a European multicenter (n=6) evaluation of three amplicon-based NGS assays targeting 11 genes recurrently mutated in chronic lymphocytic leukemia. Each assay was assessed by two centers using 48 pre-characterized chronic lymphocytic leukemia samples; libraries were sequenced on the Illumina MiSeq instrument and bioinformatics analyses were centralized. Across all centers the median percentage of target reads ≥100x ranged from 94.2-99.8%. In order to rule out assay-specific technical variability, we first assessed variant calling at the individual assay level i.e., pairwise analysis of variants detected amongst partner centers. After filtering for variants present in the paired normal sample and removal of PCR/sequencing artefacts, the panels achieved 96.2% (Multiplicom), 97.7% (TruSeq) and 90% (HaloPlex) concordance at a variant allele frequency (VAF) >0.5%. Reproducibility was assessed by looking at the inter-laboratory variation in detecting mutations and 107 of 115 (93% concordance) mutations were detected by all six centers, while the remaining eight variants (7%) were undetected by a single center. Notably, 6 of 8 of these variants concerned minor subclonal mutations (VAF <5%). We sought to investigate low-frequency mutations further by using a high-sensitivity assay containing unique molecular identifiers, which confirmed the presence of several minor subclonal mutations. Thus, while amplicon-based approaches can be adopted for somatic mutation detection with VAF >5%, after rigorous validation, the use of unique molecular identifiers may be necessary to reach a higher sensitivity and ensure consistent and accurate detection of low-frequency variants.
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Affiliation(s)
- Lesley-Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Viktor Ljungström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Enjuanes
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Diego Cortese
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aron Skaftason
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University,Ulm, Germany
| | - Katerina Stano Kozubik
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ferran Nadeu
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Marine Armand
- AP-HP, Hopital Pitie-Salpetriere, Department of Hematology, Sorbonne Université, Paris, France
| | - Jikta Malcikova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jade Forster
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Zadie Davis
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - David Oscier
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Davide Rossi
- Hematology Department, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Paolo Ghia
- Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jonathan C Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarka Pospisilova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Frederic Davi
- AP-HP, Hopital Pitie-Salpetriere, Department of Hematology, Sorbonne Université, Paris, France
| | - Elias Campo
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Kostas Stamatopoulos
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Institute of Applied Biosciences, Center for Research and Technology, Thessaloniki, Greec
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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13
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Peric J, Samaradzic N, Skodric Trifunovic V, Tosic N, Stojsic J, Pavlovic S, Jovanovic D. Genomic profiling of thymoma using a targeted high-throughput approach. Arch Med Sci 2020; 20:909-917. [PMID: 39050176 PMCID: PMC11264071 DOI: 10.5114/aoms.2020.96537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 12/21/2019] [Indexed: 07/27/2024] Open
Abstract
Introduction Thymomas and thymic carcinoma (TC) are the most common neoplasms localised in the thymus. These diseases are poorly understood, but progress made in next-generation sequencing (NGS) technology has provided novel data on their molecular pathology. Material and methods Genomic DNA was isolated from formalin-fixed paraffin-embedded tumour tissue. We investigated somatic variants in 35 thymoma patients using amplicon-based TruSeq Amplicon Cancer Panel (TSACP) that covers 48 cancer related genes. We also analysed three samples from healthy individuals by TSACP platform and 32 healthy controls using exome sequencing. Results The total number of detected variants was 4447, out of which 2906 were in the coding region (median per patient 83, range: 2-300) and 1541 were in the non-coding area (median per patient 44, range: 0-172). We identified four genes, APC, ATM, ERBB4, and SMAD4, having more than 100 protein-changing variants. Additionally, more than 70% of the analysed cases harboured protein-changing variants in SMAD4, APC, ATM, PTEN, KDR, and TP53. Moreover, this study revealed 168 recurrent variants, out of which 15 were shown to be pathogenic. Comparison to controls revealed that the variants we reported in this study were somatic thymoma-specific variants. Additionally, we found that the presence of variants in SMAD4 gene predicted shorter overall survival in thymoma patients. Conclusions The most frequently mutated genes in thymoma samples analysed in this study belong to the EGFR, ATM, and TP53 signalling pathways, regulating cell cycle check points, gene expression, and apoptosis. The results of our study complement the knowledge of thymoma molecular pathogenesis.
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Affiliation(s)
- Jelena Peric
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Natalija Samaradzic
- University Hospital of Pulmonology, Clinical Centre of Serbia, Belgrade, Serbia
| | - Vesna Skodric Trifunovic
- University Hospital of Pulmonology, Clinical Centre of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Natasa Tosic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Jelena Stojsic
- Department of Thoracopulmonary Pathology, Service of Pathology, Clinical Centre of Serbia, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Dragana Jovanovic
- University Hospital of Pulmonology, Clinical Centre of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
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14
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Torchia MT, Amakiri I, Werth P, Moschetti W. Characterization of native knee microorganisms using next-generation sequencing in patients undergoing primary total knee arthroplasty. Knee 2020; 27:1113-1119. [PMID: 31926670 DOI: 10.1016/j.knee.2019.12.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/18/2019] [Accepted: 12/17/2019] [Indexed: 02/02/2023]
Abstract
BACKGROUND Next-generation sequencing (NGS) offers improved sensitivity compared to culture-based methods for identifying organisms from synovial joints. It remains unclear whether native microorganisms exist in a joint, and positive NGS results may be interpreted as pathologic when in fact they may represent this native microbiome. The purpose of this study was to characterize the native knee microorganism profile in patients undergoing primary total knee arthroplasty (TKA). METHODS Forty consecutive patients with osteoarthritis undergoing primary total knee arthroplasty were enrolled prospectively. During TKA surgery but prior to arthrotomy, the native knee was aspirated and the fluid was sent for NGS analysis. Immediately after arthrotomy, four separate tissue samples were also sent for NGS analysis. All microbes identified by NGS were recorded. RESULTS Twelve out of forty patients (30%) had at least one positive organism identified by NGS from their native knee. Of those with positive NGS results, 9/12 (75%) had more than one organism identified (range two to 11). There were no significant differences in demographics, comorbidities, or incidence of prior knee injections between the two groups. There were 48 unique organisms identified from all patients, and the average number of organisms identified by NGS was 4.6 per patient. Four sterile water controls were all negative for organisms. CONCLUSION A proportion of patients with osteoarthritis undergoing primary total knee arthroplasty have organisms identified in their joint by NGS at the time of surgery. Organisms identified after TKA by NGS when concern for periprosthetic joint infection exists may represent the native microbiome rather than pathogenic microbes.
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Affiliation(s)
- Michael T Torchia
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, 1 Medical Center Drive, Lebanon, NH 03756, USA.
| | - Ikechukwu Amakiri
- Department of Orthopaedics, Geisel School of Medicine, Dartmouth College, 1 Rope Ferry Road, Hanover, NH 03755, USA
| | - Paul Werth
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, 1 Medical Center Drive, Lebanon, NH 03756, USA
| | - Wayne Moschetti
- Department of Orthopaedics, Dartmouth-Hitchcock Medical Center, 1 Medical Center Drive, Lebanon, NH 03756, USA; Department of Orthopaedics, Geisel School of Medicine, Dartmouth College, 1 Rope Ferry Road, Hanover, NH 03755, USA
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Abstract
PURPOSE OF REVIEW To provide the reader an understanding of the importance and limitations of prostate cancer (PCa) screening, the heritable component of PCa and the role that germline genetic markers can play in risk-adapted screening and treatment. RECENT FINDINGS Despite strong science supporting the association of germline genetic change with PCa risk and outcome, there has been a reluctance to pursue practical application of these technologies. Recent findings suggest that actionable information may now be garnered from this form of testing, which can help men at risk for and with PCa. SUMMARY This is an exciting time whereby germline genetic markers can help overcome some of the shortcomings of current PCa screening and treatment paradigms. Understanding their benefit and limitations while keeping the patient's best interest in mind will be the key for the responsible application of these exciting technologies.
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Petersen LM, Martin IW, Moschetti WE, Kershaw CM, Tsongalis GJ. Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing. J Clin Microbiol 2019; 58:e01315-19. [PMID: 31619531 PMCID: PMC6935936 DOI: 10.1128/jcm.01315-19] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, the length of time to results, and the need for technical and bioinformatics expertise. However, the recent technological innovation of nanopore sequencing from Oxford Nanopore Technologies (ONT) has the potential to address these challenges. ONT sequencing is an attractive platform for clinical laboratories to adopt due to its low cost, rapid turnaround time, and user-friendly bioinformatics pipelines. However, this method still faces the problem of base-calling accuracy compared to other platforms. This review highlights the general challenges of pathogen detection in clinical specimens by metagenomic sequencing, the advantages and disadvantages of the ONT platform, and how research to date supports the potential future use of nanopore sequencing in infectious disease diagnostics.
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Affiliation(s)
- Lauren M Petersen
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
| | - Isabella W Martin
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
| | - Wayne E Moschetti
- Dartmouth-Hitchcock Medical Center, Department of Orthopaedics and Sports Medicine, Lebanon, New Hampshire, USA
| | - Colleen M Kershaw
- Dartmouth-Hitchcock Medical Center, Department of Infectious Disease and International Health, Lebanon, New Hampshire, USA
| | - Gregory J Tsongalis
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, New Hampshire, USA
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17
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Hoefflin R, Geißler AL, Fritsch R, Claus R, Wehrle J, Metzger P, Reiser M, Mehmed L, Fauth L, Heiland DH, Erbes T, Stock F, Csanadi A, Miething C, Weddeling B, Meiss F, von Bubnoff D, Dierks C, Ge I, Brass V, Heeg S, Schäfer H, Boeker M, Rawluk J, Botzenhart EM, Kayser G, Hettmer S, Busch H, Peters C, Werner M, Duyster J, Brummer T, Boerries M, Lassmann S, von Bubnoff N. Personalized Clinical Decision Making Through Implementation of a Molecular Tumor Board: A German Single-Center Experience. JCO Precis Oncol 2018; 2:PO.18.00105. [PMID: 32913998 PMCID: PMC7446498 DOI: 10.1200/po.18.00105] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
PURPOSE Dramatic advances in our understanding of the molecular pathophysiology of cancer, along with a rapidly expanding portfolio of molecular targeted drugs, have led to a paradigm shift toward personalized, biomarker-driven cancer treatment. Here, we report the 2-year experience of the Comprehensive Cancer Center Freiburg Molecular Tumor Board (MTB), one of the first interdisciplinary molecular tumor conferences established in Europe. The role of the MTB is to recommend personalized therapy for patients with cancer beyond standard-of-care treatment. METHODS This retrospective case series includes 198 patients discussed from March 2015 through February 2017. The MTB guided individual molecular diagnostics, assessed evidence of actionability of molecular alterations, and provided therapy recommendations, including approved and off-label treatments as well as available matched clinical trials. RESULTS The majority of patients had metastatic solid tumors (73.7%), mostly progressive (77.3%) after a mean of 2.0 lines of standard treatment. Diagnostic recommendations resulted in 867 molecular diagnostic tests for 172 patients (five per case), including exome analysis in 36 cases (18.2%). With a median turnaround time of 28 days, treatment recommendations were given to 104 patients (52.5%). These included single-agent targeted therapies (42.3%), checkpoint inhibitors (37.5%), and combination therapies (18.3%). Treatment recommendations were implemented in 33 of 104 patients (31.7%), of whom 19 (57.6%) showed stable disease or partial response, including 14 patients (7.1% of the entire population) receiving off-label treatments. CONCLUSION Personalized extended molecular-guided patient care is effective for a small but clinically meaningful proportion of patients in challenging clinical situations. Limited access to targeted drugs, lack of trials, and submission at late disease stage prevents broader applicability, whereas genome-wide analyses are not a strict requirement for predictive molecular testing.
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Affiliation(s)
- Rouven Hoefflin
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Anna-Lena Geißler
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Ralph Fritsch
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Rainer Claus
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Julius Wehrle
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Patrick Metzger
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Meike Reiser
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Leman Mehmed
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Lisa Fauth
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Dieter Henrik Heiland
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Thalia Erbes
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Friedrich Stock
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Agnes Csanadi
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Cornelius Miething
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Britta Weddeling
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Frank Meiss
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Dagmar von Bubnoff
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Christine Dierks
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Isabell Ge
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Volker Brass
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Steffen Heeg
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Henning Schäfer
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Martin Boeker
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Justyna Rawluk
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Elke Maria Botzenhart
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Gian Kayser
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Simone Hettmer
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Hauke Busch
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Christoph Peters
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Martin Werner
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Justus Duyster
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Tilman Brummer
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Melanie Boerries
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Silke Lassmann
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
| | - Nikolas von Bubnoff
- All authors: University of Freiburg, Freiburg; Ralph Fritsch, Julius Wehrle, Cornelius Miething, Christoph Peters, Martin Werner, Justus Duyster, Tilman Brummer, Melanie Boerries, Silke Lassmann, and Nikolas von Bubnoff, German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg; Rainer Claus, Augsburg Medical Center, Augsburg; and Hauke Busch, University of Lübeck, Lübeck, Germany
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18
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Wang Y, Liu H, Hou Y, Zhou X, Liang L, Zhang Z, Shi H, Xu S, Hu P, Zheng Z, Liu R, Tang T, Ye F, Liang Z, Bu H. Performance validation of an amplicon-based targeted next-generation sequencing assay and mutation profiling of 648 Chinese colorectal cancer patients. Virchows Arch 2018; 472:959-968. [PMID: 29705968 DOI: 10.1007/s00428-018-2359-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/01/2018] [Accepted: 04/08/2018] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing (NGS) has become a promising approach for tumor somatic mutation detection. However, stringent validation is required for its application on clinical specimens, especially for low-quality formalin-fixed paraffin-embedded (FFPE) tissues. Here, we validated the performance of an amplicon-based targeted NGS assay, OncoAim™ DNA panel, on both commercial reference FFPE samples and clinical FFPE samples of Chinese colorectal cancer (CRC) patients. Then we profiled the mutation spectrum of 648 Chinese CRC patients in a multicenter study to explore its clinical utility. This NGS assay achieved 100% test specificity and 95-100% test sensitivity for variants with mutant allele frequency (MAF) ≥ 5% when median read depth ≥ 500×. The orthogonal methods including amplification refractory mutation system (ARMS)-PCR and Sanger sequencing validated that NGS generated three false negatives (FNs) but no false positives (FPs) among 516 clinical samples for KRAS aberration detection. Genomic profiling of Chinese CRC patients with this assay revealed that 63.3% of the tumors harbored clinically actionable alterations. Besides the commonly mutated genes including TP53 (52.82%), KRAS (46.68%), APC (24.09%), PIK3CA (18.94%), SMAD4 (9.47%), BRAF (6.15%), FBXW7 (5.32%), and NRAS (4.15%), other less frequently mutated genes were also identified. Statistically significant association of specific mutated genes with certain clinicopathological features was detected, e.g., both BRAF and PIK3CA were more prevalent in right-side CRC (p < 0.001 and p = 0.002, respectively). We concluded this targeted NGS assay is qualified for clinical practice, and our findings could help the diagnosis and prognosis of Chinese CRC patients.
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Affiliation(s)
- Yajian Wang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.,Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Haijing Liu
- Department of Pathology, Peking University Third Hospital, Beijing, 100000, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Li Liang
- Huayin Laboratory, Southern Medical University, Guangzhou, 510515, China
| | - Zhihong Zhang
- Department of Pathology, First Affiliated Hospital, Nanjing Medical University, Nanjing, 210000, China
| | - Huaiyin Shi
- Department of Pathology, Chinese PLA General Hospital and Chinese PLA Medical School, Beijing, 100000, China
| | - Sanpeng Xu
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Peizhen Hu
- Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Zuyu Zheng
- Singlera Genomics Inc., Shanghai, 201318, China
| | - Rui Liu
- Singlera Genomics Inc., Shanghai, 201318, China
| | | | - Feng Ye
- Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China. .,Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Hong Bu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.,Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.,Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, 610041, China
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