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Carrión-Estrada DA, Aguilar-Rojas A, Huerta-Yepez S, Montecillo-Aguado M, Bello M, Rojo-Domínguez A, Arechaga-Ocampo E, Briseño-Díaz P, Meraz-Ríos MA, Thompson-Bonilla MDR, Hernández-Rivas R, Vargas M. Antineoplastic effect of compounds C14 and P8 on TNBC and radioresistant TNBC cells by stabilizing the K-Ras4B G13D/PDE6δ complex. Front Oncol 2024; 14:1341766. [PMID: 38571493 PMCID: PMC10989073 DOI: 10.3389/fonc.2024.1341766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Breast cancer (BC) is the leading cause of cancer-related deaths among women, with triple-negative breast cancer (TNBC) representing one of the most aggressive and treatment-resistant subtypes. In this study, we aimed to evaluate the antitumor potential of C14 and P8 molecules in both TNBC and radioresistant TNBC cells. These compounds were chosen for their ability to stabilize the complex formed by the overactivated form of K-Ras4BG13D and its membrane transporter (PDE6δ). Methods The antitumor potential of C14 and P8 was assessed using TNBC cell lines, MDA-MB-231, and the radioresistant derivative MDA-MB-231RR, both carrying the K-Ras4B> G13D mutation. We investigated the compounds' effects on K-Ras signaling pathways, cell viability, and tumor growth in vivo. Results Western blotting analysis determined the negative impact of C14 and P8 on the activation of mutant K-Ras signaling pathways in MDA-MB-231 and MDA-MB-231RR cells. Proliferation assays demonstrated their efficacy as cytotoxic agents against K-RasG13D mutant cancer cells and in inducing apoptosis. Clonogenic assays proven their ability to inhibit TNBC and radioresistant TNBC cell clonogenicity. In In vivo studies, C14 and P8 inhibited tumor growth and reduced proliferation, angiogenesis, and cell cycle progression markers. Discussion These findings suggest that C14 and P8 could serve as promising adjuvant treatments for TNBC, particularly for non-responders to standard therapies. By targeting overactivated K-Ras and its membrane transporter, these compounds offer potential therapeutic benefits against TNBC, including its radioresistant form. Further research and clinical trials are warranted to validate their efficacy and safety as novel TNBC treatments.
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Affiliation(s)
- Dayan A. Carrión-Estrada
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-I.P.N.), Mexico City, Mexico
| | - Arturo Aguilar-Rojas
- Medical Research Unit in Reproductive Medicine, Mexican Social Security Institute (IMSS), High Specialty Medical Unit in Gynecology and Obstetrics No. 4 Dr. Luis Castelazo Ayala, Mexico City, Mexico
| | - Sara Huerta-Yepez
- Research Unit in Oncological Diseases, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Mayra Montecillo-Aguado
- Research Unit in Oncological Diseases, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Martiniano Bello
- Laboratory for the Design and Development of New Drugs and Biotechnological Innovation, Higher School of Medicine, National Polytechnic Institute, Mexico City, Mexico
| | - Arturo Rojo-Domínguez
- Department of Natural Sciences, Metropolitan Autonomous University Cuajimalpa Unit, Mexico City, Mexico
| | - Elena Arechaga-Ocampo
- Department of Natural Sciences, Metropolitan Autonomous University Cuajimalpa Unit, Mexico City, Mexico
| | - Paola Briseño-Díaz
- Department of Biochemistry of the Faculty of Medicine of the National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Marco Antonio Meraz-Ríos
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-I.P.N.), Mexico City, Mexico
| | - María del Rocío Thompson-Bonilla
- Biomedical and Transnational Research, Genomic Medicine Laboratory, Hospital 1° de Octubre, Institute of Security and Social Services of State Workers (ISSSTE), Mexico City, Mexico
| | - Rosaura Hernández-Rivas
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-I.P.N.), Mexico City, Mexico
| | - Miguel Vargas
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-I.P.N.), Mexico City, Mexico
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Li S, Gu Y, Geng Z, Li K, Hu Y, Liu Q, Fu R, Liu P. Tweezer PCR: A Highly Specific Method for Accurate Identification of Low-Abundance Mutations. Anal Chem 2023; 95:17679-17690. [PMID: 37971891 DOI: 10.1021/acs.analchem.3c03467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Somatic mutation is a valuable biomarker for tracking tumor progression and migration due to its distinctive feature in various tumors and its wide distribution throughout body fluids. However, accurately detecting somatic mutations from the abundant DNA of noncancerous origins remains a practical challenge in the clinic. Herein, we developed an ultraspecific method, called tweezer PCR, for detecting low-abundance mutations inspired by the design of DNA origami. The high specificity of tweezer PCR relies on a tweezer-shaped primer containing six basic functional units: a primer, a hairpin, a linker, a blocker, a spacer, and a toehold. After optimizing the structure of the tweezer-shaped primer and enhancing its specificity by adding additional Mg2+ and Na+, tweezer PCR distinguished as low as 20 copies of mutations from 2 million copies of wild-type templates per test. By testing synthesized plasmids and plasma samples gathered from nonsmall-cell lung cancer patients, tweezer PCR showed higher specificity and robustness for detecting low-copy-number mutations in contrast with digital droplet PCR. Additionally, the need for conventional instruments makes tweezer PCR a practically accessible method for testing low-abundance mutations. Because of its numerous advantages, we believe that tweezer PCR offers a precise, robust, and pragmatic tool for cancer screening, prognosis, and genotyping in the clinic.
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Affiliation(s)
- Shanglin Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- Changping Laboratory, Beijing 102206, China
| | - Yin Gu
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing 100094, China
| | - Zhi Geng
- Shimadzu Research Laboratory (Shanghai) Co. Ltd, Shanghai 201206, China
| | - Kaiyi Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yawei Hu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- Changping Laboratory, Beijing 102206, China
| | - Qiang Liu
- Beijing Haidian Hospital, Beijing 100080, China
| | - Rongxin Fu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- Changping Laboratory, Beijing 102206, China
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Oliveira BB, Costa B, Morão B, Faias S, Veigas B, Pereira LP, Albuquerque C, Maio R, Cravo M, Fernandes AR, Baptista PV. Combining the amplification refractory mutation system and high-resolution melting analysis for KRAS mutation detection in clinical samples. Anal Bioanal Chem 2023; 415:2849-2863. [PMID: 37097304 PMCID: PMC10185647 DOI: 10.1007/s00216-023-04696-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023]
Abstract
The success of personalized medicine depends on the discovery of biomarkers that allow oncologists to identify patients that will benefit from a particular targeted drug. Molecular tests are mostly performed using tumor samples, which may not be representative of the tumor's temporal and spatial heterogeneity. Liquid biopsies, and particularly the analysis of circulating tumor DNA, are emerging as an interesting means for diagnosis, prognosis, and predictive biomarker discovery. In this study, the amplification refractory mutation system (ARMS) coupled with high-resolution melting analysis (HRMA) was developed for detecting two of the most relevant KRAS mutations in codon 12. After optimization with commercial cancer cell lines, KRAS mutation screening was validated in tumor and plasma samples collected from patients with pancreatic ductal adenocarcinoma (PDAC), and the results were compared to those obtained by Sanger sequencing (SS) and droplet digital polymerase chain reaction (ddPCR). The developed ARMS-HRMA methodology stands out for its simplicity and reduced time to result when compared to both SS and ddPCR but showing high sensitivity and specificity for the detection of mutations in tumor and plasma samples. In fact, ARMS-HRMA scored 3 more mutations compared to SS (tumor samples T6, T7, and T12) and one more compared to ddPCR (tumor sample T7) in DNA extracted from tumors. For ctDNA from plasma samples, insufficient genetic material prevented the screening of all samples. Still, ARMS-HRMA allowed for scoring more mutations in comparison to SS and 1 more mutation in comparison to ddPCR (plasma sample P7). We propose that ARMS-HRMA might be used as a sensitive, specific, and simple method for the screening of low-level mutations in liquid biopsies, suitable for improving diagnosis and prognosis schemes.
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Affiliation(s)
- Beatriz B Oliveira
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Beatriz Costa
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | | | | | - Bruno Veigas
- AlmaScience, Campus de Caparica, 2829-519, Caparica, Portugal
| | - Lucília Pebre Pereira
- Unidade de Investigação Em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Rua Prof Lima Basto, 1099-023, Lisbon, Portugal
| | - Cristina Albuquerque
- Unidade de Investigação Em Patobiologia Molecular, Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Rua Prof Lima Basto, 1099-023, Lisbon, Portugal
| | - Rui Maio
- Hospital da Luz-Lisboa, Lisbon, Portugal
- Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Marília Cravo
- Hospital da Luz-Lisboa, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
| | - Pedro Viana Baptista
- UCIBIO, Dept. Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
- i4HB, Associate Laboratory - Institute for Health and Bioeconomy, Faculdade de Ciências E Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal.
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Chen S, Sun Y, Fan F, Chen S, Zhang Y, Zhang Y, Meng X, Lin JM. Present status of microfluidic PCR chip in nucleic acid detection and future perspective. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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5
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Batra U, Nathany S, Sharma M, BP A, Jose JT, Singh H, Mattoo S, Mehta A. KRAS mutated Non-Small Lung Carcinoma: A Real World Context from the Indian subcontinent. Cancer Med 2022; 12:2869-2874. [PMID: 36069080 PMCID: PMC9939094 DOI: 10.1002/cam4.5193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/08/2022] [Accepted: 08/19/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND KRAS, although a common variant of occurrence (~20% of non-small-cell lung carcinoma [NSCLC]) has been untargetable, owing to the molecular structure which inherently prevents drug binding. KRAS mutations in NSCLC are associated with distinct clinical profiles including smokers and mucinous histology. KRAS G12C mutations account for ~40% KRAS altered NSCLC, but NSCLC being a geographically diverse disease, the features may be distinct in this part of the world. This is a single-center experience of KRAS-mutated NSCLC including clinical, imaging, pathologic features, and treatment patterns and outcomes. METHODS This is a single-center retrospective study of KRAS-mutated NSCLC. The clinicopathological features and outcomes were retrieved and collated from the medical record archives of the hospital. RESULTS Fifty (30.6%) patients with advanced-stage NSCLC with alterations in the KRAS gene were enrolled in the 163 patients who were tested for KRAS alterations. The median age was 61 years. Molecular detection revealed three main types of KRAS mutations viz-a-vis: G12C in 17 (34%), G12V in 9 (18%), and G12D in 6 (12%) patients. Comparing G12C versus the non-G12C mutated cases, co-mutations were common in the non-G12C subgroup (p < 0.05). Among the 36, who were treated at our center, all received chemotherapy as the first line with a median progression-free survival (PFS)of 5.4 months. The PFS of G12C was higher than the non-G12C subgroup (6.4 vs 3.8 months). CONCLUSION This is the largest single-center experience from the Indian subcontinent for KRAS-mutated NSCLC with distinct clinical features. It highlights the unmet need for G12C inhibitors in our country, where prevalence is equivalent to the West.
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Affiliation(s)
- Ullas Batra
- Medical OncologyRajiv Gandhi Cancer Institute and Research CenterNew DelhiIndia
| | - Shrinidhi Nathany
- Molecular DiagnosticsRajiv Gandhi Cancer Institute and Research CenterNew DelhiIndia
| | - Mansi Sharma
- Medical OncologyRajiv Gandhi Cancer Institute and Research CenterNew DelhiIndia
| | - Amrith BP
- Medical OncologyRajiv Gandhi Cancer Institute and Research CenterNew DelhiIndia
| | - Joslia T. Jose
- Medical OncologyRajiv Gandhi Cancer Institute and Research CenterNew DelhiIndia
| | - Harkirat Singh
- Medical OncologyRajiv Gandhi Cancer Institute and Research CenterNew DelhiIndia
| | - Sakshi Mattoo
- Molecular DiagnosticsRajiv Gandhi Cancer Institute and Research CenterNew DelhiIndia
| | - Anurag Mehta
- Laboratory ServicesRajiv Gandhi Cancer Institute and Research CenterNew DelhiIndia
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The potential of PIK3CA, KRAS, BRAF, and APC hotspot mutations as a non-invasive detection method for colorectal cancer. Mol Cell Probes 2022; 63:101807. [DOI: 10.1016/j.mcp.2022.101807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 02/07/2023]
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Ritu K, Kumar P, Singh A, Nupur K, Spalgias S, Mrigpuri P, Rajkumar. Untangling the KRAS mutated lung cancer subsets and its therapeutic implications. MOLECULAR BIOMEDICINE 2021; 2:40. [PMID: 34918209 PMCID: PMC8677854 DOI: 10.1186/s43556-021-00061-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
The Kirsten rat sarcoma virus transforming protein (KRAS) mutations (predominate in codons 12, 13, and 61) and genomically drive nearly one-third of lung carcinomas. These mutations have complex functions in tumorigenesis, and influence the tumor response to chemotherapy and tyrosine kinase inhibitors resulting in a poorer patient prognosis. Recent attempts using targeted therapies against KRAS alone have met with little success. The existence of specific subsets of lung cancer based on KRAS mutations and coexisting mutations are suggested. Their interactions need further elaboration before newer promising targeted therapies for KRAS mutant lung cancers can be used as earlier lines of therapy. We summarize the existing knowledge of KRAS mutations and their coexisting mutations that is relevant to lung cancer treatment, in this review. We elaborate on the prognostic impact of clinical and pathologic characteristics of lung cancer patients associated with KRAS mutations. We briefly review the currently available techniques for KRAS mutation detection on biopsy and cytology samples. Finally, we discuss the new therapeutic strategies for targeting KRAS-mutant non-small cell lung cancer (NSCLC). These may herald a new era in the treatment of KRASG12Cmutated NSCLC as well as be helpful to develop demographic subsets to predict targeted therapies and prognosis of lung cancer patients.
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Lakatos G, Köhne CH, Bodoky G. Current therapy of advanced colorectal cancer according to RAS/RAF mutational status. Cancer Metastasis Rev 2021; 39:1143-1157. [PMID: 32648137 DOI: 10.1007/s10555-020-09913-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Colorectal cancer is a clinically and molecularly heterogeneous disease. Currently, extended RAS and BRAF mutation testing is obligatory in routine clinical practice before starting any treatment in the metastatic setting. Treatment decision making also includes assessment of the clinical condition of the patient, definition of the treatment goal, and consideration of the primary tumor site. Biological treatment is part of the first-line drug combination unless contraindicated. Mutational status is significantly associated with the outcome of patients and is strongly predictive for anti-EGFR-targeted therapy. The prognosis of RAS mutant CRC is clearly inferior to wild-type cases. RAS remains an elusive target, and specific treatment options are not yet available. Recently, promising results of a direct KRAS G12C inhibitor have been reported; however, further confirmation is needed. The biomarker landscape in mCRC is evolving; new promising markers are awaited with the chance of more precise targeted treatment.
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Affiliation(s)
- Gábor Lakatos
- Department of Oncology, South-Pest Hospital Centre - National Institute for Infectology and Haematology, Budapest, Hungary.
| | - Claus-Henning Köhne
- Klinikum Oldenburg, University Clinic of Oncology and Haematology, Oldenburg, Germany
| | - György Bodoky
- Department of Oncology, South-Pest Hospital Centre - National Institute for Infectology and Haematology, Budapest, Hungary
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KRAS Mutations in Papillary Fibroelastomas: A Study of 50 Cases With Etiologic and Diagnostic Implications. Am J Surg Pathol 2020; 44:626-632. [PMID: 32141886 DOI: 10.1097/pas.0000000000001448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Papillary fibroelastoma (PFE) is an increasingly recognized cardiac tumor. Despite its prevalence, controversy exists as to whether it represents a reactive or neoplastic process due to histopathologic similarities with Lambl excrescences (LEs), an accepted reactive phenomenon. Recently, KRAS mutations were reported in a small collection of PFEs, but the incidence of mutations and conditions in which they arise in are unknown. Furthermore, the relationship between PFE and LE has yet to be investigated. Institutional archives were queried for cases of PFE (2001-2017). Paraffin-embedded tissue was microdissected for tumor isolation. Prospectively identified LEs (2018) were collected and wholly isolated. Extracted DNA underwent droplet digital polymerase chain reaction analysis of the most common KRAS mutations (codons 12/13 and 61). Relevant clinical information was abstracted from the medical record. Fifty-two PFEs were tested from 50 patients (32 women). The median patient age was 67 years. Seventeen (33%) PFEs harbored pathogenic variants in tested KRAS codons (12 in codons 12/13; 5 in codon 61). Mutations were mutually exclusive. No clinical or pathologic correlates differed significantly from cases without detectable pathogenic variants. No pathogenic mutation were detected in LEs (n=20; P=0.002). Herein, we report on the largest series of PFE tested for KRAS mutations and present the largest cohort of KRAS-mutant PFEs to date, providing evidence in support of the notion that at least a subset of PFEs represents neoplasia. Moreover, the lack of KRAS mutations in LEs provides evidence as to the separate etiology of this accepted reactive lesion.
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Akagi Y, Tachibana T, Orita Y, Gion Y, Marunaka H, Makino T, Miki K, Akisada N, Yoshino T, Nishizaki K, Sato Y. KRAS mutations in tongue squamous cell carcinoma. Acta Otolaryngol 2019; 139:647-651. [PMID: 31066593 DOI: 10.1080/00016489.2019.1610574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Background: p16INK4a (p16) expression in tongue cancer (TC) is reportedly not associated with human papilloma virus (HPV). Mutations of KRAS in cancer cells are most frequently observed within codon 12. However, few reports have investigated the association between KRAS mutations and p16 status in TC. Objectives: This study aimed to evaluate the influence of KRAS mutations on TC. Methods: Clinical records and surgically resected specimens of 85 TC patients were analyzed. Tumor samples were analyzed for mutations of KRAS located within codons 12 and 13. p16 staining was performed and considered positive in cases with moderate to strong nuclear and cytoplasmic staining. Results: Positive p16 staining was observed in 10 cases (11.8%). A KRAS mutation was detected in one case (1.2%). The case with KRAS mutation showed negative p16 staining. Despite being at an early stage, the patient died of lung metastasis at 43 months from initial treatment. Conclusions and Significance: KRAS mutations are not associated with p16 expression in TC and may predict poor prognosis in TC patients. Further analysis of mutations in regions other than codons 12 and 13 of KRAS will be necessary to determine the relationship between KRAS mutations and prognosis of this disease.
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Affiliation(s)
- Yusuke Akagi
- Department of Otolaryngology, National Hospital Organization Okayama Medical Center, Okayama, Japan
| | - Tomoyasu Tachibana
- Department of Otolaryngology, Japanese Red Cross Society Himeji Hospital, Hyogo, Japan
| | - Yorihisa Orita
- Department of Otolaryngology Head and Neck Surgery, Kumamoto University Graduate School of Medicine, Kumamoto, Japan
| | - Yuka Gion
- Division of Pathophysiology, Okayama University Graduate School of Health Sciences, Okayama, Japan
| | - Hidenori Marunaka
- Department of Otolaryngology, Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Takuma Makino
- Department of Otolaryngology, Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kentaro Miki
- Department of Otolaryngology, Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Naoki Akisada
- Department of Otolaryngology, Japanese Red Cross Okayama Hospital, Japan, Okayama
| | - Tadashi Yoshino
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kazunori Nishizaki
- Department of Otolaryngology, Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yasuharu Sato
- Division of Pathophysiology, Okayama University Graduate School of Health Sciences, Okayama, Japan
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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Jouini R, Ferchichi M, BenBrahim E, Ayari I, Khanchel F, Koubaa W, Saidi O, Allani R, Chadli-Debbiche A. KRAS and NRAS pyrosequencing screening in Tunisian colorectal cancer patients in 2015. Heliyon 2019; 5:e01330. [PMID: 30949599 PMCID: PMC6430077 DOI: 10.1016/j.heliyon.2019.e01330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 02/23/2019] [Accepted: 03/06/2019] [Indexed: 02/07/2023] Open
Abstract
Background Mutations in KRAS and NRAS often result in constitutive activation of RAS in the epidermal growth factor receptor (EGFR) signaling pathway. Mutations in KRAS exon 2 (codon 12–13) predict resistance to anti-EGFR targeted therapy in patients with metastatic colorectal carcinoma (mCRC). However, it's currently known that a significant proportion of mCRC have RAS mutations outside KRAS exon 2, particularly in exons 3 and 4 of KRAS and exons 2, 3 and 4 of NRAS. No data about RAS mutations outside KRAS exon 2 are available for Tunisian mCRC. The aim of this study was to analyze RAS, using pyrosequencing, in nine hotspots mutations in Tunisian patients with mCRC. Methods A series of 131 mCRC was enrolled. Nine hotspots sites mutations of KRAS and NRAS were analyzed (KRAS: codons 12–13, codons 59–61, codon 117 and codon 146, NRAS: codons 12–13, codon 59, codon 61, codon 117 and codon 146) using Therascreen KRAS and RAS extension pyrosequencing kits. Results Analysis was successful in 129 cases (98.5%). Mutations were observed in 97 cases (75.2%) dominated by those in KRAS exon 2 (86.6%). KRAS G12V was the most dominated mutation, observed in 25 cases (25.8%), and followed by KRAS G12S and KRAS G12D, each in 17 cases (17.5%). Mutations outside of KRAS exon 2 presented 13.4% of mutated cases and almost a third (28.8%) of KRAS exon 2 wild type mCRC. Among those, 9 cases (69.3%) carried mutations in NRAS exons 2, 3 and 4 and 4 cases (30.7%) in KRAS exons 3 and 4. Conclusions RAS mutations outside exon 2 of KRAS should be included in routine practice, since they predict also response to anti-EGFR. That would make certain these patients benefit from appropriate testing and treatment. In addition unjustified expenses of anti-EGFR targeted therapy could be avoided.
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Affiliation(s)
- Raja Jouini
- Pathology Department, Habib Thameur Hospital, Tunis, Tunisia
- University of Medicine, Farhat Hached Campus, Tunis El Manar, Tunisia
| | - Marwa Ferchichi
- Pathology Department, Habib Thameur Hospital, Tunis, Tunisia
- University of Sciences, Farhat Hached Campus, Tunis El Manar, Tunisia
- Corresponding author.
| | - Ehsen BenBrahim
- Pathology Department, Habib Thameur Hospital, Tunis, Tunisia
| | - Imen Ayari
- Pathology Department, Habib Thameur Hospital, Tunis, Tunisia
- University of Sciences, Farhat Hached Campus, Tunis El Manar, Tunisia
| | - Fatma Khanchel
- Pathology Department, Habib Thameur Hospital, Tunis, Tunisia
| | - Wafa Koubaa
- Pathology Department, Habib Thameur Hospital, Tunis, Tunisia
| | | | - Riadh Allani
- University of Medicine, Farhat Hached Campus, Tunis El Manar, Tunisia
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Chang XY, Wu Y, Li Y, Wang J, Chen J. Intraductal papillary mucinous neoplasms of the pancreas: Clinical association with KRAS. Mol Med Rep 2018; 17:8061-8068. [PMID: 29658583 PMCID: PMC5983980 DOI: 10.3892/mmr.2018.8875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 01/18/2018] [Indexed: 12/30/2022] Open
Abstract
Intraductal papillary mucinous neoplasms of the pancreas (IPMN) are among the most important precancerous lesions in the pancreas. V‑Ki‑ras 2 Kirsten rat sarcoma viral oncogene homolog (KRAS) is one of the most important genes involved in pancreatic neoplasms, and exhibits a high mutation rate in pancreatic ductal adenocarcinomas and pancreatic intraepithelial neoplasia. The present study aimed to further elucidate the associations among IPMN subtypes (gastric, intestinal, pancreatobiliary and oncocytic), pathological classifications [low‑grade, intermediate‑grade, and high‑grade IPMN, and associated minimally invasive carcinoma (invasive depth ≤0.5 cm) and advanced invasive carcinoma (invasive depth >0.5 cm)]. A total of 56 cases of IPMN were studied using scorpion amplified refractory mutation system analysis of KRAS mutations, pathological features and prognosis. KRAS mutations were identified in 50% (28/56 cases). The frequency was 60% (9/15 cases) in gastric‑type, 52.6% (10/19 cases) in intestinal‑type, 47.3% (9/19 cases) in pancreatobiliary‑type and zero (0/3 cases) in oncocytic‑type IPMN. Except for oncocytic type IPMN, the frequencies of KRAS mutations in IPMN with low, intermediate and high grade, and IPMN‑associated carcinoma were 58.3% (7/12 cases), 27.3% (3/11 cases), 80% (4/5 cases) and 56% (14/25 cases), respectively. With more advanced dysplasia and invasion, the prevalence of KRAS mutations in intestinal‑type IPMN increased (P=0.012). The Kaplan‑Meier survival curve demonstrated that survival rate was not associated with KRAS mutation (log‑rank test; P=0.308). The prevalence of KRAS mutations was lowest in intestinal‑type IPMN, and was in proportion to the degree of dysplasia and invasion. Therefore, KRAS mutation in IPMN does not correlate with histological subtype, dysplasia grade, depth of invasion or survival.
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Affiliation(s)
- Xiao Yan Chang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tsinghua University, Beijing 100730, P.R. China
| | - Yan Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tsinghua University, Beijing 100730, P.R. China
| | - Yuan Li
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tsinghua University, Beijing 100730, P.R. China
| | - Jing Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tsinghua University, Beijing 100730, P.R. China
| | - Jie Chen
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tsinghua University, Beijing 100730, P.R. China
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Guarnaccia M, Iemmolo R, San Biagio F, Alessi E, Cavallaro S. Genotyping of KRAS Mutational Status by the In-Check Lab-on-Chip Platform. SENSORS 2018; 18:s18010131. [PMID: 29304017 PMCID: PMC5795341 DOI: 10.3390/s18010131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/14/2017] [Accepted: 12/31/2017] [Indexed: 12/20/2022]
Abstract
The KRAS oncogene is involved in the pathogenesis of several types of cancer, particularly colorectal cancer (CRC). The most frequent mutations in this gene are associated with poor survival, increased tumor aggressiveness and resistance to therapy with anti-epidermal growth factor receptor (EGFR) antibodies. For this reason, KRAS mutation testing has become increasingly common in clinical practice for personalized cancer treatments of CRC patients. Detection methods for KRAS mutations are currently expensive, laborious, time-consuming and often lack of diagnostic sensitivity and specificity. In this study, we describe the development of a Lab-on-Chip assay for genotyping of KRAS mutational status. This assay, based on the In-Check platform, integrates microfluidic handling, a multiplex polymerase chain reaction (PCR) and a low-density microarray. This integrated sample-to-result system enables the detection of KRAS point mutations, including those occurring in codons 12 and 13 of exon 2, 59 and 61 of exon 3, 117 and 146 of exon 4. Thanks to its miniaturization, automation, rapid analysis, minimal risk of sample contamination, increased accuracy and reproducibility of results, this Lab-on-Chip platform may offer immediate opportunities to simplify KRAS genotyping into clinical routine.
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Affiliation(s)
- Maria Guarnaccia
- Institute of Neurological Sciences, Italian National Research Council, Via Paolo Gaifami 18, 95126 Catania, Italy.
| | - Rosario Iemmolo
- Institute of Neurological Sciences, Italian National Research Council, Via Paolo Gaifami 18, 95126 Catania, Italy.
| | | | - Enrico Alessi
- Analog, MEMS & Sensor Group-HealthCare Business Development Unit, STMicroelectronics, Stradale Primosole 50, 95121 Catania, Italy.
| | - Sebastiano Cavallaro
- Institute of Neurological Sciences, Italian National Research Council, Via Paolo Gaifami 18, 95126 Catania, Italy.
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14
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Sherwood JL, Brown H, Rettino A, Schreieck A, Clark G, Claes B, Agrawal B, Chaston R, Kong BSG, Choppa P, Nygren AOH, Deras IL, Kohlmann A. Key differences between 13 KRAS mutation detection technologies and their relevance for clinical practice. ESMO Open 2017; 2:e000235. [PMID: 29018576 PMCID: PMC5623342 DOI: 10.1136/esmoopen-2017-000235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/18/2022] Open
Abstract
Introduction This study assessed KRAS mutation detection and functional characteristics across 13 distinct technologies and assays available in clinical practice, in a blinded manner. Methods Five distinct KRAS-mutant cell lines were used to study five clinically relevant KRAS mutations: p.G12C, p.G12D, p.G12V, p.G13D and p.Q61H. 50 cell line admixtures with low (50 and 100) mutant KRAS allele copies at 20%, 10%, 5%, 1% and 0.5% frequency were processed using quantitative PCR (qPCR) (n=3), matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF) (n=2), next-generation sequencing (NGS) (n=6), digital PCR (n=1) and Sanger capillary sequencing (n=1) assays. Important performance differences were revealed, particularly assay sensitivity and turnaround time. Results Overall 406/728 data points across all 13 technologies were identified correctly. Successful genotyping of admixtures ranged from 0% (Sanger sequencing) to 100% (NGS). 5/6 NGS platforms reported similar allelic frequency for each sample. One NGS assay detected mutations down to a frequency of 0.5% and correctly identified all 56 samples (Oncomine Focus Assay, Thermo Fisher Scientific). One qPCR (Idylla, Biocartis) and MALDI-TOF (UltraSEEK, Agena Bioscience) assay identified 96% (all 100 copies and 23/25 at 50 copies input) and 92% (23/25 at 100 copies and 23/25 at 50 copies input) of samples, respectively. The digital PCR assay (KRAS PrimePCR ddPCR, Bio-Rad Laboratories) identified 60% (100 copies) and 52% (50 copies) of samples correctly. Turnaround time from sample to results ranged from ~2 hours (Idylla CE-IVD) to 2 days (TruSight Tumor 15 and Sentosa CE-IVD), to 2 weeks for certain NGS assays; the level of required expertise ranged from minimal (Idylla CE-IVD) to high for some technologies. Discussion This comprehensive parallel assessment used high molecular weight cell line DNA as a model system to address key questions for a laboratory when implementing routine KRAS testing. As most of the technologies are available for additional molecular biomarkers, this study may be informative for other applications.
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Affiliation(s)
- James L Sherwood
- Precision Medicine and Genomics, Innovative Medicines and Early Development Biotech, AstraZeneca, Cambridge, UK
| | - Helen Brown
- Precision Medicine and Genomics, Innovative Medicines and Early Development Biotech, AstraZeneca, Cambridge, UK
| | - Alessandro Rettino
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | | | - Graeme Clark
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Research Campus, Cambridge, UK
| | | | | | | | - Benjamin S G Kong
- Thermo Fisher Scientific, Clinical Sequencing Division, West Sacramento, California, UK
| | - Paul Choppa
- Thermo Fisher Scientific, Clinical Sequencing Division, West Sacramento, California, UK
| | | | | | - Alexander Kohlmann
- Precision Medicine and Genomics, Innovative Medicines and Early Development Biotech, AstraZeneca, Cambridge, UK
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15
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Rapid and accurate detection of KRAS mutations in colorectal cancers using the isothermal-based optical sensor for companion diagnostics. Oncotarget 2017; 8:83860-83871. [PMID: 29137388 PMCID: PMC5663560 DOI: 10.18632/oncotarget.20038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/25/2017] [Indexed: 01/23/2023] Open
Abstract
Although KRAS mutational status testing is becoming a companion diagnostic tool for managing patients with colorectal cancer (CRC), there are still several difficulties when analyzing KRAS mutations using the existing assays, particularly with regard to low sensitivity, its time-consuming, and the need for large instruments. We developed a rapid, sensitive, and specific mutation detection assay based on the bio-photonic sensor termed ISAD (isothermal solid-phase amplification/detection), and used it to analyze KRAS gene mutations in human clinical samples. To validate the ISAD-KRAS assay for use in clinical diagnostics, we examined for hotspot KRAS mutations (codon 12 and codon 13) in 70 CRC specimens using PCR and direct sequencing methods. In a serial dilution study, ISAD-KRAS could detect mutations in a sample containing only 1% of the mutant allele in a mixture of wild-type DNA, whereas both PCR and direct sequencing methods could detect mutations in a sample containing approximately 30% of mutant cells. The results of the ISAD-KRAS assay from 70 clinical samples matched those from PCR and direct sequencing, except in 5 cases, wherein ISAD-KRAS could detect mutations that were not detected by PCR and direct sequencing. We also found that the sensitivity and specificity of ISAD-KRAS were 100% within 30 min. The ISAD-KRAS assay provides a rapid, highly sensitive, and label-free method for KRAS mutation testing, and can serve as a robust and near patient testing approach for the rapid detection of patients most likely to respond to anti-EGFR drugs.
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16
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Chuerduangphui J, Pientong C, Patarapadungkit N, Chotiyano A, Vatanasapt P, Kongyingyoes B, Promthet S, Swangphon P, Bumrungthai S, Pimson C, Ekalaksananan T. Amplification of EGFR and cyclin D1 genes associated with human papillomavirus infection in oral squamous cell carcinoma. Med Oncol 2017; 34:148. [DOI: 10.1007/s12032-017-1010-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/20/2017] [Indexed: 12/28/2022]
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17
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Sepulveda AR, Hamilton SR, Allegra CJ, Grody W, Cushman-Vokoun AM, Funkhouser WK, Kopetz SE, Lieu C, Lindor NM, Minsky BD, Monzon FA, Sargent DJ, Singh VM, Willis J, Clark J, Colasacco C, Bryan Rumble R, Temple-Smolkin R, B Ventura C, Nowak JA. Molecular Biomarkers for the Evaluation of Colorectal Cancer: Guideline From the American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology. Arch Pathol Lab Med 2017; 141:625-657. [PMID: 28165284 DOI: 10.5858/arpa.2016-0554-cp] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVES - To develop evidence-based guideline recommendations through a systematic review of the literature to establish standard molecular biomarker testing of colorectal cancer (CRC) tissues to guide epidermal growth factor receptor (EGFR) therapies and conventional chemotherapy regimens. METHODS - The American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology convened an expert panel to develop an evidence-based guideline to establish standard molecular biomarker testing and guide therapies for patients with CRC. A comprehensive literature search that included more than 4,000 articles was conducted. RESULTS - Twenty-one guideline statements were established. CONCLUSIONS - Evidence supports mutational testing for EGFR signaling pathway genes, since they provide clinically actionable information as negative predictors of benefit to anti-EGFR monoclonal antibody therapies for targeted therapy of CRC. Mutations in several of the biomarkers have clear prognostic value. Laboratory approaches to operationalize CRC molecular testing are presented.
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Affiliation(s)
- Antonia R Sepulveda
- From the 1 Department of Pathology and Cell Biology, Columbia University, New York, NY
| | | | - Carmen J Allegra
- 5 Division of Hematology and Oncology, University of Florida Medical Center, Gainesville
| | - Wayne Grody
- 6 Departments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics, UCLA Medical Center, Los Angeles, CA
| | | | - William K Funkhouser
- 8 Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill
| | | | - Christopher Lieu
- 9 Division of Medical Oncology, University of Colorado Denver School of Medicine, Denver
| | | | - Bruce D Minsky
- 4 Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston
| | | | - Daniel J Sargent
- 12 Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | - Joseph Willis
- 14 Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Jennifer Clark
- 15 ASCP Institute for Science, Technology, and Policy, American Society for Clinical Pathology, Washington, DC
| | - Carol Colasacco
- 16 Laboratory and Pathology Quality Center, College of American Pathologists, Northfield, IL
| | - R Bryan Rumble
- 17 American Society of Clinical Oncology, Alexandria, VA
| | | | - Christina B Ventura
- 16 Laboratory and Pathology Quality Center, College of American Pathologists, Northfield, IL
| | - Jan A Nowak
- From the 1 Department of Pathology and Cell Biology, Columbia University, New York, NY
- 2 Department of Pathology
- 3 Department of Gastrointestinal (GI) Medical Oncology
- 4 Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston
- 5 Division of Hematology and Oncology, University of Florida Medical Center, Gainesville
- 6 Departments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics, UCLA Medical Center, Los Angeles, CA
- 7 Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
- 8 Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill
- 9 Division of Medical Oncology, University of Colorado Denver School of Medicine, Denver
- 10 Department of Medical Genetics, Mayo Clinic, Scottsdale, AZ
- 11 Castle Biosciences, Friendswood, TX
- 12 Department of Health Sciences Research, Mayo Clinic, Rochester, MN
- 13 Biocept, San Diego, CA
- 14 Department of Pathology, Case Western Reserve University, Cleveland, OH
- 15 ASCP Institute for Science, Technology, and Policy, American Society for Clinical Pathology, Washington, DC
- 16 Laboratory and Pathology Quality Center, College of American Pathologists, Northfield, IL
- 17 American Society of Clinical Oncology, Alexandria, VA
- 18 Association for Molecular Pathology, Bethesda, MD
- 19 Department of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, NY
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18
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Sepulveda AR, Hamilton SR, Allegra CJ, Grody W, Cushman-Vokoun AM, Funkhouser WK, Kopetz SE, Lieu C, Lindor NM, Minsky BD, Monzon FA, Sargent DJ, Singh VM, Willis J, Clark J, Colasacco C, Rumble RB, Temple-Smolkin R, Ventura CB, Nowak JA. Molecular Biomarkers for the Evaluation of Colorectal Cancer. Am J Clin Pathol 2017; 147:221-260. [PMID: 28165529 PMCID: PMC7263311 DOI: 10.1093/ajcp/aqw209] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Objectives: To develop evidence-based guideline recommendations through a systematic review of the literature to establish standard molecular biomarker testing of colorectal cancer (CRC) tissues to guide epidermal growth factor receptor (EGFR) therapies and conventional chemotherapy regimens. Methods: The American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology convened an expert panel to develop an evidence-based guideline to establish standard molecular biomarker testing and guide therapies for patients with CRC. A comprehensive literature search that included more than 4,000 articles was conducted. Results: Twenty-one guideline statements were established. Conclusions: Evidence supports mutational testing for EGFR signaling pathway genes, since they provide clinically actionable information as negative predictors of benefit to anti-EGFR monoclonal antibody therapies for targeted therapy of CRC. Mutations in several of the biomarkers have clear prognostic value. Laboratory approaches to operationalize CRC molecular testing are presented.
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Affiliation(s)
- Antonia R. Sepulveda
- From theDepartment of Pathology and Cell Biology, Columbia University, New York, NY; Departments of
| | | | - Carmen J. Allegra
- Division of Hematology and Oncology, University of Florida Medical Center, Gainesville
| | - Wayne Grody
- Departments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics UCLA Medical Center, Los Angeles, CA
| | | | - William K. Funkhouser
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill
| | | | - Christopher Lieu
- Division of Medical Oncology, University of Colorado Denver School of Medicine, Denver
| | | | - Bruce D. Minsky
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston
| | | | | | | | - Joseph Willis
- Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Jennifer Clark
- ASCP Institute for Science, Technology, and Policy, American Society for Clinical Pathology, Washington, DC
| | - Carol Colasacco
- Laboratory and Pathology Quality Center, College of American Pathologists, Northfield, IL
| | | | | | - Christina B. Ventura
- Laboratory and Pathology Quality Center, College of American Pathologists, Northfield, IL
| | - Jan A. Nowak
- Department of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, NY
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19
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Sepulveda AR, Hamilton SR, Allegra CJ, Grody W, Cushman-Vokoun AM, Funkhouser WK, Kopetz SE, Lieu C, Lindor NM, Minsky BD, Monzon FA, Sargent DJ, Singh VM, Willis J, Clark J, Colasacco C, Rumble RB, Temple-Smolkin R, Ventura CB, Nowak JA. Molecular Biomarkers for the Evaluation of Colorectal Cancer: Guideline From the American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology. J Mol Diagn 2017; 19:187-225. [PMID: 28185757 PMCID: PMC5971222 DOI: 10.1016/j.jmoldx.2016.11.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES To develop evidence-based guideline recommendations through a systematic review of the literature to establish standard molecular biomarker testing of colorectal cancer (CRC) tissues to guide epidermal growth factor receptor (EGFR) therapies and conventional chemotherapy regimens. METHODS The American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology convened an expert panel to develop an evidence-based guideline to establish standard molecular biomarker testing and guide therapies for patients with CRC. A comprehensive literature search that included more than 4,000 articles was conducted. RESULTS Twenty-one guideline statements were established. CONCLUSIONS Evidence supports mutational testing for EGFR signaling pathway genes, since they provide clinically actionable information as negative predictors of benefit to anti-EGFR monoclonal antibody therapies for targeted therapy of CRC. Mutations in several of the biomarkers have clear prognostic value. Laboratory approaches to operationalize CRC molecular testing are presented. Key Words: Molecular diagnostics; Gastrointestinal; Histology; Genetics; Oncology.
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Affiliation(s)
- Antonia R Sepulveda
- Department of Pathology and Cell Biology, Columbia University, New York, NY.
| | - Stanley R Hamilton
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston
| | - Carmen J Allegra
- Division of Hematology and Oncology, University of Florida Medical Center, Gainesville
| | - Wayne Grody
- Departments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics, UCLA Medical Center, Los Angeles, CA
| | | | - William K Funkhouser
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill
| | - Scott E Kopetz
- Department of Gastrointestinal (GI) Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Christopher Lieu
- Division of Medical Oncology, University of Colorado Denver School of Medicine, Denver
| | | | - Bruce D Minsky
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston
| | | | - Daniel J Sargent
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | - Joseph Willis
- Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Jennifer Clark
- ASCP Institute for Science, Technology, and Policy, American Society for Clinical Pathology, Washington, DC
| | - Carol Colasacco
- Laboratory and Pathology Quality Center, College of American Pathologists, Northfield, IL
| | | | | | - Christina B Ventura
- Laboratory and Pathology Quality Center, College of American Pathologists, Northfield, IL
| | - Jan A Nowak
- Department of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, NY
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20
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Sepulveda AR, Hamilton SR, Allegra CJ, Grody W, Cushman-Vokoun AM, Funkhouser WK, Kopetz SE, Lieu C, Lindor NM, Minsky BD, Monzon FA, Sargent DJ, Singh VM, Willis J, Clark J, Colasacco C, Rumble RB, Temple-Smolkin R, Ventura CB, Nowak JA. Molecular Biomarkers for the Evaluation of Colorectal Cancer: Guideline From the American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and the American Society of Clinical Oncology. J Clin Oncol 2017; 35:1453-1486. [PMID: 28165299 DOI: 10.1200/jco.2016.71.9807] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Purpose Molecular testing of colorectal cancers (CRCs) to improve patient care and outcomes of targeted and conventional therapies has been the center of many recent studies, including clinical trials. Evidence-based recommendations for the molecular testing of CRC tissues to guide epidermal growth factor receptor (EGFR) -targeted therapies and conventional chemotherapy regimens are warranted in clinical practice. The purpose of this guideline is to develop evidence-based recommendations to help establish standard molecular biomarker testing for CRC through a systematic review of the literature. Methods The American Society for Clinical Pathology (ASCP), College of American Pathologists (CAP), Association for Molecular Pathology (AMP), and the American Society of Clinical Oncology (ASCO) convened an Expert Panel to develop an evidence-based guideline to help establish standard molecular biomarker testing, guide targeted therapies, and advance personalized care for patients with CRC. A comprehensive literature search that included over 4,000 articles was conducted to gather data to inform this guideline. Results Twenty-one guideline statements (eight recommendations, 10 expert consensus opinions and three no recommendations) were established. Recommendations Evidence supports mutational testing for genes in the EGFR signaling pathway, since they provide clinically actionable information as negative predictors of benefit to anti-EGFR monoclonal antibody therapies for targeted therapy of CRC. Mutations in several of the biomarkers have clear prognostic value. Laboratory approaches to operationalize molecular testing for predictive and prognostic molecular biomarkers involve selection of assays, type of specimens to be tested, timing of ordering of tests and turnaround time for testing results. Additional information is available at: www.asco.org/CRC-markers-guideline and www.asco.org/guidelineswiki.
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Affiliation(s)
- Antonia R Sepulveda
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Stanley R Hamilton
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Carmen J Allegra
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Wayne Grody
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Allison M Cushman-Vokoun
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - William K Funkhouser
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Scott E Kopetz
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Christopher Lieu
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Noralane M Lindor
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Bruce D Minsky
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Federico A Monzon
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Daniel J Sargent
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Veena M Singh
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Joseph Willis
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Jennifer Clark
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Carol Colasacco
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - R Bryan Rumble
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Robyn Temple-Smolkin
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Christina B Ventura
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
| | - Jan A Nowak
- Antonia R. Sepulveda, Columbia University, New York, NY; Stanley R. Hamilton, Scott E. Kopetz, and Bruce D. Minsky, University of Texas MD Anderson Cancer Center, Houston, TX; Carmen J. Allegra, University of Florida Medical Center, Gainesville, FL; Wayne Grody, UCLA Medical Center, Los Angeles, CA; Allison M. Cushman-Vokoun, University of Nebraska Medical Center, Omaha, NE; William K. Funkhouser, University of North Carolina School of Medicine, Chapel Hill, NC; Christopher Lieu, University of Colorado Denver School of Medicine, Denver, CO; Noralane M. Lindor, Mayo Clinic, Scottsdale, AZ; Federico A. Monzon, Castle Biosciences, Friendswood, TX; Daniel J. Sargent, Mayo Clinic, Rochester, MN; Veena M. Singh, Biocept, San Diego, CA; Joseph Willis, Case Western Reserve University, Cleveland, OH; Jennifer Clark, American Society for Clinical Pathology, Washington, DC; Carol Colasacco and Christina B. Ventura, College of American Pathologists, Northfield, IL; R. Bryan Rumble, American Society of Clinical Oncology, Alexandria, VA; Robyn Temple-Smolkin, Association for Molecular Pathology, Bethesda, MD; and Jan A. Nowak, Roswell Park Cancer Institute, Buffalo, NY
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21
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Loree JM, Kopetz S, Raghav KPS. Current companion diagnostics in advanced colorectal cancer; getting a bigger and better piece of the pie. J Gastrointest Oncol 2017; 8:199-212. [PMID: 28280626 PMCID: PMC5334060 DOI: 10.21037/jgo.2017.01.01] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/18/2016] [Indexed: 12/19/2022] Open
Abstract
While the treatment of colorectal cancer continues to rely heavily on conventional cytotoxic therapy, an increasing number of targeted agents are under development. Many of these treatments require companion diagnostic tests in order to define an appropriate population that will derive benefit. In addition, a growing number of biomarkers provide prognostic information about a patient's malignancy. As we learn more about these biomarkers and their assays, selecting the appropriate companion diagnostic becomes increasingly important. In the case of many biomarkers, there are numerous assays which could provide the same information to a treating physician, however each assay has strengths and weaknesses. Institutions must balance cost, assay sensitivity, turn-around time, and labor resources when selecting which assay to offer. In this review we will discuss the current state of companion diagnostics available in metastatic colorectal cancer and explore emerging biomarkers and their assays. We will focus on KRAS, BRAF, HER2, and PIK3CA testing, as well as microsatellite stability assessment and multigene panels.
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Affiliation(s)
- Jonathan M Loree
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kanwal P S Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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22
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Denis JA, Patroni A, Guillerm E, Pépin D, Benali-Furet N, Wechsler J, Manceau G, Bernard M, Coulet F, Larsen AK, Karoui M, Lacorte JM. Droplet digital PCR of circulating tumor cells from colorectal cancer patients can predict KRAS mutations before surgery. Mol Oncol 2016; 10:1221-31. [PMID: 27311775 PMCID: PMC5423194 DOI: 10.1016/j.molonc.2016.05.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/13/2016] [Accepted: 05/29/2016] [Indexed: 01/24/2023] Open
Abstract
In colorectal cancer (CRC), KRAS mutations are a strong negative predictor for treatment with the EGFR-targeted antibodies cetuximab and panitumumab. Since it can be difficult to obtain appropriate tumor tissues for KRAS genotyping, alternative methods are required. Circulating tumor cells (CTCs) are believed to be representative of the tumor in real time. In this study we explored the capacity of a size-based device for capturing CTCs coupled with a multiplex KRAS screening assay using droplet digital PCR (ddPCR). We showed that it is possible to detect a mutant ratio of 0.05% and less than one KRAS mutant cell per mL total blood with ddPCR compared to about 0.5% and 50-75 cells for TaqMeltPCR and HRM. Next, CTCs were isolated from the blood of 35 patients with CRC at various stage of the disease. KRAS genotyping was successful for 86% (30/35) of samples with a KRAS codon 12/13 mutant ratio of 57% (17/30). In contrast, only one patient was identified as KRAS mutant when size-based isolation was combined with HRM or TaqMeltPCR. KRAS status was then determined for the 26 available formalin-fixed paraffin-embedded tumors using standard procedures. The concordance between the CTCs and the corresponding tumor tissues was 77% with a sensitivity of 83%. Taken together, the data presented here suggest that is feasible to detect KRAS mutations in CTCs from blood samples of CRC patients which are predictive for those found in the tumor. The minimal invasive nature of this procedure in combination with the high sensitivity of ddPCR might provide in the future an opportunity to monitor patients throughout the course of disease on multiple levels including early detection, prognosis, treatment and relapse as well as to obtain mechanistic insight with respect to tumor invasion and metastasis.
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Affiliation(s)
- Jérôme Alexandre Denis
- Sorbonne Universités, UPMC Univ. Paris 06, F-75005, Paris, France; Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Oncology and Endocrine Biochemistry, Paris, France; Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine, Institut National de la Santé et de la Recherche Médicale (INSERM) U938, Institut Universitaire de Cancérologie (IUC), Université Pierre et Marie Curie (UPMC), Sorbonne Universities, Paris, France.
| | - Alexia Patroni
- Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Digestive and Hepato-Pancreato-Biliary Surgery, Paris, France
| | - Erell Guillerm
- Sorbonne Universités, UPMC Univ. Paris 06, F-75005, Paris, France; Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Oncogenetics and Molecular Angiogenetics, Paris, France
| | - Dominique Pépin
- Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Oncology and Endocrine Biochemistry, Paris, France
| | | | | | - Gilles Manceau
- Sorbonne Universités, UPMC Univ. Paris 06, F-75005, Paris, France; Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Digestive and Hepato-Pancreato-Biliary Surgery, Paris, France
| | - Maguy Bernard
- Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Oncology and Endocrine Biochemistry, Paris, France
| | - Florence Coulet
- Sorbonne Universités, UPMC Univ. Paris 06, F-75005, Paris, France; Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Oncogenetics and Molecular Angiogenetics, Paris, France
| | - Annette K Larsen
- Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine, Institut National de la Santé et de la Recherche Médicale (INSERM) U938, Institut Universitaire de Cancérologie (IUC), Université Pierre et Marie Curie (UPMC), Sorbonne Universities, Paris, France
| | - Mehdi Karoui
- Sorbonne Universités, UPMC Univ. Paris 06, F-75005, Paris, France; Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Digestive and Hepato-Pancreato-Biliary Surgery, Paris, France
| | - Jean-Marc Lacorte
- Sorbonne Universités, UPMC Univ. Paris 06, F-75005, Paris, France; Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Department of Oncology and Endocrine Biochemistry, Paris, France; INSERM, UMR_S 1166, Institute of Cardiometabolism and Nutrition, ICAN, Paris, France
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23
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Xu S, Duan Y, Lou L, Tang F, Shou J, Wang G. Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay. Oncol Lett 2016; 12:4238-4244. [PMID: 27895798 DOI: 10.3892/ol.2016.5184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/05/2016] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to explore the influence of T790M neighboring single nucleotide polymorphism (SNP) on the sensitivity of amplification refractory mutation system (ARMS)-based T790M mutation assay. Three ARMS-quantitative polymerase chain reaction (qPCR) systems (system 1 had a forward ARMS primer without rs1050171, system 2 included a forward ARMS primer with rs1050171 and system 3 contained the above two forward ARMS primers) were used to detect the T790M mutation in two series plasmid samples and genomic DNA (gDNA) of the cell line H1975. A total of 670 formalin-fixed paraffin-embedded (FFPE) tumor samples from non-small cell lung cancer patients were used to detect the epidermal growth factor receptor (EGFR) gene T790M mutation by direct sequencing and ARMS-qPCR. The ARMS-qPCR system 1 effectively detected samples with as low as 1% T790M mutant plasmid 1 (without rs1050171) and with 50% T790M mutant plasmid 2 (with rs1050171), while the ARMS-qPCR system 2 detected samples with 20 and 50% T790M mutant plasmid 1, in addition to samples with 1% T790M mutant plasmid 2. For the ARMS-qPCR system 3, samples with as low as 1% T790M mutant plasmids 1 or 2 were effectively detected. For gDNA analysis of the cell line H1975, the T790M mutation was effectively detected by the ARMS-qPCR systems 2 and 3 (~50% mutation rate), but was detected with a low mutation abundance by the ARMS-qPCR system 1 (~1% mutation rate). Of the 670 FFPE samples, 5 cases were identified to have the T790M mutation by sequencing and by the ARMS-qPCR system 1. One sample (named N067), which was considered as T790M-negative by sequencing, was demonstrated to have the T790M mutation using the ARMS-qPCR system 1. Sample N094, which was variant homozygous for rs1050171 and was indicated to be T790M-negative by sequencing and by the ARMS-qPCR system 1, was identified to have the T790M mutation with the ARMS-qPCR system 3. The A-variant allele frequency of rs1050171 was observed to be 28.2% in the 670 FFPE tumor samples, while the presence of rs148188503 (c. C2355T, p. T785T) was observed in sample N558, and a novel SNP with a base substitution (c. T2375C) at position 792 (p. L792P) in exon 20 of the EGFR gene was observed in sample N310. rs1050171 is a high-frequency SNP located near T790M, and the mutation statuses of rs1050171 appear to influence the sensitivity of the ARMS-based T790M detection system, thus generating a 14.3% false-negative rate (1/7). The present study proposes the risk that target neighboring SNPs (as far as 8 bp away in the present study) may exert on the sensitivity of ARMS-based detection methods.
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Affiliation(s)
- Sanpeng Xu
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yaqi Duan
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Liping Lou
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Fengjuan Tang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Juan Shou
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Guoping Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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Matsunaga M, Kaneta T, Miwa K, Ichikawa W, Fujita KI, Nagashima F, Furuse J, Kage M, Akagi Y, Sasaki Y. A comparison of four methods for detecting KRAS mutations in formalin-fixed specimens from metastatic colorectal cancer patients. Oncol Lett 2016; 12:150-156. [PMID: 27347117 DOI: 10.3892/ol.2016.4576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/29/2016] [Indexed: 12/24/2022] Open
Abstract
There is currently no standard method for the detection of Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation status in colorectal tumors. In the present study, we compared the KRAS mutation detection ability of four methods: direct sequencing, Scorpion-ARMS assaying, pyrosequencing and multi-analyte profiling (Luminex xMAP). We evaluated 73 cases of metastatic colorectal cancer (mCRC) resistant to irinotecan, oxaliplatin and fluoropyrimidine that were enrolled in an all-case study of cetuximab. The KRAS mutation detection capacity of the four analytical methods was compared using DNA samples extracted from tumor tissue, and the detection success rate and concordance of the detection results were evaluated. KRAS mutations were detected by direct sequencing, Scorpion-ARMS assays, pyrosequencing and Luminex xMAP at success rates of 93.2%, 97.3%, 95.9% and 94.5%, respectively. The concordance rates of the detection results by Scorpion-ARMS, pyrosequencing and Luminex xMAP with those of direct sequencing were 0.897, 0.923 and 0.900 (κ statistics), respectively. The direct sequencing method could not determine KRAS mutation status in five DNA samples. Of these, Scorpion-ARMS, pyrosequencing and Luminex xMAP successfully detected three, two and one KRAS mutation statuses, respectively. Three cases demonstrated inconsistent results, whereby Luminex xMAP detected mutated KRAS in two samples while wild-type KRAS was detected by the other methods. In the remaining case, direct sequencing detected wild-type KRAS, which was identified as mutated KRAS by the other methods. In conclusion, we confirmed that Scorpion-ARMS, pyrosequencing and Luminex xMAP were equally reliable in detecting KRAS mutation status in mCRC. However, in rare cases, the KRAS status was differentially diagnosed using these methods.
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Affiliation(s)
- Mototsugu Matsunaga
- Multidisciplinary Treatment Cancer Center, Kurume University Hospital, Kurume, Fukuoka 830-0011, Japan
| | - Toshikado Kaneta
- Division of Medical Oncology, Department of Internal Medicine, Showa University Hospital, Hatanodai, Shinagawa, Tokyo 142-8666, Japan
| | - Keisuke Miwa
- Multidisciplinary Treatment Cancer Center, Kurume University Hospital, Kurume, Fukuoka 830-0011, Japan
| | - Wataru Ichikawa
- Division of Medical Oncology, Department of Internal Medicine, Showa University Hospital, Hatanodai, Shinagawa, Tokyo 142-8666, Japan
| | - Ken-Ichi Fujita
- Division of Medical Oncology, Department of Internal Medicine, Showa University Hospital, Hatanodai, Shinagawa, Tokyo 142-8666, Japan
| | - Fumio Nagashima
- Department of Medical Oncology, Kyorin University School of Medicine, Hinkawa, Mitaka, Tokyo 181-8611, Japan
| | - Junji Furuse
- Department of Medical Oncology, Kyorin University School of Medicine, Hinkawa, Mitaka, Tokyo 181-8611, Japan
| | - Masayoshi Kage
- Department of Diagnostic Pathology, Kurume University Hospital, Kurume, Fukuoka 830-0011, Japan
| | - Yoshito Akagi
- Department of Surgery, Kurume University Hospital, Kurume, Fukuoka 830-0011, Japan
| | - Yasutsuna Sasaki
- Division of Medical Oncology, Department of Internal Medicine, Showa University Hospital, Hatanodai, Shinagawa, Tokyo 142-8666, Japan
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Dong YJ, Cai YR, Zhou LJ, Su D, Mu J, Chen XJ, Zhang LI. Association between the histological subtype of lung adenocarcinoma, EGFR/KRAS mutation status and the ALK rearrangement according to the novel IASLC/ATS/ERS classification. Oncol Lett 2016; 11:2552-2558. [PMID: 27073516 DOI: 10.3892/ol.2016.4233] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 01/27/2016] [Indexed: 01/11/2023] Open
Abstract
The present study aimed to investigate the association between epidermal growth factor receptor (EGFR)/Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations, anaplastic lymphoma receptor tyrosine kinase (ALK) rearrangements and the morphological characteristics of lung adenocarcinoma (LAC), according to the International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society (IASLC/ATS/ERS) classification in a large group of patients with primary LAC. A total of 200 patients with invasive LAC who had undergone complete resections at the Beijing Chest Hospital (Beijing, China) were randomly selected. The morphology of the samples was reassessed in 5% increments by two pathologists, according to the IASLC/ATS/ERS scheme. EGFR and KRAS mutations were tested by direct DNA sequencing. ALK rearrangements were screened by immunohistochemistry on a Benchmark XT stainer. The data revealed that EGFR and KRAS mutations, and ALK rearrangements were identified in 46.0% (92/200), 9.0% (18/200) and 11.5% (23/200) of the patients, respectively. The EGFR/KRAS mutations and ALK rearrangements were mostly exclusive. However, 1 patient exhibited the coexistence of the EGFR (at exon 20) and KRAS (codon 12) mutations, and another patient exhibited the coexistence of the EGFR mutation (at exon 21) and the ALK gene fusion. EGFR mutations were indicated to be closely associated with the acinar predominant (43/77; 55.8%; P=0.030) and papillary predominant (26/49; 53.1%; P=0.006) subtypes. KRAS mutations were more commonly associated with the solid predominant subtype (9/52; 17.3%; P=0.023) and invasive mucinous LAC (5/10; 50.0%; P=0.004), and less commonly associated with the acinar predominant subtype (1/77; 1.3%; P=0.002). ALK rearrangements more commonly occurred in the solid predominant subtype compared with other subtypes (13/52; 25%; P=0.002), and less commonly occurred in the papillary predominant subtype (1/49; 2.0%; P=0.004). Tumors harboring ALK rearrangements were characterized by signet-ring cell (7/9; 77.8%; P<0.0001) and cribriform (7/12; 58.3%; P<0.0001) patterns. The association between the mutation status and histological subtype in LAC was distinct. The predominant subtype according to the IASLC/ATS/ERS classification provided important information for gene mutations and integrated clinical findings to improve the treatment of LAC patients.
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Affiliation(s)
- Yu-Jie Dong
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
| | - Yi-Ran Cai
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
| | - Li-Juan Zhou
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
| | - Dan Su
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
| | - Jing Mu
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
| | - Xue-Jing Chen
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
| | - L I Zhang
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
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Huang JF, Zeng DZ, Duan GJ, Shi Y, Deng GH, Xia H, Xu HQ, Zhao N, Fu WL, Huang Q. Single-Tubed Wild-Type Blocking Quantitative PCR Detection Assay for the Sensitive Detection of Codon 12 and 13 KRAS Mutations. PLoS One 2015; 10:e0145698. [PMID: 26701781 PMCID: PMC4689371 DOI: 10.1371/journal.pone.0145698] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023] Open
Abstract
The high degree of intra-tumor heterogeneity has meant that it is important to develop sensitive and selective assays to detect low-abundance KRAS mutations in metastatic colorectal carcinoma (mCRC) patients. As a major potential source of tumor DNA in the aforementioned genotyping assays, it was necessary to conduct an analysis on both the quality and quantity of DNA extracted from formalin-fixed paraffin-embedded (FFPE). Therefore, four commercial FFPE DNA extraction kits were initially compared with respect to their ability to facilitate extraction of amplifiable DNA. The results showed that TrimGen kits showed the greatest performance in relation to the quality and quantity of extracted FFPE DNA solutions. Using DNA extracted by TrimGen kits as a template for tumor genotyping, a real-time wild-type blocking PCR (WTB-PCR) assay was subsequently developed to detect the aforementioned KRAS mutations in mCRC patients. The results showed that WTB-PCR facilitated the detection of mutated alleles at a ratio of 1:10,000 (i.e. 0.01%) wild-type alleles. When the assay was subsequently used to test 49 mCRC patients, the results showed that the mutation detection levels of the WTB-PCR assay (61.8%; 30/49) were significantly higher than that of traditional PCR (38.8%; 19/49). Following the use of the real-time WTB-PCR assay, the ΔCq method was used to quantitatively analyze the mutation levels associated with KRAS in each FFPE sample. The results showed that the mutant levels ranged from 53.74 to 0.12% in the patients analyzed. In conclusion, the current real-time WTB-PCR is a rapid, simple, and low-cost method that permits the detection of trace amounts of the mutated KRAS gene.
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Affiliation(s)
- Jun-Fu Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Dong-Zhu Zeng
- Department of General Surgery, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Guang-Jie Duan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Yan Shi
- Department of General Surgery, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Guo-Hong Deng
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Han Xia
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Han-Qing Xu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Na Zhao
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
| | - Wei-Ling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
- * E-mail: (QH); (W-LF)
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, P. R. China
- * E-mail: (QH); (W-LF)
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Kriegsmann M, Arens N, Endris V, Weichert W, Kriegsmann J. Detection of KRAS, NRAS and BRAF by mass spectrometry - a sensitive, reliable, fast and cost-effective technique. Diagn Pathol 2015; 10:132. [PMID: 26220423 PMCID: PMC4518505 DOI: 10.1186/s13000-015-0364-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 07/09/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND According to current clinical guidelines mutational analysis for KRAS and NRAS is recommended prior to EGFR-directed therapy of colorectal cancer (CRC) in the metastatic setting. Therefore, reliable, fast, sensitive and cost-effective methods for routine tissue based molecular diagnostics are required that allow the assessment of the CRC mutational status in a high throughput fashion. METHODS We have developed a custom designed assay for routine mass-spectrometric (MS) (MassARRAY, Agena Bioscience) analysis to test the presence/absence of 18 KRAS, 14 NRAS and 4 BRAF mutations. We have applied this assay to 93 samples from patients with CRC and have compared the results with Sanger sequencing and a chip hybridization assay (KRAS LCD-array Kit, Chipron). In cases with discordant results, next-generation sequencing (NGS) was performed. RESULTS MS detected a KRAS mutation in 46/93 (49%), a NRAS mutation in 2/93 (2%) and a BRAF mutation in 1/93 (1%) of the cases. MS results were in agreement with results obtained by combination of the two other methods in 92 (99%) of 93 cases. In 1/93 (1%) of the cases a G12V mutation has been detected by Sanger sequencing and MS, but not by the chip assay. In this case, NGS has confirmed the G12V mutation in KRAS. CONCLUSIONS Mutational analysis by MS is a reliable method for routine diagnostic use, which can be easily extended for testing of additional mutations.
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Affiliation(s)
- Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
| | | | - Volker Endris
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
| | - Wilko Weichert
- Institute of Pathology, University of Heidelberg, INF 224, Heidelberg, Germany.
- National Center of Tumor Diseases, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Jörg Kriegsmann
- Institute of Molecular Pathology, Trier, Germany.
- MVZ for Histology, Cytology and Molecular Diagnostics, Trier, Germany.
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28
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Cancer risk and overall survival in mismatch repair proficient hereditary non-polyposis colorectal cancer, Lynch syndrome and sporadic colorectal cancer. Fam Cancer 2015; 13:109-19. [PMID: 24061861 DOI: 10.1007/s10689-013-9683-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Mismatch repair proficient hereditary non-polyposis colorectal cancer (MSS-HNPCC) encloses a heterogeneous group of families consisting of different unknown genetic syndromes and/or aggregations cases. The lack of information about the hereditability of cancer risk in these families makes it difficult to carry out an individualized Genetic Counseling. Therefore, deep description of such families becomes important for a better classification and search for underlying susceptibility causes. The aim of this study is to describe and compare the clinical, morphological features, tumor KRAS status and overall survival in MSS-HNPCC, Lynch and sporadic colorectal cancer. A total of 37 MSS-HNPCC families, 50 Lynch families and 612 sporadic CRC were included. Clinical and morphological data were evaluated by reviewing medical and pathology reports of 55, 69 and 102 tumors respectively. KRAS/BRAF status were detected by allele specific real-time PCR. Standardized incidence ratios (SIR) were calculated among 602 MSS-HNPCC relatives and 668 Lynch relatives. Main features distinguishing MSS-HNPCC were diagnosis age (55.1 ± 12.6), preferential distal location (76%), polyp detection (45%) and familial colorectal cancer incidence (SIR = 6.6). In addition, we found increased incidences rates for kidney, stomach and uterus tumors. KRAS mutation rates were similar in the study populations (48.8 ± 5.8) but higher than those described before by Sanger sequencing. MSS-HNPCC overall survival was similar to Lynch in B Dukes' stage tumors and between Lynch and sporadic in C stage tumors. Anatomical and morphological data of MSS-HNPCC are consistent with other described populations. Our studies disclose an increased HNPCC-extracolonic tumors incidence and improved overall survival in MSS-HNPCC families.
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29
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Li Z, Liu XW, Chi ZC, Sun BS, Cheng Y, Cheng LW. Detection of K-ras Mutations in Predicting Efficacy of Epidermal Growth Factor Receptor Tyrosine Kinase (EGFR-TK) Inhibitor in Patients with Metastatic Colorectal Cancer. PLoS One 2015; 10:e0101019. [PMID: 25950441 PMCID: PMC4423938 DOI: 10.1371/journal.pone.0101019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 06/02/2014] [Indexed: 12/27/2022] Open
Abstract
Epidermal growth factor receptor tyrosine kinase (EGFR-TK) inhibitors are useful in treating different advanced human cancers; however, their clinical efficacy varies. This study detected K-ras mutations to predict the efficacy of EGFR-TK inhibitor cetuximab treatment on Chinese patients with metastatic colorectal cancer (mCRC). A total of 87 patients with metastatic colorectal cancer were treated with cetuximab for 2-16 months, in combination with chemotherapy between August 2008 and July 2012, and tissue samples were used to detect K-ras mutations. The data showed that K-ras mutation occurred in 27/87 (31%). The objective response rates and disease control rate in K-ras wild type and mutant patients were 42% (25/60) versus 11% (3/27) (p<0.05) and 60% (36/60) versus 26% (7/27) (p<0.05), respectively. Patients with the wild-type K-ras had significantly higher median survival times and progression-free survival, than patients with mutated K-ras (21 months versus 17 months, p=0.017; 10 months versus 6 months, p=0.6). These findings suggest that a high frequency of K-ras mutations occurs in Chinese mCRC patients and that K-ras mutation is required to select patients for eligibility for cetuximab therapy. Further prospective studies using a large sample size are needed to confirm these preliminary findings.
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Affiliation(s)
- Ze Li
- Department of Gastrointestinal Surgery, Cancer Hospital of Jilin Province, Changchun, Jilin, China
| | - Xue-Wei Liu
- Department of Gastrointestinal Surgery, Cancer Hospital of Jilin Province, Changchun, Jilin, China
| | - Zhao-Cheng Chi
- Department of Gastrointestinal Surgery, Cancer Hospital of Jilin Province, Changchun, Jilin, China
| | - Bao-Sheng Sun
- Department of Gastrointestinal Surgery, Cancer Hospital of Jilin Province, Changchun, Jilin, China
| | - Ying Cheng
- Department of Gastrointestinal Surgery, Cancer Hospital of Jilin Province, Changchun, Jilin, China
- * E-mail: (L-WC); (YC)
| | - Long-Wei Cheng
- Department of Gastrointestinal Surgery, Cancer Hospital of Jilin Province, Changchun, Jilin, China
- * E-mail: (L-WC); (YC)
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30
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Affiliation(s)
- Chloe E Atreya
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA
| | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX
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31
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Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection. Biotechniques 2015; 58:126-34. [DOI: 10.2144/000114264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 12/17/2014] [Indexed: 11/23/2022] Open
Abstract
The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations.
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32
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Taniguchi H, Yamazaki K, Yoshino T, Muro K, Yatabe Y, Watanabe T, Ebi H, Ochiai A, Baba E, Tsuchihara K. Japanese Society of Medical Oncology Clinical Guidelines: RAS (KRAS/NRAS) mutation testing in colorectal cancer patients. Cancer Sci 2015; 106:324-7. [PMID: 25800101 PMCID: PMC4376442 DOI: 10.1111/cas.12595] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 12/13/2014] [Accepted: 12/15/2014] [Indexed: 01/08/2023] Open
Abstract
The Japanese guidelines for the testing of KRAS mutations in colorectal cancer have been used for the past 5 years. However, new findings of RAS (KRAS/NRAS) mutations that can further predict the therapeutic effects of anti-epidermal growth factor receptor (EGFR) antibody therapy necessitated a revision of the guidelines. The revised guidelines included the following five basic requirements for RAS mutation testing to highlight a patient group in which anti-EGFR antibody therapy may be ineffective: First, anti-EGFR antibody therapy may not offer survival benefit and/or tumor shrinkage to patients with expanded RAS mutations. Thus, current methods to detect KRAS exon 2 (codons 12 and 13) mutations are insufficient for selecting appropriate candidates for this therapy. Additional testing of extended KRAS/NRAS mutations is recommended. Second, repeated tests are not required for the detection; tissue materials of either primary or metastatic lesions are applicable for RAS mutation testing. Evaluating RAS mutations prior to anti-EGFR antibody therapy is recommended. Third, direct sequencing with manual dissection or allele-specific PCR-based methods is currently applicable for RAS mutation testing. Fourth, thinly sliced sections of formalin-fixed, paraffin-embedded tissue blocks are applicable for RAS mutation testing. One section stained with H&E should be provided to histologically determine whether the tissue contains sufficient amount of tumor cells for testing. Finally, RAS mutation testing must be performed in laboratories with appropriate testing procedures and specimen management practices.
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Affiliation(s)
- Hiroya Taniguchi
- Department of Clinical Oncology, Aichi Cancer Center HospitalAichi, Japan
| | - Kentaro Yamazaki
- Division of Gastrointestinal Oncology, Shizuoka Cancer CenterShizuoka, Japan
| | - Takayuki Yoshino
- Department of Gastrointestinal Oncology, National Cancer Center Hospital EastChiba, Japan
| | - Kei Muro
- Department of Clinical Oncology, Aichi Cancer Center HospitalAichi, Japan
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center HospitalAichi, Japan
| | - Toshiaki Watanabe
- Department of Surgical Oncology, Graduate School of Medicine and Faculty of Medicine, The University of TokyoTokyo, Japan
| | - Hiromichi Ebi
- Division of Medical Oncology, Cancer Research Institute, Kanazawa UniversityIshikawa, Japan
| | - Atsushi Ochiai
- Department of Pathology and Clinical Laboratories, National Cancer Center HospitalTokyo, Japan
| | - Eishi Baba
- Department of Comprehensive Clinical Oncology, Faculty of Medical Sciences, Kyushu UniversityFukuoka, Japan
| | - Katsuya Tsuchihara
- Division of Translational Research, Exploratory Oncology Research and Clinical Trial Center, National Cancer CenterChiba, Japan
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Li-Chang HH, Kasaian K, Ng Y, Lum A, Kong E, Lim H, Jones SJ, Huntsman DG, Schaeffer DF, Yip S. Retrospective review using targeted deep sequencing reveals mutational differences between gastroesophageal junction and gastric carcinomas. BMC Cancer 2015; 15:32. [PMID: 25656989 PMCID: PMC4322811 DOI: 10.1186/s12885-015-1021-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 01/14/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Adenocarcinomas of both the gastroesophageal junction and stomach are molecularly complex, but differ with respect to epidemiology, etiology and survival. There are few data directly comparing the frequencies of single nucleotide mutations in cancer-related genes between the two sites. Sequencing of targeted gene panels may be useful in uncovering multiple genomic aberrations using a single test. METHODS DNA from 92 gastroesophageal junction and 75 gastric adenocarcinoma resection specimens was extracted from formalin-fixed paraffin-embedded tissue. Targeted deep sequencing of 46 cancer-related genes was performed through emulsion PCR followed by semiconductor-based sequencing. Gastroesophageal junction and gastric carcinomas were contrasted with respect to mutational profiles, immunohistochemistry and in situ hybridization, as well as corresponding clinicopathologic data. RESULTS Gastroesophageal junction carcinomas were associated with younger age, more frequent intestinal-type histology, more frequent p53 overexpression, and worse disease-free survival on multivariable analysis. Among all cases, 145 mutations were detected in 31 genes. TP53 mutations were the most common abnormality detected, and were more common in gastroesophageal junction carcinomas (42% vs. 27%, p = 0.036). Mutations in the Wnt pathway components APC and CTNNB1 were more common among gastric carcinomas (16% vs. 3%, p = 0.006), and gastric carcinomas were more likely to have ≥3 driver mutations detected (11% vs. 2%, p = 0.044). Twenty percent of cases had potentially actionable mutations identified. R132H and R132C missense mutations in the IDH1 gene were observed, and are the first reported mutations of their kind in gastric carcinoma. CONCLUSIONS Panel sequencing of routine pathology material can yield mutational information on several driver genes, including some for which targeted therapies are available. Differing rates of mutations and clinicopathologic differences support a distinction between adenocarcinomas that arise in the gastroesophageal junction and those that arise in the stomach proper.
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Affiliation(s)
- Hector H Li-Chang
- University of British Columbia, Vancouver, Canada.
- Division of Anatomic Pathology, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 855 12 Ave W, Vancouver, BC, V5Z 1 M9, Canada.
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.
| | - Katayoon Kasaian
- University of British Columbia, Vancouver, Canada.
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada.
| | - Ying Ng
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada.
| | - Amy Lum
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada.
| | - Esther Kong
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada.
| | - Howard Lim
- University of British Columbia, Vancouver, Canada.
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, Canada.
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada.
| | - David G Huntsman
- University of British Columbia, Vancouver, Canada.
- Division of Anatomic Pathology, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 855 12 Ave W, Vancouver, BC, V5Z 1 M9, Canada.
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada.
| | - David F Schaeffer
- University of British Columbia, Vancouver, Canada.
- Division of Anatomic Pathology, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 855 12 Ave W, Vancouver, BC, V5Z 1 M9, Canada.
| | - Stephen Yip
- University of British Columbia, Vancouver, Canada.
- Division of Anatomic Pathology, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, 855 12 Ave W, Vancouver, BC, V5Z 1 M9, Canada.
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, Canada.
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34
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Mohamed Suhaimi NA, Foong YM, Lee DYS, Phyo WM, Cima I, Lee EXW, Goh WL, Lim WY, Chia KS, Kong SL, Gong M, Lim B, Hillmer AM, Koh PK, Ying JY, Tan MH. Non-invasive sensitive detection of KRAS and BRAF mutation in circulating tumor cells of colorectal cancer patients. Mol Oncol 2015; 9:850-60. [PMID: 25605225 DOI: 10.1016/j.molonc.2014.12.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/22/2014] [Accepted: 12/27/2014] [Indexed: 12/28/2022] Open
Abstract
Characterization of genetic alterations in tumor biopsies serves as useful biomarkers in prognosis and treatment management. Circulating tumor cells (CTCs) obtained non-invasively from peripheral blood could serve as a tumor proxy. Using a label-free CTC enrichment strategy that we have established, we aimed to develop sensitive assays for qualitative assessment of tumor genotype in patients. Blood consecutively obtained from 44 patients with local and advanced colorectal cancer and 18 healthy donors were enriched for CTCs using a size-based microsieve technology. To screen for CTC mutations, we established high-resolution melt (HRM) and allele-specific PCR (ASPCR) KRAS-codon 12/13- and BRAF-codon 600- specific assays, and compared the performance with pyrosequencing and Sanger sequencing. For each patient, the resulting CTC genotypes were compared with matched tumor and normal tissues. Both HRM and ASPCR could detect as low as 1.25% KRAS- or BRAF-mutant alleles. HRM detected 14/44 (31.8%) patients with KRAS mutation in CTCs and 5/44 (11.3%) patients having BRAF mutation in CTCs. ASPCR detected KRAS and BRAF mutations in CTCs of 10/44 (22.7%) and 1/44 (2.3%) patients respectively. There was an increased detection of mutation in blood using these two methods. Comparing tumor tissues and CTCs mutation status using HRM, we observed 84.1% concordance in KRAS genotype (p = 0.000129, Fishers' exact test; OR = 38.7, 95% CI = 4.05-369) and 90.9% (p = 0.174) concordance in BRAF genotype. Our results demonstrate that CTC enrichment, coupled with sensitive mutation detection methods, may allow rapid, sensitive and non-invasive assessment of tumor genotype.
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Affiliation(s)
| | - Yu Miin Foong
- Institute of Bioengineering and Nanotechnology, Singapore
| | | | - Wai Min Phyo
- Institute of Bioengineering and Nanotechnology, Singapore
| | - Igor Cima
- Institute of Bioengineering and Nanotechnology, Singapore
| | | | - Wei Lin Goh
- Fortis Surgical Hospital Singapore, Singapore
| | - Wei-Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Kee Seng Chia
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | | | - Min Gong
- Genome Institute of Singapore, Singapore
| | - Bing Lim
- Genome Institute of Singapore, Singapore
| | | | - Poh Koon Koh
- Institute of Bioengineering and Nanotechnology, Singapore; Fortis Surgical Hospital Singapore, Singapore
| | - Jackie Y Ying
- Institute of Bioengineering and Nanotechnology, Singapore
| | - Min-Han Tan
- Institute of Bioengineering and Nanotechnology, Singapore; National Cancer Centre Singapore, Singapore.
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Liu YP, Wu HY, Yang X, Xu HQ, Chen D, Huang Q, Fu WL. Diagnostic accuracy of high resolution melting analysis for detection of KRAS mutations: a systematic review and meta-analysis. Sci Rep 2014; 4:7521. [PMID: 25515911 PMCID: PMC4268648 DOI: 10.1038/srep07521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/27/2014] [Indexed: 01/01/2023] Open
Abstract
Increasing evidence points to a negative correlation between KRAS mutations and patients' responses to anti-EGFR monoclonal antibody treatment. Therefore, patients must undergo KRAS mutation detection to be eligible for treatment. High resolution melting analysis (HRM) is gaining increasing attention in KRAS mutation detection. However, its accuracy has not been systematically evaluated. We conducted a meta-analysis of published articles, involving 13 articles with 1,520 samples, to assess its diagnostic accuracy compared with DNA sequencing. The quality of included articles was assessed using the revised Quality Assessment for Studies of Diagnostic Accuracy (QUADAS-2) tools. Random effects models were applied to analyze the performance of pooled characteristics. The overall sensitivity and specificity of HRM were 0.99 (95% confidence interval [CI]: 0.98-1.00) and 0.96 (95%CI: 0.94-0.97), respectively. The area under the summary receiver operating characteristic curve was 0.996. High sensitivity and specificity, less labor, rapid turn-around and the closed-tube format of HRM make it an attractive choice for rapid detection of KRAS mutations in clinical practice. The burden of DNA sequencing can be reduced dramatically by the implementation of HRM, but positive results still need to be sequenced for diagnostic confirmation.
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Affiliation(s)
- Yue-Ping Liu
- 1] Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China [2] Department of Laboratory Medicine, 477TH Hospital of PLA, Xiangyang City, 400013, Hubei Province, PR China
| | - Hai-Yan Wu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
| | - Xiang Yang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
| | - Han-Qing Xu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
| | - Dong Chen
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
| | - Wei-Ling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, PR China
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Abstract
Activating mutation of KRAS plays a significant role in the pathogenesis of common human malignancies and molecular testing of KRAS mutation has emerged as an essential biomarker in the current practice of clinical oncology. The presence of KRAS mutation is generally associated with clinical aggressiveness of the cancer and reduced survival of the patient. Therapeutically, KRAS mutation testing has maximum utility in stratifying metastatic colorectal carcinoma and lung cancer patients for treatment with targeted therapy. Diagnostically, KRAS mutation testing is useful in the workup of pancreaticobiliary and thyroid cancers, particularly using cytological specimens. In the era of precision medicine, the role of KRAS mutation testing is poised to expand, likely in a setting of combinatorial therapeutic strategy and requiring additional mutation testing of its upstream and/or downstream effectors.
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Affiliation(s)
- Sudhir Perincheri
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520-8023, USA
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Yi S, Zhuang Y, Zhou J, Ma H, Huang J, Wang L, Zhu W, Kang S, Guo L, Guo F. A comparison of epidermal growth factor receptor mutation testing methods in different tissue types in non-small cell lung cancer. Int J Mol Med 2014; 34:464-74. [PMID: 24891042 DOI: 10.3892/ijmm.2014.1789] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/12/2014] [Indexed: 11/06/2022] Open
Abstract
The detection of somatic epidermal growth factor receptor (EGFR) mutations is valuable when an appropriate therapy, either EGFR-tyrosine kinase inhibitor (TKI) therapy or chemotherapy, for patients with advanced non-small cell lung cancer (NSCLC) needs to be selected. Although it is well‑understood that EGFR mutation detection is significant for the decision‑making regarding treatment, no consensus on the methodology that should be the most preferebale for detecting mutations in clinical practice has been reached. The presence of false positives due to the technique carried out for mutation analysis affects the accurate estimation of response EGFR-TKI therapy. Furthermore, false negatives directly exclude the potential application of an EGFR-TKI. In the present study, we present the results of detecting EGFR mutations in individual sample types using three different low- or high-sensitivity techniques. We suggest that the choice of the method used should be made based on the type of the sample. Our results revealed that EGFR mutations were less frequently detected in bronchoscopic biopsies, regardless of the method used. However, the amplification refractory mutation system (ARMS) was optimal owing to the small amount of DNA prepared for biopsy. The cytology sample was a valuable alternative to traditional samples, given that a sensitive method for detecting mutations was used. For surgical resections, the testing method may be selected based on the expertise of each laboratory, but direct sequencing is highly recommended. We also suggest that two methods should be used sequentially (the screening and targeted methods) in clinical practice due to the presence of non-neglected discordance between any method from its own benefits and drawbacks.
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Affiliation(s)
- Suqin Yi
- Central Laboratory, The First Affiliated Hospital of Soochow University, Suzhou 215006, P.R. China
| | - Yuan Zhuang
- Central Laboratory, The First Affiliated Hospital of Soochow University, Suzhou 215006, P.R. China
| | - Jun Zhou
- Central Laboratory, The First Affiliated Hospital of Soochow University, Suzhou 215006, P.R. China
| | - Haitao Ma
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, P.R. China
| | - Jianan Huang
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou 215006, P.R. China
| | - Lin Wang
- Department of Special Requirements Ward, The First Affiliated Hospital of Soochow University, Suzhou 215006, P.R. China
| | - Weidong Zhu
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou 215006, P.R. China
| | - Suya Kang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou 215006, P.R. China
| | - Linchuan Guo
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou 215006, P.R. China
| | - Feng Guo
- Central Laboratory, The First Affiliated Hospital of Soochow University, Suzhou 215006, P.R. China
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Balschun K, Wenke AK, Röcken C, Haag J. Detection of KRAS and BRAF mutations in advanced colorectal cancer by allele-specific single-base primer extension. Expert Rev Mol Diagn 2014; 11:799-802. [DOI: 10.1586/erm.11.75] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Katharina Balschun
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, D-24105 Kiel, Germany
| | - Ann-Kathrin Wenke
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, D-24105 Kiel, Germany
| | - Christoph Röcken
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, D-24105 Kiel, Germany
| | - Jochen Haag
- Institute of Pathology, Christian-Albrechts-University, Arnold-Heller-Str. 3, D-24105 Kiel, Germany
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Molinari F, Frattini M. KRASmutational test for metastatic colorectal cancer patients: not just a technical problem. Expert Rev Mol Diagn 2014; 12:123-6. [DOI: 10.1586/erm.11.94] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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A Multicenter Blinded Study Evaluating EGFR and KRAS Mutation Testing Methods in the Clinical Non–Small Cell Lung Cancer Setting—IFCT/ERMETIC2 Project Part 1. J Mol Diagn 2014; 16:45-55. [DOI: 10.1016/j.jmoldx.2013.07.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 07/04/2013] [Accepted: 07/30/2013] [Indexed: 11/22/2022] Open
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Aisner DL, Nguyen TT, Paskulin DD, Le AT, Haney J, Schulte N, Chionh F, Hardingham J, Mariadason J, Tebbutt N, Doebele RC, Weickhardt AJ, Varella-Garcia M. ROS1 and ALK fusions in colorectal cancer, with evidence of intratumoral heterogeneity for molecular drivers. Mol Cancer Res 2013; 12:111-8. [PMID: 24296758 DOI: 10.1158/1541-7786.mcr-13-0479-t] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
UNLABELLED Activated anaplastic lymphoma kinase (ALK) and ROS1 tyrosine kinases, through gene fusions, have been found in lung adenocarcinomas and are highly sensitive to selective kinase inhibitors. This study aimed at identifying the presence of these rearrangements in human colorectal adenocarcinoma specimens using a 4-target, 4-color break-apart FISH assay to simultaneously determine the genomic status of ALK and ROS1. Among the clinical colorectal cancer specimens analyzed, rearrangement-positive cases for both ALK and ROS1 were observed. The fusion partner for ALK was identified as EML4 and the fusion partner for one of the ROS1-positive cases was SLC34A2, the partner for the other ROS1-positive case remains to be identified. A small fraction of specimens presented duplicated or clustered copies of native ALK and ROS1. In addition, rearrangements were detected in samples that also harbored KRAS and BRAF mutations in two of the three cases. Interestingly, the ALK-positive specimen displayed marked intratumoral heterogeneity and rearrangement was also identified in regions of high-grade dysplasia. Despite the additional oncogenic events and tumor heterogeneity observed, elucidation of the first cases of ROS1 rearrangements and confirmation of ALK rearrangements support further evaluation of these genomic fusions as potential therapeutic targets in colorectal cancer. IMPLICATIONS ROS1 and ALK fusions occur in colorectal cancer and may have substantial impact in therapy selection.
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Affiliation(s)
- Dara L Aisner
- University of Colorado School of Medicine Anschutz Medical Campus, 12801 East 17th Avenue, L18-8118, Mail Stop 8117, Aurora, CO 80045.
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Beyond the standard of care: the role of cytopathology in molecular testing of cancer. Cancer Treat Res 2013. [PMID: 24092374 DOI: 10.1007/978-3-642-38850-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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43
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Malapelle U, Carlomagno C, de Luca C, Bellevicine C, Troncone G. KRAS testing in metastatic colorectal carcinoma: challenges, controversies, breakthroughs and beyond. J Clin Pathol 2013; 67:1-9. [DOI: 10.1136/jclinpath-2013-201835] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Blons H, Rouleau E, Charrier N, Chatellier G, Côté JF, Pages JC, de Fraipont F, Boyer JC, Merlio JP, Morel A, Gorisse MC, de Cremoux P, Leroy K, Milano G, Ouafik L, Merlin JL, Le Corre D, Aucouturier P, Sabourin JC, Nowak F, Frebourg T, Emile JF, Durand-Zaleski I, Laurent-Puig P. Performance and cost efficiency of KRAS mutation testing for metastatic colorectal cancer in routine diagnosis: the MOKAECM study, a nationwide experience. PLoS One 2013; 8:e68945. [PMID: 23935912 PMCID: PMC3723748 DOI: 10.1371/journal.pone.0068945] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 06/04/2013] [Indexed: 12/13/2022] Open
Abstract
Purpose Rapid advances in the understanding of cancer biology have transformed drug development thus leading to the approval of targeted therapies and to the development of molecular tests to select patients that will respond to treatments. KRAS status has emerged as a negative predictor of clinical benefit from anti-EGFR antibodies in colorectal cancer, and anti-EGFR antibodies use was limited to KRAS wild type tumors. In order to ensure wide access to tumor molecular profiling, the French National Cancer Institute (INCa) has set up a national network of 28 regional molecular genetics centers. Concurrently, a nationwide external quality assessment for KRAS testing (MOKAECM) was granted to analyze reproducibility and costs. Methods 96 cell-line DNAs and 24 DNA samples from paraffin embedded tumor tissues were sent to 40 French laboratories. A total of 5448 KRAS results were collected and analyzed and a micro-costing study was performed on sites for 5 common methods by an independent team of health economists. Results This work provided a baseline picture of the accuracy and reliability of KRAS analysis in routine testing conditions at a nationwide level. Inter-laboratory Kappa values were >0.8 for KRAS results despite differences detection methods and the use of in-house technologies. Specificity was excellent with only one false positive in 1128 FFPE data, and sensitivity was higher for targeted techniques as compared to Sanger sequencing based methods that were dependent upon local expertise. Estimated reagent costs per patient ranged from €5.5 to €19.0. Conclusion The INCa has set-up a network of public laboratories dedicated to molecular oncology tests. Our results showed almost perfect agreements in KRAS testing at a nationwide level despite different testing methods ensuring a cost-effective equal access to personalized colorectal cancer treatment.
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Affiliation(s)
- Hélène Blons
- UMR-S775, INSERM, Paris, France
- Université Paris Descartes, Paris, France
- Assistance Publique Hôpitaux de Paris Department of biology, Hôpital Européen Georges Pompidou, Paris, France
| | | | - Nathanaël Charrier
- Assistance Publique Hôpitaux de Paris, Henri Mondor-Albert Chenevier Hospitals, Department of Public Health, Creteil; URCEco Ile de France, Paris, France
| | - Gilles Chatellier
- Université Paris Descartes, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, URC Paris, France
| | - Jean-François Côté
- EA4340, Université de Versailles St Quentin en Yvelines; Assistance Publique Hôpitaux de Paris Hôpital Ambroise Paré, Department of Pathology; Boulogne-Billancourt, France
| | - Jean-Christophe Pages
- INSERM U966, Université François Rabelais de Tours, Faculté de Médecine, Tours, France
| | | | | | - Jean Philippe Merlio
- Bordeaux University Hospital Segalene Department of Tumor Biology, Pessac; Bordeaux University EA 2406, Bordeaux, France
| | - Alain Morel
- Cancer Center Paul Papin; INSERM U892; University of Angers, Angers, France
| | | | - Patricia de Cremoux
- Assistance Publique Hôpitaux de Paris, Saint Louis Hospital, Molecular oncology unit, Department of biochemistry, Paris, France
| | - Karen Leroy
- Assistance Publique Hôpitaux de Paris Department of pathology Henri Mondor Hospital, Creteil, France
| | | | - L’Houcine Ouafik
- Aix-Marseille Université, Inserm-CRO2 UMR911, AP-HM, CHU Nord, Service de Transfert d’Oncologie Biologique, Marseille, France
| | | | | | - Pascaline Aucouturier
- Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, URC Paris, France
| | - Jean-Christophe Sabourin
- Rouen University Hospital Department of surgical and molecular pathology; Inserm U1079, Rouen, France
| | | | - Thierry Frebourg
- Rouen University Hospital Department of Genetics, Inserm U614, Rouen, France
| | - Jean-François Emile
- EA4340, Université de Versailles St Quentin en Yvelines; Assistance Publique Hôpitaux de Paris Hôpital Ambroise Paré, Department of Pathology; Boulogne-Billancourt, France
| | - Isabelle Durand-Zaleski
- Assistance Publique Hôpitaux de Paris, Henri Mondor-Albert Chenevier Hospitals, Department of Public Health, Creteil; URCEco Ile de France, Paris, France
| | - Pierre Laurent-Puig
- UMR-S775, INSERM, Paris, France
- Université Paris Descartes, Paris, France
- Assistance Publique Hôpitaux de Paris Department of biology, Hôpital Européen Georges Pompidou, Paris, France
- * E-mail:
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Smith DL, Lamy A, Beaudenon-Huibregtse S, Sesboüé R, Laosinchai-Wolf W, Sabourin JC, Labourier E. A multiplex technology platform for the rapid analysis of clinically actionable genetic alterations and validation for BRAF p.V600E detection in 1549 cytologic and histologic specimens. Arch Pathol Lab Med 2013; 138:371-8. [PMID: 23808402 DOI: 10.5858/arpa.2013-0002-oa] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Current clinicopathologic assessment of malignant neoplastic diseases entails the analysis of specific genetic alterations that provide diagnostic, prognostic, or therapy-determining information. OBJECTIVE To develop and validate a robust molecular method to detect clinically relevant mutations in various tissue types and anatomic pathology specimens. DESIGN Genes of interest were amplified by multiplex polymerase chain reaction and sequence variants identified by liquid bead array cytometry. The BRAF assay was fully characterized by using plasmids and genomic DNA extracted from cell lines, metastatic colorectal cancer formalin-fixed, paraffin-embedded (FFPE) tissues, and thyroid nodule fine-needle aspirates. RESULTS Qualitative multiplex assays for 22 different mutations in the BRAF, HRAS, KRAS, NRAS, or EGFR genes were established. The high signal-to-noise ratio of the technology enabled reproducible detection of BRAF c.1799T>A (p.V600E) at 0.5% mutant allele in 20 ng of genomic DNA. Precision studies with multiple operators and instruments showed very high repeatability and reproducibility with 100% (98.7%-100%) qualitative agreement among 292 individual measures in 38 runs. Evaluation of 1549 representative pathologic specimens in 2 laboratories relative to independent reference methods resulted in 99.0% (97.6%-99.6%) agreement for colorectal FFPE tissues (n = 416) and 98.9% (98.2%-99.4%) for thyroid fine-needle aspiration specimens (n = 1133) with an overall diagnostic odds ratio of 10 856 (2451-48 078). CONCLUSIONS The multiplex assay system is a sensitive and reliable method to detect BRAF c.1799T>A mutation in colorectal and thyroid lesions. This optimized technology platform is suitable for the rapid analysis of clinically actionable genetic alterations in cytologic and histologic specimens.
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Affiliation(s)
- David L Smith
- From Asuragen Inc, Austin, Texas, (Drs Smith, Beaudenon-Huibregtse, Laosinchai-Wolf, and Labourier); the Department of Pathology, Rouen University Hospital, Rouen, France (Drs Lamy and Sabourin); and INSERM U1079, Faculty of Medicine, Rouen University, Rouen, France (Dr Sesboüé)
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Li Z, Chen Y, Wang D, Wang G, He L, Suo J. Detection of KRAS mutations and their associations with clinicopathological features and survival in Chinese colorectal cancer patients. J Int Med Res 2013; 40:1589-98. [PMID: 22971512 DOI: 10.1177/147323001204000439] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE Mutation of the KRAS (v-Kiras2 Kirsten rat sarcoma viral oncogene homologue) gene plays an important role in colorectal tumorigenesis. This study examined associations between KRAS gene mutations and clinicopathological and survival data in Chinese patients with colorectal cancer (CRC). METHODS CRC patients were recruited for the detection of KRAS gene mutations using polymerase chain reaction and DNA sequencing. Data on clinicopathological features and survival times were collected. RESULTS The study included 78 CRC patients. The overall mutation frequency of the KRAS gene at codons 12 and 13 was 33.3% (26/78). KRAS gene mutations were significantly associated with poor tumour differentiation and liver metastasis. Patients with the wild-type KRAS gene had significantly higher median survival times than patients with KRAS gene mutations (35.05 months versus 25.72 months). Those with KRAS gene mutations at codons 12 or 13 did not have significantly different median survival times (25.69 months versus 20.67 months, respectively). CONCLUSIONS These findings suggest that a high frequency of KRAS gene mutations exists in Chinese patients with CRC, and that such mutations are associated with poor survival, tumour differentiation and liver metastasis in CRC patients.
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Affiliation(s)
- Z Li
- Department of Gastrointestinal Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
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Hagan S, Orr MCM, Doyle B. Targeted therapies in colorectal cancer-an integrative view by PPPM. EPMA J 2013; 4:3. [PMID: 23356214 PMCID: PMC3584939 DOI: 10.1186/1878-5085-4-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 12/26/2012] [Indexed: 12/12/2022]
Abstract
In developed countries, colorectal cancer (CRC) is the third most common malignancy, but it is the second most frequent cause of cancer-related death. Clinicians are still faced with numerous challenges in the treatment of this disease, and future approaches which target the molecular features of the disorder will be critical for success in this disease setting. Genetic analyses of many solid tumours have shown that up to 100 protein-encoding genes are mutated. Within CRC, numerous genetic alterations have been identified in a number of pathways. Therefore, understanding the molecular pathology of CRC may present information on potential routes for treatment and may also provide valuable prognostic information. This will be particularly pertinent for molecularly targeted treatments, such as anti-vascular endothelial growth factor therapies and anti-epidermal growth factor receptor (EGFR) monoclonal antibody therapy. KRAS and BRAF mutations have been shown to predict response to anti-EGFR therapy. As EGFR can also signal via the phosphatidylinositol 3-kinase (PI3K) kinase pathway, there is considerable interest in the potential roles of members of this pathway (such as PI3K and PTEN) in predicting treatment response. Therefore, a combined approach of new techniques that allow identification of these biomarkers alongside interdisciplinary approaches to the treatment of advanced CRC will aid in the treatment decision-making process and may also serve to guide future therapeutic approaches.
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Affiliation(s)
- Suzanne Hagan
- Department of Life Sciences Glasgow, Caledonian University, Glasgow, G4 0BA, UK
| | - Maria C M Orr
- Personalised Healthcare and Biomarkers, AstraZeneca, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - Brendan Doyle
- Department of Histopathology, Trinity College, St. James's Hospital, Dublin, 8, Ireland
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Improving the limit of detection for Sanger sequencing: a comparison of methodologies for KRAS variant detection. Biotechniques 2013; 53:182-188. [PMID: 22963480 DOI: 10.2144/000113913] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 07/27/2012] [Indexed: 11/23/2022] Open
Abstract
Fluorescent dye terminator Sanger sequencing (FTSS), with detection by automated capillary electrophoresis (CE), has long been regarded as the gold standard for variant detection. However, software analysis and base-calling algorithms used to detect mutations were largely optimized for resequencing applications in which different alleles were expected as heterozygous mixtures of 50%. Increasingly, the requirements for variant detection are an analytic sensitivity for minor alleles of <20%, in particular, when assessing the mutational status of heterogeneous tumor samples. Here, we describe a simple modification to the FTSS workflow that improves the limit of detection of cell-line gDNA mixtures from 50%-20% to 5% for G>A transitions and from 50%-5% to 5% for G>C and G>T transversions. In addition, we use two different sample types to compare the limit of detection of sequence variants in codons 12 and 13 of the KRAS gene between Sanger sequencing and other methodologies including shifted termination assay (STA) detection, single-base extension (SBE), pyrosequencing (PS), high- resolution melt (HRM), and real-time PCR (qPCR).
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Altimari A, de Biase D, De Maglio G, Gruppioni E, Capizzi E, Degiovanni A, D’Errico A, Pession A, Pizzolitto S, Fiorentino M, Tallini G. 454 next generation-sequencing outperforms allele-specific PCR, Sanger sequencing, and pyrosequencing for routine KRAS mutation analysis of formalin-fixed, paraffin-embedded samples. Onco Targets Ther 2013; 6:1057-64. [PMID: 23950653 PMCID: PMC3741083 DOI: 10.2147/ott.s42369] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Detection of KRAS mutations in archival pathology samples is critical for therapeutic appropriateness of anti-EGFR monoclonal antibodies in colorectal cancer. We compared the sensitivity, specificity, and accuracy of Sanger sequencing, ARMS-Scorpion (TheraScreen®) real-time polymerase chain reaction (PCR), pyrosequencing, chip array hybridization, and 454 next-generation sequencing to assess KRAS codon 12 and 13 mutations in 60 nonconsecutive selected cases of colorectal cancer. Twenty of the 60 cases were detected as wild-type KRAS by all methods with 100% specificity. Among the 40 mutated cases, 13 were discrepant with at least one method. The sensitivity was 85%, 90%, 93%, and 92%, and the accuracy was 90%, 93%, 95%, and 95% for Sanger sequencing, TheraScreen real-time PCR, pyrosequencing, and chip array hybridization, respectively. The main limitation of Sanger sequencing was its low analytical sensitivity, whereas TheraScreen real-time PCR, pyrosequencing, and chip array hybridization showed higher sensitivity but suffered from the limitations of predesigned assays. Concordance between the methods was k = 0.79 for Sanger sequencing and k > 0.85 for the other techniques. Tumor cell enrichment correlated significantly with the abundance of KRAS-mutated deoxyribonucleic acid (DNA), evaluated as ΔCt for TheraScreen real-time PCR (P = 0.03), percentage of mutation for pyrosequencing (P = 0.001), ratio for chip array hybridization (P = 0.003), and percentage of mutation for 454 next-generation sequencing (P = 0.004). Also, 454 next-generation sequencing showed the best cross correlation for quantification of mutation abundance compared with all the other methods (P < 0.001). Our comparison showed the superiority of next-generation sequencing over the other techniques in terms of sensitivity and specificity. Next-generation sequencing will replace Sanger sequencing as the reference technique for diagnostic detection of KRAS mutation in archival tumor tissues.
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Affiliation(s)
- Annalisa Altimari
- Laboratory of Molecular Oncologic and Transplantation Pathology, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Dario de Biase
- Laboratory of Molecular Pathology, Anatomic Pathology, Bellaria Hospital, Bologna, Italy
| | - Giovanna De Maglio
- Department of Pathology, S. Maria della Misericordia Hospital, Udine, Italy
| | - Elisa Gruppioni
- Laboratory of Molecular Oncologic and Transplantation Pathology, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Elisa Capizzi
- Laboratory of Molecular Oncologic and Transplantation Pathology, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Alessio Degiovanni
- Laboratory of Molecular Oncologic and Transplantation Pathology, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Antonia D’Errico
- Laboratory of Molecular Oncologic and Transplantation Pathology, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Annalisa Pession
- Laboratory of Molecular Pathology, Anatomic Pathology, Bellaria Hospital, Bologna, Italy
| | - Stefano Pizzolitto
- Department of Pathology, S. Maria della Misericordia Hospital, Udine, Italy
| | - Michelangelo Fiorentino
- Laboratory of Molecular Oncologic and Transplantation Pathology, S. Orsola-Malpighi Hospital, Bologna, Italy
- Correspondence: Michelangelo Fiorentino, Istituto Oncologico Addarii, Viale Ercolani 4/2, 40138, Bologna, Italy, Tel +39 05 1636 3781, Fax +39 05 1636 3782, Email
| | - Giovanni Tallini
- Laboratory of Molecular Pathology, Anatomic Pathology, Bellaria Hospital, Bologna, Italy
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Shackelford RE, Whitling NA, McNab P, Japa S, Coppola D. KRAS Testing: A Tool for the Implementation of Personalized Medicine. Genes Cancer 2012; 3:459-66. [PMID: 23264846 DOI: 10.1177/1947601912460547] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 08/14/2012] [Indexed: 12/21/2022] Open
Abstract
Activating point mutations in codons 12, 13, and 61 of the KRAS proto-oncogene are common in colorectal, non-small cell lung, pancreatic, and thyroid cancers. Constitutively activated KRAS mutations are strongly associated with a resistance to anti-epidermal growth factor receptor (EGFR) therapies, such as panitumumab and cetuximab used for treating metastatic colorectal carcinoma and EGFR tyrosine inhibitors used for advanced non-small cell lung cancers. Since anti-EGFR therapies are costly and may exert deleterious effects on individuals without activating mutations, KRAS mutation testing is recommended prior to the initiation of anti-EGFR therapy for these malignancies. The goal of this review is to summarize the KRAS mutation testing methods. Testing is now routinely requested in the clinical practice to provide data to assign the most appropriate anticancer chemotherapy for each given patient. Review of the most relevant literature was performed. Several areas were considered: ordering of the test, selection of the sample to be tested, and review of the testing methodologies. We found that several different methods are used for clinical KRAS mutation testing. Each of the methodologies is described, and information is provided about their performance, cost, turnaround times, detection limits, sensitivities, and specificities. We also provided "tips" for the appropriate selection and preparation of the sample to be tested. This is an important aspect of KRAS testing for clinical use, as the results of the test will affect clinical decisions with consequences for the patient.
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